Starting phenix.real_space_refine on Tue Aug 26 03:32:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rqy_24640/08_2025/7rqy_24640_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rqy_24640/08_2025/7rqy_24640.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7rqy_24640/08_2025/7rqy_24640_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rqy_24640/08_2025/7rqy_24640_neut_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7rqy_24640/08_2025/7rqy_24640.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rqy_24640/08_2025/7rqy_24640.map" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.011 sd= 0.135 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 8 5.49 5 S 80 5.16 5 C 11016 2.51 5 N 2620 2.21 5 O 2940 1.98 5 H 15388 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32052 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 7877 Classifications: {'peptide': 525} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 511} Chain breaks: 2 Unresolved non-hydrogen bonds: 243 Unresolved non-hydrogen angles: 301 Unresolved non-hydrogen dihedrals: 202 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'TYR:plan': 2, 'ASN:plan1': 4, 'GLU:plan': 8, 'ASP:plan': 10, 'ARG:plan': 5, 'GLN:plan1': 1, 'PHE:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 138 Chain: "B" Number of atoms: 7877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 7877 Classifications: {'peptide': 525} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 511} Chain breaks: 2 Unresolved non-hydrogen bonds: 243 Unresolved non-hydrogen angles: 301 Unresolved non-hydrogen dihedrals: 202 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'TYR:plan': 2, 'ASN:plan1': 4, 'GLU:plan': 8, 'ASP:plan': 10, 'ARG:plan': 5, 'GLN:plan1': 1, 'PHE:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 138 Chain: "A" Number of atoms: 136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 136 Unusual residues: {'6EU': 1, '6OU': 2, 'LBN': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 62 Planarities with less than four sites: {'LBN:plan-3': 1, '6OU:plan-1': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 168 Unusual residues: {'6EU': 1, '6OU': 3, 'LBN': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 81 Planarities with less than four sites: {'LBN:plan-3': 1, '6OU:plan-1': 2} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 111 Unusual residues: {'6EU': 1, '6OU': 1, 'LBN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 38 Planarities with less than four sites: {'6OU:plan-1': 1, 'LBN:plan-3': 1} Unresolved non-hydrogen planarities: 6 Restraints were copied for chains: D, C Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N ALA A 204 " occ=0.50 ... (8 atoms not shown) pdb=" HB3 ALA A 204 " occ=0.50 residue: pdb=" N ALA B 204 " occ=0.50 ... (8 atoms not shown) pdb=" HB3 ALA B 204 " occ=0.50 residue: pdb=" N ALA C 204 " occ=0.50 ... (8 atoms not shown) pdb=" HB3 ALA C 204 " occ=0.50 residue: pdb=" N ALA D 204 " occ=0.50 ... (8 atoms not shown) pdb=" HB3 ALA D 204 " occ=0.50 Time building chain proxies: 15.13, per 1000 atoms: 0.47 Number of scatterers: 32052 At special positions: 0 Unit cell: (124.509, 123.48, 109.074, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 80 16.00 P 8 15.00 O 2940 8.00 N 2620 7.00 C 11016 6.00 H 15388 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 386 " - pdb=" SG CYS A 390 " distance=2.07 Simple disulfide: pdb=" SG CYS B 386 " - pdb=" SG CYS B 390 " distance=2.07 Simple disulfide: pdb=" SG CYS D 386 " - pdb=" SG CYS D 390 " distance=2.07 Simple disulfide: pdb=" SG CYS C 386 " - pdb=" SG CYS C 390 " distance=2.07 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.88 Conformation dependent library (CDL) restraints added in 957.3 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3976 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 4 sheets defined 66.3% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 203 through 212 Processing helix chain 'A' and resid 213 through 224 removed outlier: 3.716A pdb=" N GLY A 224 " --> pdb=" O LEU A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 258 Processing helix chain 'A' and resid 260 through 270 Processing helix chain 'A' and resid 286 through 294 Processing helix chain 'A' and resid 298 through 320 removed outlier: 3.609A pdb=" N LYS A 303 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE A 304 " --> pdb=" O ASP A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 344 Processing helix chain 'A' and resid 345 through 354 Processing helix chain 'A' and resid 362 through 366 removed outlier: 4.096A pdb=" N LEU A 365 " --> pdb=" O CYS A 362 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N SER A 366 " --> pdb=" O ARG A 363 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 362 through 366' Processing helix chain 'A' and resid 394 through 401 removed outlier: 3.597A pdb=" N ILE A 399 " --> pdb=" O VAL A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 429 removed outlier: 4.019A pdb=" N ARG A 420 " --> pdb=" O GLU A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 454 removed outlier: 3.501A pdb=" N TYR A 435 " --> pdb=" O LYS A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 500 removed outlier: 3.609A pdb=" N PHE A 489 " --> pdb=" O GLY A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 504 No H-bonds generated for 'chain 'A' and resid 502 through 504' Processing helix chain 'A' and resid 505 through 510 removed outlier: 3.770A pdb=" N ASP A 509 " --> pdb=" O SER A 505 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER A 510 " --> pdb=" O LEU A 506 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 505 through 510' Processing helix chain 'A' and resid 510 through 531 removed outlier: 3.583A pdb=" N LEU A 515 " --> pdb=" O TYR A 511 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE A 516 " --> pdb=" O SER A 512 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER A 520 " --> pdb=" O PHE A 516 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N MET A 523 " --> pdb=" O GLN A 519 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE A 531 " --> pdb=" O VAL A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 551 removed outlier: 3.692A pdb=" N SER A 540 " --> pdb=" O GLU A 536 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N PHE A 543 " --> pdb=" O ALA A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 559 removed outlier: 3.687A pdb=" N THR A 556 " --> pdb=" O LEU A 553 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG A 557 " --> pdb=" O TYR A 554 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY A 558 " --> pdb=" O TYR A 555 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE A 559 " --> pdb=" O THR A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 575 removed outlier: 3.901A pdb=" N VAL A 567 " --> pdb=" O GLY A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 599 removed outlier: 3.607A pdb=" N VAL A 586 " --> pdb=" O PHE A 582 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N PHE A 587 " --> pdb=" O VAL A 583 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE A 599 " --> pdb=" O VAL A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 642 removed outlier: 3.690A pdb=" N PHE A 640 " --> pdb=" O GLU A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 671 removed outlier: 3.574A pdb=" N ILE A 661 " --> pdb=" O ALA A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 691 removed outlier: 3.527A pdb=" N LEU A 678 " --> pdb=" O LEU A 674 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN A 691 " --> pdb=" O ASN A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 712 removed outlier: 3.639A pdb=" N LEU A 699 " --> pdb=" O ASN A 695 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N PHE A 712 " --> pdb=" O THR A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 720 removed outlier: 4.290A pdb=" N PHE A 720 " --> pdb=" O MET A 716 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 212 Processing helix chain 'B' and resid 213 through 224 removed outlier: 3.716A pdb=" N GLY B 224 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 258 Processing helix chain 'B' and resid 260 through 270 Processing helix chain 'B' and resid 286 through 294 Processing helix chain 'B' and resid 298 through 320 removed outlier: 3.609A pdb=" N LYS B 303 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE B 304 " --> pdb=" O ASP B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 344 Processing helix chain 'B' and resid 345 through 354 Processing helix chain 'B' and resid 362 through 366 removed outlier: 4.096A pdb=" N LEU B 365 " --> pdb=" O CYS B 362 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N SER B 366 " --> pdb=" O ARG B 363 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 362 through 366' Processing helix chain 'B' and resid 394 through 401 removed outlier: 3.597A pdb=" N ILE B 399 " --> pdb=" O VAL B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 429 removed outlier: 4.018A pdb=" N ARG B 420 " --> pdb=" O GLU B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 454 Processing helix chain 'B' and resid 468 through 500 removed outlier: 3.609A pdb=" N PHE B 489 " --> pdb=" O GLY B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 504 No H-bonds generated for 'chain 'B' and resid 502 through 504' Processing helix chain 'B' and resid 505 through 510 removed outlier: 3.770A pdb=" N ASP B 509 " --> pdb=" O SER B 505 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER B 510 " --> pdb=" O LEU B 506 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 505 through 510' Processing helix chain 'B' and resid 510 through 531 removed outlier: 3.584A pdb=" N LEU B 515 " --> pdb=" O TYR B 511 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE B 516 " --> pdb=" O SER B 512 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER B 520 " --> pdb=" O PHE B 516 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N MET B 523 " --> pdb=" O GLN B 519 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE B 531 " --> pdb=" O VAL B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 551 removed outlier: 3.691A pdb=" N SER B 540 " --> pdb=" O GLU B 536 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE B 543 " --> pdb=" O ALA B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 559 removed outlier: 3.688A pdb=" N THR B 556 " --> pdb=" O LEU B 553 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG B 557 " --> pdb=" O TYR B 554 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY B 558 " --> pdb=" O TYR B 555 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE B 559 " --> pdb=" O THR B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 575 removed outlier: 3.900A pdb=" N VAL B 567 " --> pdb=" O GLY B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 599 removed outlier: 3.607A pdb=" N VAL B 586 " --> pdb=" O PHE B 582 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N PHE B 587 " --> pdb=" O VAL B 583 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE B 599 " --> pdb=" O VAL B 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 642 removed outlier: 3.690A pdb=" N PHE B 640 " --> pdb=" O GLU B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 671 removed outlier: 3.574A pdb=" N ILE B 661 " --> pdb=" O ALA B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 674 through 691 removed outlier: 3.527A pdb=" N LEU B 678 " --> pdb=" O LEU B 674 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLN B 691 " --> pdb=" O ASN B 687 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 712 removed outlier: 3.639A pdb=" N LEU B 699 " --> pdb=" O ASN B 695 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N PHE B 712 " --> pdb=" O THR B 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 720 removed outlier: 4.290A pdb=" N PHE B 720 " --> pdb=" O MET B 716 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 212 Processing helix chain 'C' and resid 213 through 224 removed outlier: 3.715A pdb=" N GLY C 224 " --> pdb=" O LEU C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 258 Processing helix chain 'C' and resid 260 through 270 Processing helix chain 'C' and resid 286 through 294 Processing helix chain 'C' and resid 298 through 320 removed outlier: 3.609A pdb=" N LYS C 303 " --> pdb=" O VAL C 299 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE C 304 " --> pdb=" O ASP C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 344 Processing helix chain 'C' and resid 345 through 354 Processing helix chain 'C' and resid 362 through 366 removed outlier: 4.096A pdb=" N LEU C 365 " --> pdb=" O CYS C 362 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N SER C 366 " --> pdb=" O ARG C 363 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 362 through 366' Processing helix chain 'C' and resid 394 through 401 removed outlier: 3.597A pdb=" N ILE C 399 " --> pdb=" O VAL C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 429 removed outlier: 4.019A pdb=" N ARG C 420 " --> pdb=" O GLU C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 454 removed outlier: 3.501A pdb=" N TYR C 435 " --> pdb=" O LYS C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 500 removed outlier: 3.609A pdb=" N PHE C 489 " --> pdb=" O GLY C 485 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 504 No H-bonds generated for 'chain 'C' and resid 502 through 504' Processing helix chain 'C' and resid 505 through 510 removed outlier: 3.770A pdb=" N ASP C 509 " --> pdb=" O SER C 505 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER C 510 " --> pdb=" O LEU C 506 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 505 through 510' Processing helix chain 'C' and resid 510 through 531 removed outlier: 3.583A pdb=" N LEU C 515 " --> pdb=" O TYR C 511 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N PHE C 516 " --> pdb=" O SER C 512 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER C 520 " --> pdb=" O PHE C 516 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N MET C 523 " --> pdb=" O GLN C 519 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE C 531 " --> pdb=" O VAL C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 536 through 551 removed outlier: 3.692A pdb=" N SER C 540 " --> pdb=" O GLU C 536 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE C 543 " --> pdb=" O ALA C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 559 removed outlier: 3.688A pdb=" N THR C 556 " --> pdb=" O LEU C 553 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG C 557 " --> pdb=" O TYR C 554 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY C 558 " --> pdb=" O TYR C 555 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE C 559 " --> pdb=" O THR C 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 563 through 575 removed outlier: 3.901A pdb=" N VAL C 567 " --> pdb=" O GLY C 563 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 599 removed outlier: 3.606A pdb=" N VAL C 586 " --> pdb=" O PHE C 582 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N PHE C 587 " --> pdb=" O VAL C 583 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE C 599 " --> pdb=" O VAL C 595 " (cutoff:3.500A) Processing helix chain 'C' and resid 629 through 642 removed outlier: 3.690A pdb=" N PHE C 640 " --> pdb=" O GLU C 636 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 671 removed outlier: 3.574A pdb=" N ILE C 661 " --> pdb=" O ALA C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 674 through 691 removed outlier: 3.527A pdb=" N LEU C 678 " --> pdb=" O LEU C 674 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN C 691 " --> pdb=" O ASN C 687 " (cutoff:3.500A) Processing helix chain 'C' and resid 692 through 712 removed outlier: 3.640A pdb=" N LEU C 699 " --> pdb=" O ASN C 695 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N PHE C 712 " --> pdb=" O THR C 708 " (cutoff:3.500A) Processing helix chain 'C' and resid 712 through 720 removed outlier: 4.289A pdb=" N PHE C 720 " --> pdb=" O MET C 716 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 212 Processing helix chain 'D' and resid 213 through 224 removed outlier: 3.715A pdb=" N GLY D 224 " --> pdb=" O LEU D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 258 Processing helix chain 'D' and resid 260 through 270 Processing helix chain 'D' and resid 286 through 294 Processing helix chain 'D' and resid 298 through 320 removed outlier: 3.608A pdb=" N LYS D 303 " --> pdb=" O VAL D 299 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE D 304 " --> pdb=" O ASP D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 344 Processing helix chain 'D' and resid 345 through 354 Processing helix chain 'D' and resid 362 through 366 removed outlier: 4.096A pdb=" N LEU D 365 " --> pdb=" O CYS D 362 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N SER D 366 " --> pdb=" O ARG D 363 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 362 through 366' Processing helix chain 'D' and resid 394 through 401 removed outlier: 3.597A pdb=" N ILE D 399 " --> pdb=" O VAL D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 429 removed outlier: 4.018A pdb=" N ARG D 420 " --> pdb=" O GLU D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 454 removed outlier: 3.501A pdb=" N TYR D 435 " --> pdb=" O LYS D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 468 through 500 removed outlier: 3.608A pdb=" N PHE D 489 " --> pdb=" O GLY D 485 " (cutoff:3.500A) Processing helix chain 'D' and resid 502 through 504 No H-bonds generated for 'chain 'D' and resid 502 through 504' Processing helix chain 'D' and resid 505 through 510 removed outlier: 3.771A pdb=" N ASP D 509 " --> pdb=" O SER D 505 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER D 510 " --> pdb=" O LEU D 506 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 505 through 510' Processing helix chain 'D' and resid 510 through 531 removed outlier: 3.584A pdb=" N LEU D 515 " --> pdb=" O TYR D 511 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE D 516 " --> pdb=" O SER D 512 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER D 520 " --> pdb=" O PHE D 516 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N MET D 523 " --> pdb=" O GLN D 519 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE D 531 " --> pdb=" O VAL D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 551 removed outlier: 3.691A pdb=" N SER D 540 " --> pdb=" O GLU D 536 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N PHE D 543 " --> pdb=" O ALA D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 559 removed outlier: 3.688A pdb=" N THR D 556 " --> pdb=" O LEU D 553 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG D 557 " --> pdb=" O TYR D 554 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY D 558 " --> pdb=" O TYR D 555 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE D 559 " --> pdb=" O THR D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 563 through 575 removed outlier: 3.902A pdb=" N VAL D 567 " --> pdb=" O GLY D 563 " (cutoff:3.500A) Processing helix chain 'D' and resid 580 through 599 removed outlier: 3.607A pdb=" N VAL D 586 " --> pdb=" O PHE D 582 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N PHE D 587 " --> pdb=" O VAL D 583 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE D 599 " --> pdb=" O VAL D 595 " (cutoff:3.500A) Processing helix chain 'D' and resid 629 through 642 removed outlier: 3.691A pdb=" N PHE D 640 " --> pdb=" O GLU D 636 " (cutoff:3.500A) Processing helix chain 'D' and resid 655 through 671 removed outlier: 3.574A pdb=" N ILE D 661 " --> pdb=" O ALA D 657 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 691 removed outlier: 3.527A pdb=" N LEU D 678 " --> pdb=" O LEU D 674 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN D 691 " --> pdb=" O ASN D 687 " (cutoff:3.500A) Processing helix chain 'D' and resid 692 through 712 removed outlier: 3.640A pdb=" N LEU D 699 " --> pdb=" O ASN D 695 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N PHE D 712 " --> pdb=" O THR D 708 " (cutoff:3.500A) Processing helix chain 'D' and resid 712 through 720 removed outlier: 4.291A pdb=" N PHE D 720 " --> pdb=" O MET D 716 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 372 through 374 removed outlier: 3.639A pdb=" N TRP A 372 " --> pdb=" O SER A 379 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL A 377 " --> pdb=" O TYR A 374 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N ASP A 737 " --> pdb=" O VAL A 728 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N VAL A 728 " --> pdb=" O ASP A 737 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 372 through 374 removed outlier: 3.639A pdb=" N TRP B 372 " --> pdb=" O SER B 379 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL B 377 " --> pdb=" O TYR B 374 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N ASP B 737 " --> pdb=" O VAL B 728 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N VAL B 728 " --> pdb=" O ASP B 737 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 372 through 374 removed outlier: 3.638A pdb=" N TRP C 372 " --> pdb=" O SER C 379 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL C 377 " --> pdb=" O TYR C 374 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N ASP C 737 " --> pdb=" O VAL C 728 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N VAL C 728 " --> pdb=" O ASP C 737 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 372 through 374 removed outlier: 3.639A pdb=" N TRP D 372 " --> pdb=" O SER D 379 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL D 377 " --> pdb=" O TYR D 374 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N ASP D 737 " --> pdb=" O VAL D 728 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N VAL D 728 " --> pdb=" O ASP D 737 " (cutoff:3.500A) 913 hydrogen bonds defined for protein. 2715 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.04 Time building geometry restraints manager: 3.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 15368 1.04 - 1.23: 601 1.23 - 1.43: 6749 1.43 - 1.63: 9570 1.63 - 1.83: 160 Bond restraints: 32448 Sorted by residual: bond pdb=" CAS 6EU A 901 " pdb=" CAX 6EU A 901 " ideal model delta sigma weight residual 1.334 1.606 -0.272 2.00e-02 2.50e+03 1.84e+02 bond pdb=" CAS 6EU D 901 " pdb=" CAX 6EU D 901 " ideal model delta sigma weight residual 1.334 1.605 -0.271 2.00e-02 2.50e+03 1.84e+02 bond pdb=" CAS 6EU B 901 " pdb=" CAX 6EU B 901 " ideal model delta sigma weight residual 1.334 1.605 -0.271 2.00e-02 2.50e+03 1.84e+02 bond pdb=" CAS 6EU C 902 " pdb=" CAX 6EU C 902 " ideal model delta sigma weight residual 1.334 1.605 -0.271 2.00e-02 2.50e+03 1.84e+02 bond pdb=" CAW 6EU C 902 " pdb=" CBA 6EU C 902 " ideal model delta sigma weight residual 1.339 1.519 -0.180 2.00e-02 2.50e+03 8.10e+01 ... (remaining 32443 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.17: 57591 3.17 - 6.33: 353 6.33 - 9.50: 44 9.50 - 12.66: 20 12.66 - 15.83: 8 Bond angle restraints: 58016 Sorted by residual: angle pdb=" N GLU B 391 " pdb=" CA GLU B 391 " pdb=" C GLU B 391 " ideal model delta sigma weight residual 111.02 118.42 -7.40 1.22e+00 6.72e-01 3.68e+01 angle pdb=" N GLU C 391 " pdb=" CA GLU C 391 " pdb=" C GLU C 391 " ideal model delta sigma weight residual 111.02 118.40 -7.38 1.22e+00 6.72e-01 3.66e+01 angle pdb=" N GLU A 391 " pdb=" CA GLU A 391 " pdb=" C GLU A 391 " ideal model delta sigma weight residual 111.02 118.37 -7.35 1.22e+00 6.72e-01 3.63e+01 angle pdb=" N GLU D 391 " pdb=" CA GLU D 391 " pdb=" C GLU D 391 " ideal model delta sigma weight residual 111.02 118.36 -7.34 1.22e+00 6.72e-01 3.62e+01 angle pdb=" CAM 6EU B 901 " pdb=" CAV 6EU B 901 " pdb=" CBD 6EU B 901 " ideal model delta sigma weight residual 115.62 99.79 15.83 3.00e+00 1.11e-01 2.78e+01 ... (remaining 58011 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.05: 15356 33.05 - 66.11: 500 66.11 - 99.16: 44 99.16 - 132.21: 12 132.21 - 165.27: 8 Dihedral angle restraints: 15920 sinusoidal: 8304 harmonic: 7616 Sorted by residual: dihedral pdb=" C1 LBN B 902 " pdb=" O1 LBN B 902 " pdb=" P1 LBN B 902 " pdb=" O3 LBN B 902 " ideal model delta sinusoidal sigma weight residual -84.60 80.67 -165.27 1 3.00e+01 1.11e-03 2.10e+01 dihedral pdb=" C1 LBN A 902 " pdb=" O1 LBN A 902 " pdb=" P1 LBN A 902 " pdb=" O3 LBN A 902 " ideal model delta sinusoidal sigma weight residual -84.60 80.64 -165.24 1 3.00e+01 1.11e-03 2.10e+01 dihedral pdb=" C1 LBN C 903 " pdb=" O1 LBN C 903 " pdb=" P1 LBN C 903 " pdb=" O3 LBN C 903 " ideal model delta sinusoidal sigma weight residual -84.60 80.62 -165.22 1 3.00e+01 1.11e-03 2.10e+01 ... (remaining 15917 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 2563 0.089 - 0.178: 53 0.178 - 0.267: 12 0.267 - 0.357: 14 0.357 - 0.446: 14 Chirality restraints: 2656 Sorted by residual: chirality pdb=" CAO 6EU B 901 " pdb=" CAJ 6EU B 901 " pdb=" CAR 6EU B 901 " pdb=" CAW 6EU B 901 " both_signs ideal model delta sigma weight residual False -2.24 -2.68 0.45 2.00e-01 2.50e+01 4.97e+00 chirality pdb=" CAO 6EU A 901 " pdb=" CAJ 6EU A 901 " pdb=" CAR 6EU A 901 " pdb=" CAW 6EU A 901 " both_signs ideal model delta sigma weight residual False -2.24 -2.68 0.44 2.00e-01 2.50e+01 4.93e+00 chirality pdb=" C2 LBN B 902 " pdb=" C1 LBN B 902 " pdb=" C3 LBN B 902 " pdb=" O7 LBN B 902 " both_signs ideal model delta sigma weight residual False -2.36 -2.81 0.44 2.00e-01 2.50e+01 4.93e+00 ... (remaining 2653 not shown) Planarity restraints: 4880 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 687 " 0.158 2.00e-02 2.50e+03 1.57e-01 3.69e+02 pdb=" CG ASN B 687 " -0.012 2.00e-02 2.50e+03 pdb=" OD1 ASN B 687 " -0.150 2.00e-02 2.50e+03 pdb=" ND2 ASN B 687 " -0.001 2.00e-02 2.50e+03 pdb="HD21 ASN B 687 " -0.221 2.00e-02 2.50e+03 pdb="HD22 ASN B 687 " 0.226 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 687 " -0.157 2.00e-02 2.50e+03 1.57e-01 3.69e+02 pdb=" CG ASN D 687 " 0.012 2.00e-02 2.50e+03 pdb=" OD1 ASN D 687 " 0.150 2.00e-02 2.50e+03 pdb=" ND2 ASN D 687 " 0.001 2.00e-02 2.50e+03 pdb="HD21 ASN D 687 " 0.221 2.00e-02 2.50e+03 pdb="HD22 ASN D 687 " -0.226 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 687 " 0.158 2.00e-02 2.50e+03 1.57e-01 3.69e+02 pdb=" CG ASN C 687 " -0.012 2.00e-02 2.50e+03 pdb=" OD1 ASN C 687 " -0.150 2.00e-02 2.50e+03 pdb=" ND2 ASN C 687 " -0.001 2.00e-02 2.50e+03 pdb="HD21 ASN C 687 " -0.221 2.00e-02 2.50e+03 pdb="HD22 ASN C 687 " 0.226 2.00e-02 2.50e+03 ... (remaining 4877 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 1849 2.20 - 2.80: 63275 2.80 - 3.40: 86163 3.40 - 4.00: 111679 4.00 - 4.60: 173355 Nonbonded interactions: 436321 Sorted by model distance: nonbonded pdb=" O ILE B 209 " pdb="HE22 GLN B 260 " model vdw 1.600 2.450 nonbonded pdb=" O ILE C 209 " pdb="HE22 GLN C 260 " model vdw 1.600 2.450 nonbonded pdb=" O ILE A 209 " pdb="HE22 GLN A 260 " model vdw 1.600 2.450 nonbonded pdb=" O ILE D 209 " pdb="HE22 GLN D 260 " model vdw 1.601 2.450 nonbonded pdb=" OD1 ASP B 296 " pdb=" HG1 THR B 298 " model vdw 1.621 2.450 ... (remaining 436316 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 197 through 752) selection = (chain 'B' and resid 197 through 752) selection = (chain 'C' and resid 197 through 752) selection = (chain 'D' and resid 197 through 752) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.200 Extract box with map and model: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 36.280 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.272 17064 Z= 0.533 Angle : 0.943 15.830 23212 Z= 0.431 Chirality : 0.054 0.446 2656 Planarity : 0.004 0.055 2844 Dihedral : 17.875 165.267 6260 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.70 (0.18), residues: 2076 helix: 0.13 (0.15), residues: 1288 sheet: -4.09 (0.44), residues: 56 loop : -1.06 (0.20), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 428 TYR 0.010 0.001 TYR C 309 PHE 0.013 0.001 PHE D 448 TRP 0.006 0.001 TRP D 372 HIS 0.002 0.001 HIS C 364 Details of bonding type rmsd covalent geometry : bond 0.01059 (17060) covalent geometry : angle 0.94201 (23204) SS BOND : bond 0.03920 ( 4) SS BOND : angle 2.05012 ( 8) hydrogen bonds : bond 0.20761 ( 913) hydrogen bonds : angle 7.39452 ( 2715) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Evaluate side-chains 205 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 561 GLN cc_start: 0.8034 (mp10) cc_final: 0.7426 (pm20) REVERT: A 677 MET cc_start: 0.8428 (ttp) cc_final: 0.8028 (ttm) REVERT: B 552 MET cc_start: 0.8883 (mtt) cc_final: 0.8452 (mtt) REVERT: B 677 MET cc_start: 0.8374 (ttp) cc_final: 0.8057 (ttm) REVERT: C 552 MET cc_start: 0.8818 (mtt) cc_final: 0.8434 (mtt) REVERT: C 677 MET cc_start: 0.8330 (ttp) cc_final: 0.7935 (ttm) REVERT: C 703 ILE cc_start: 0.8639 (mt) cc_final: 0.8376 (mt) REVERT: D 592 SER cc_start: 0.8910 (t) cc_final: 0.8471 (m) REVERT: D 677 MET cc_start: 0.8404 (ttp) cc_final: 0.8083 (ttm) outliers start: 0 outliers final: 0 residues processed: 205 average time/residue: 0.2307 time to fit residues: 75.0221 Evaluate side-chains 164 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 0.5980 chunk 107 optimal weight: 40.0000 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 7.9990 chunk 200 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 2.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 HIS A 676 ASN A 687 ASN B 498 GLN B 676 ASN B 687 ASN C 378 HIS C 498 GLN C 676 ASN C 687 ASN D 378 HIS D 676 ASN D 687 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.219759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.187778 restraints weight = 47033.856| |-----------------------------------------------------------------------------| r_work (start): 0.4094 rms_B_bonded: 1.41 r_work: 0.3535 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3205 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3204 r_free = 0.3204 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3204 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 17064 Z= 0.181 Angle : 0.589 7.426 23212 Z= 0.305 Chirality : 0.035 0.143 2656 Planarity : 0.004 0.053 2844 Dihedral : 16.202 164.402 2952 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.38 % Allowed : 7.27 % Favored : 92.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.18), residues: 2076 helix: 0.57 (0.15), residues: 1296 sheet: -4.19 (0.39), residues: 56 loop : -0.98 (0.20), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 432 TYR 0.014 0.001 TYR D 309 PHE 0.011 0.001 PHE B 448 TRP 0.007 0.001 TRP C 549 HIS 0.004 0.001 HIS C 378 Details of bonding type rmsd covalent geometry : bond 0.00403 (17060) covalent geometry : angle 0.58854 (23204) SS BOND : bond 0.00752 ( 4) SS BOND : angle 0.59759 ( 8) hydrogen bonds : bond 0.05082 ( 913) hydrogen bonds : angle 4.84394 ( 2715) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Evaluate side-chains 183 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 177 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 677 MET cc_start: 0.8803 (ttp) cc_final: 0.8391 (ttm) REVERT: B 677 MET cc_start: 0.8723 (ttp) cc_final: 0.8360 (ttm) REVERT: C 677 MET cc_start: 0.8653 (ttp) cc_final: 0.8244 (ttm) REVERT: D 311 GLU cc_start: 0.7197 (mm-30) cc_final: 0.6995 (tt0) REVERT: D 677 MET cc_start: 0.8784 (ttp) cc_final: 0.8383 (ttm) outliers start: 6 outliers final: 4 residues processed: 179 average time/residue: 0.2708 time to fit residues: 75.5952 Evaluate side-chains 173 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 169 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 320 HIS Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain C residue 378 HIS Chi-restraints excluded: chain D residue 378 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 50 optimal weight: 10.0000 chunk 44 optimal weight: 0.9990 chunk 175 optimal weight: 6.9990 chunk 40 optimal weight: 0.9980 chunk 2 optimal weight: 40.0000 chunk 94 optimal weight: 6.9990 chunk 100 optimal weight: 9.9990 chunk 77 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 197 optimal weight: 0.7980 chunk 172 optimal weight: 10.0000 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 378 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.221054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 113)---------------| | r_work = 0.3951 r_free = 0.3951 target = 0.171983 restraints weight = 47181.576| |-----------------------------------------------------------------------------| r_work (start): 0.3916 rms_B_bonded: 1.40 r_work: 0.3476 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3142 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3142 r_free = 0.3142 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3142 r_free = 0.3142 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3142 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17064 Z= 0.133 Angle : 0.505 5.630 23212 Z= 0.265 Chirality : 0.033 0.138 2656 Planarity : 0.004 0.061 2844 Dihedral : 14.840 171.238 2952 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.44 % Allowed : 8.27 % Favored : 91.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.18), residues: 2076 helix: 1.05 (0.15), residues: 1296 sheet: -4.03 (0.39), residues: 56 loop : -0.97 (0.20), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 432 TYR 0.014 0.001 TYR B 309 PHE 0.009 0.001 PHE B 448 TRP 0.005 0.001 TRP C 697 HIS 0.023 0.002 HIS D 378 Details of bonding type rmsd covalent geometry : bond 0.00279 (17060) covalent geometry : angle 0.50517 (23204) SS BOND : bond 0.00370 ( 4) SS BOND : angle 0.83209 ( 8) hydrogen bonds : bond 0.04331 ( 913) hydrogen bonds : angle 4.41365 ( 2715) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Evaluate side-chains 179 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 172 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 677 MET cc_start: 0.8787 (ttp) cc_final: 0.8389 (ttm) REVERT: B 677 MET cc_start: 0.8747 (ttp) cc_final: 0.8363 (ttm) REVERT: C 378 HIS cc_start: 0.7385 (m90) cc_final: 0.7018 (m90) REVERT: C 561 GLN cc_start: 0.7848 (mp10) cc_final: 0.7098 (pm20) REVERT: C 677 MET cc_start: 0.8706 (ttp) cc_final: 0.8275 (ttm) REVERT: D 304 PHE cc_start: 0.7797 (t80) cc_final: 0.7238 (t80) REVERT: D 311 GLU cc_start: 0.7284 (mm-30) cc_final: 0.7021 (tt0) REVERT: D 677 MET cc_start: 0.8782 (ttp) cc_final: 0.8388 (ttm) outliers start: 7 outliers final: 6 residues processed: 177 average time/residue: 0.2574 time to fit residues: 72.6905 Evaluate side-chains 169 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 163 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 687 ASN Chi-restraints excluded: chain B residue 320 HIS Chi-restraints excluded: chain B residue 378 HIS Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain D residue 378 HIS Chi-restraints excluded: chain D residue 646 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 25 optimal weight: 0.1980 chunk 55 optimal weight: 50.0000 chunk 44 optimal weight: 1.9990 chunk 68 optimal weight: 7.9990 chunk 163 optimal weight: 30.0000 chunk 45 optimal weight: 0.9990 chunk 124 optimal weight: 9.9990 chunk 34 optimal weight: 1.9990 chunk 165 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 overall best weight: 1.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 498 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.219667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.171588 restraints weight = 47067.013| |-----------------------------------------------------------------------------| r_work (start): 0.3918 rms_B_bonded: 1.37 r_work: 0.3487 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3239 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3239 r_free = 0.3239 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3239 r_free = 0.3239 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3239 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17064 Z= 0.148 Angle : 0.503 6.603 23212 Z= 0.263 Chirality : 0.034 0.129 2656 Planarity : 0.003 0.060 2844 Dihedral : 14.235 174.118 2952 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.50 % Allowed : 9.84 % Favored : 89.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.18), residues: 2076 helix: 1.26 (0.15), residues: 1300 sheet: -3.67 (0.41), residues: 56 loop : -1.04 (0.20), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 575 TYR 0.009 0.001 TYR B 309 PHE 0.011 0.001 PHE D 304 TRP 0.007 0.001 TRP C 372 HIS 0.011 0.001 HIS C 378 Details of bonding type rmsd covalent geometry : bond 0.00335 (17060) covalent geometry : angle 0.50279 (23204) SS BOND : bond 0.00361 ( 4) SS BOND : angle 1.44292 ( 8) hydrogen bonds : bond 0.03806 ( 913) hydrogen bonds : angle 4.19938 ( 2715) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Evaluate side-chains 175 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 167 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 561 GLN cc_start: 0.7930 (mp10) cc_final: 0.7239 (pm20) REVERT: B 677 MET cc_start: 0.8821 (ttp) cc_final: 0.8452 (ttm) REVERT: C 378 HIS cc_start: 0.7492 (m90) cc_final: 0.7163 (m90) REVERT: C 561 GLN cc_start: 0.7926 (mp10) cc_final: 0.7102 (pm20) REVERT: C 677 MET cc_start: 0.8791 (ttp) cc_final: 0.8337 (ttm) REVERT: D 311 GLU cc_start: 0.7231 (mm-30) cc_final: 0.6995 (tt0) REVERT: D 677 MET cc_start: 0.8825 (ttp) cc_final: 0.8449 (ttm) outliers start: 8 outliers final: 5 residues processed: 173 average time/residue: 0.2405 time to fit residues: 67.2495 Evaluate side-chains 169 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 164 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 687 ASN Chi-restraints excluded: chain B residue 320 HIS Chi-restraints excluded: chain B residue 378 HIS Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain D residue 378 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 193 optimal weight: 2.9990 chunk 107 optimal weight: 50.0000 chunk 129 optimal weight: 0.0170 chunk 102 optimal weight: 7.9990 chunk 197 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 29 optimal weight: 0.1980 chunk 185 optimal weight: 0.1980 chunk 89 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 187 optimal weight: 0.8980 overall best weight: 0.6620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 410 HIS C 410 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.222603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 124)---------------| | r_work = 0.3951 r_free = 0.3951 target = 0.171656 restraints weight = 47304.594| |-----------------------------------------------------------------------------| r_work (start): 0.3927 rms_B_bonded: 1.39 r_work: 0.3503 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3161 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3161 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 17064 Z= 0.092 Angle : 0.458 4.945 23212 Z= 0.239 Chirality : 0.032 0.119 2656 Planarity : 0.003 0.050 2844 Dihedral : 13.760 175.642 2952 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.81 % Allowed : 9.90 % Favored : 89.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.18), residues: 2076 helix: 1.65 (0.15), residues: 1296 sheet: -3.43 (0.43), residues: 56 loop : -1.02 (0.20), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 432 TYR 0.010 0.001 TYR B 309 PHE 0.007 0.001 PHE A 712 TRP 0.005 0.001 TRP A 549 HIS 0.009 0.001 HIS B 378 Details of bonding type rmsd covalent geometry : bond 0.00198 (17060) covalent geometry : angle 0.45736 (23204) SS BOND : bond 0.00695 ( 4) SS BOND : angle 0.88790 ( 8) hydrogen bonds : bond 0.03342 ( 913) hydrogen bonds : angle 3.94110 ( 2715) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Evaluate side-chains 177 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 164 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 339 LEU cc_start: 0.8028 (tt) cc_final: 0.7797 (tp) REVERT: B 561 GLN cc_start: 0.7948 (mp10) cc_final: 0.7242 (pm20) REVERT: B 677 MET cc_start: 0.8793 (ttp) cc_final: 0.8406 (ttm) REVERT: C 561 GLN cc_start: 0.7896 (mp10) cc_final: 0.7105 (pm20) REVERT: C 677 MET cc_start: 0.8759 (ttp) cc_final: 0.8354 (ttm) REVERT: D 311 GLU cc_start: 0.7210 (mm-30) cc_final: 0.6966 (tt0) REVERT: D 503 LEU cc_start: 0.7969 (mt) cc_final: 0.7621 (tp) REVERT: D 677 MET cc_start: 0.8805 (ttp) cc_final: 0.8446 (ttm) outliers start: 13 outliers final: 6 residues processed: 172 average time/residue: 0.2154 time to fit residues: 61.1991 Evaluate side-chains 165 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 159 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 687 ASN Chi-restraints excluded: chain B residue 320 HIS Chi-restraints excluded: chain B residue 378 HIS Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain D residue 378 HIS Chi-restraints excluded: chain D residue 646 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 122 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 161 optimal weight: 20.0000 chunk 105 optimal weight: 9.9990 chunk 201 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 134 optimal weight: 0.0000 chunk 32 optimal weight: 1.9990 chunk 114 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 overall best weight: 1.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.219853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.171494 restraints weight = 47006.239| |-----------------------------------------------------------------------------| r_work (start): 0.3909 rms_B_bonded: 1.38 r_work: 0.3474 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3212 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3212 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17064 Z= 0.150 Angle : 0.485 6.403 23212 Z= 0.251 Chirality : 0.034 0.119 2656 Planarity : 0.003 0.049 2844 Dihedral : 14.044 178.227 2952 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.63 % Allowed : 9.84 % Favored : 89.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.88 (0.18), residues: 2076 helix: 1.66 (0.15), residues: 1296 sheet: -3.29 (0.45), residues: 56 loop : -1.07 (0.20), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 575 TYR 0.008 0.001 TYR C 530 PHE 0.009 0.001 PHE D 448 TRP 0.006 0.001 TRP C 740 HIS 0.007 0.001 HIS C 378 Details of bonding type rmsd covalent geometry : bond 0.00341 (17060) covalent geometry : angle 0.48478 (23204) SS BOND : bond 0.00505 ( 4) SS BOND : angle 1.19420 ( 8) hydrogen bonds : bond 0.03516 ( 913) hydrogen bonds : angle 3.96180 ( 2715) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Evaluate side-chains 176 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 166 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 339 LEU cc_start: 0.8054 (tt) cc_final: 0.7824 (tp) REVERT: C 259 ASN cc_start: 0.5370 (t0) cc_final: 0.4944 (m-40) REVERT: C 561 GLN cc_start: 0.7989 (mp10) cc_final: 0.7137 (pm20) REVERT: C 677 MET cc_start: 0.8807 (ttp) cc_final: 0.8426 (ttm) REVERT: D 311 GLU cc_start: 0.7237 (mm-30) cc_final: 0.6992 (tt0) REVERT: D 503 LEU cc_start: 0.7974 (mt) cc_final: 0.7606 (tp) outliers start: 10 outliers final: 7 residues processed: 174 average time/residue: 0.2124 time to fit residues: 60.3160 Evaluate side-chains 172 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 165 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 687 ASN Chi-restraints excluded: chain B residue 320 HIS Chi-restraints excluded: chain B residue 378 HIS Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain C residue 378 HIS Chi-restraints excluded: chain D residue 378 HIS Chi-restraints excluded: chain D residue 387 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 118 optimal weight: 4.9990 chunk 175 optimal weight: 5.9990 chunk 129 optimal weight: 0.6980 chunk 64 optimal weight: 8.9990 chunk 205 optimal weight: 20.0000 chunk 189 optimal weight: 2.9990 chunk 52 optimal weight: 40.0000 chunk 60 optimal weight: 10.0000 chunk 200 optimal weight: 1.9990 chunk 153 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.215930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.184282 restraints weight = 47210.559| |-----------------------------------------------------------------------------| r_work (start): 0.4063 rms_B_bonded: 1.49 r_work: 0.3475 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3094 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3094 r_free = 0.3094 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3094 r_free = 0.3094 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3094 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 17064 Z= 0.278 Angle : 0.589 8.739 23212 Z= 0.299 Chirality : 0.039 0.178 2656 Planarity : 0.004 0.045 2844 Dihedral : 14.727 177.582 2952 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.75 % Allowed : 10.09 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.18), residues: 2076 helix: 1.21 (0.14), residues: 1300 sheet: -3.45 (0.44), residues: 56 loop : -1.14 (0.20), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 579 TYR 0.012 0.002 TYR C 530 PHE 0.016 0.002 PHE D 448 TRP 0.005 0.001 TRP C 549 HIS 0.006 0.001 HIS C 378 Details of bonding type rmsd covalent geometry : bond 0.00647 (17060) covalent geometry : angle 0.58832 (23204) SS BOND : bond 0.00309 ( 4) SS BOND : angle 1.23803 ( 8) hydrogen bonds : bond 0.04348 ( 913) hydrogen bonds : angle 4.23008 ( 2715) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Evaluate side-chains 184 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 172 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 339 LEU cc_start: 0.8025 (tt) cc_final: 0.7797 (tp) REVERT: B 369 PHE cc_start: 0.7778 (m-10) cc_final: 0.7513 (m-10) REVERT: C 259 ASN cc_start: 0.5625 (t0) cc_final: 0.5180 (m-40) REVERT: C 677 MET cc_start: 0.8927 (ttp) cc_final: 0.8683 (ttm) REVERT: D 503 LEU cc_start: 0.7921 (mt) cc_final: 0.7571 (tp) outliers start: 12 outliers final: 10 residues processed: 180 average time/residue: 0.2462 time to fit residues: 69.9623 Evaluate side-chains 179 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 169 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 687 ASN Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain B residue 320 HIS Chi-restraints excluded: chain B residue 378 HIS Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain C residue 378 HIS Chi-restraints excluded: chain D residue 378 HIS Chi-restraints excluded: chain D residue 646 ASP Chi-restraints excluded: chain D residue 689 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 175 optimal weight: 5.9990 chunk 206 optimal weight: 20.0000 chunk 151 optimal weight: 2.9990 chunk 155 optimal weight: 20.0000 chunk 5 optimal weight: 20.0000 chunk 179 optimal weight: 2.9990 chunk 83 optimal weight: 0.2980 chunk 105 optimal weight: 8.9990 chunk 187 optimal weight: 0.6980 chunk 113 optimal weight: 10.0000 chunk 128 optimal weight: 0.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 498 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.218497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 100)---------------| | r_work = 0.3913 r_free = 0.3913 target = 0.168245 restraints weight = 47114.210| |-----------------------------------------------------------------------------| r_work (start): 0.3882 rms_B_bonded: 1.41 r_work: 0.3421 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3137 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3137 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 17064 Z= 0.148 Angle : 0.502 6.972 23212 Z= 0.258 Chirality : 0.034 0.118 2656 Planarity : 0.003 0.045 2844 Dihedral : 14.247 177.126 2952 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.81 % Allowed : 10.28 % Favored : 88.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.18), residues: 2076 helix: 1.47 (0.15), residues: 1300 sheet: -3.30 (0.46), residues: 56 loop : -1.13 (0.20), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 409 TYR 0.010 0.001 TYR B 565 PHE 0.009 0.001 PHE D 448 TRP 0.006 0.001 TRP C 549 HIS 0.007 0.001 HIS C 378 Details of bonding type rmsd covalent geometry : bond 0.00339 (17060) covalent geometry : angle 0.50144 (23204) SS BOND : bond 0.00292 ( 4) SS BOND : angle 1.05673 ( 8) hydrogen bonds : bond 0.03587 ( 913) hydrogen bonds : angle 4.01077 ( 2715) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Evaluate side-chains 180 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 167 time to evaluate : 0.670 Fit side-chains revert: symmetry clash REVERT: A 339 LEU cc_start: 0.7981 (tt) cc_final: 0.7756 (tp) REVERT: B 369 PHE cc_start: 0.7754 (m-10) cc_final: 0.7451 (m-10) REVERT: C 259 ASN cc_start: 0.5509 (t0) cc_final: 0.5042 (m-40) REVERT: C 677 MET cc_start: 0.8834 (ttp) cc_final: 0.8616 (ttm) REVERT: D 503 LEU cc_start: 0.7917 (mt) cc_final: 0.7566 (tp) outliers start: 13 outliers final: 10 residues processed: 178 average time/residue: 0.2188 time to fit residues: 62.3123 Evaluate side-chains 176 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 166 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 687 ASN Chi-restraints excluded: chain B residue 320 HIS Chi-restraints excluded: chain B residue 378 HIS Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain C residue 378 HIS Chi-restraints excluded: chain D residue 378 HIS Chi-restraints excluded: chain D residue 468 THR Chi-restraints excluded: chain D residue 646 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 59 optimal weight: 30.0000 chunk 193 optimal weight: 0.9990 chunk 177 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 8 optimal weight: 10.0000 chunk 81 optimal weight: 0.6980 chunk 171 optimal weight: 0.0070 chunk 161 optimal weight: 20.0000 chunk 137 optimal weight: 2.9990 chunk 154 optimal weight: 0.7980 chunk 62 optimal weight: 5.9990 overall best weight: 0.9002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.219386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 118)---------------| | r_work = 0.3924 r_free = 0.3924 target = 0.169489 restraints weight = 47021.237| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 1.35 r_work: 0.3422 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3170 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3170 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 17064 Z= 0.105 Angle : 0.465 5.558 23212 Z= 0.241 Chirality : 0.032 0.139 2656 Planarity : 0.003 0.045 2844 Dihedral : 13.695 177.231 2952 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.44 % Allowed : 10.65 % Favored : 88.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.18), residues: 2076 helix: 1.77 (0.15), residues: 1300 sheet: -3.22 (0.47), residues: 56 loop : -1.09 (0.20), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 409 TYR 0.018 0.001 TYR C 309 PHE 0.009 0.001 PHE C 304 TRP 0.007 0.001 TRP C 549 HIS 0.007 0.001 HIS C 378 Details of bonding type rmsd covalent geometry : bond 0.00236 (17060) covalent geometry : angle 0.46499 (23204) SS BOND : bond 0.00189 ( 4) SS BOND : angle 0.96948 ( 8) hydrogen bonds : bond 0.03195 ( 913) hydrogen bonds : angle 3.83963 ( 2715) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Evaluate side-chains 172 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 165 time to evaluate : 0.758 Fit side-chains revert: symmetry clash REVERT: A 339 LEU cc_start: 0.7953 (tt) cc_final: 0.7740 (tp) REVERT: B 369 PHE cc_start: 0.7670 (m-10) cc_final: 0.7381 (m-10) REVERT: C 259 ASN cc_start: 0.5400 (t0) cc_final: 0.4924 (m-40) REVERT: D 424 ASP cc_start: 0.7756 (t0) cc_final: 0.7469 (t0) REVERT: D 503 LEU cc_start: 0.7902 (mt) cc_final: 0.7531 (tp) outliers start: 7 outliers final: 7 residues processed: 171 average time/residue: 0.2270 time to fit residues: 61.8266 Evaluate side-chains 172 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 165 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 687 ASN Chi-restraints excluded: chain B residue 320 HIS Chi-restraints excluded: chain B residue 378 HIS Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain C residue 378 HIS Chi-restraints excluded: chain D residue 378 HIS Chi-restraints excluded: chain D residue 646 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 17 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 202 optimal weight: 3.9990 chunk 191 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 172 optimal weight: 8.9990 chunk 54 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 14 optimal weight: 7.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.219081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 106)---------------| | r_work = 0.3939 r_free = 0.3939 target = 0.170979 restraints weight = 47426.086| |-----------------------------------------------------------------------------| r_work (start): 0.3920 rms_B_bonded: 1.39 r_work: 0.3487 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3452 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3452 r_free = 0.3452 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3452 r_free = 0.3452 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3452 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 17064 Z= 0.138 Angle : 0.478 6.398 23212 Z= 0.247 Chirality : 0.033 0.120 2656 Planarity : 0.003 0.045 2844 Dihedral : 13.737 177.661 2952 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.44 % Allowed : 10.78 % Favored : 88.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.98 (0.18), residues: 2076 helix: 1.76 (0.15), residues: 1300 sheet: -3.25 (0.47), residues: 56 loop : -1.09 (0.20), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 409 TYR 0.008 0.001 TYR A 351 PHE 0.008 0.001 PHE D 448 TRP 0.004 0.001 TRP A 549 HIS 0.007 0.001 HIS C 378 Details of bonding type rmsd covalent geometry : bond 0.00317 (17060) covalent geometry : angle 0.47802 (23204) SS BOND : bond 0.00283 ( 4) SS BOND : angle 0.82369 ( 8) hydrogen bonds : bond 0.03312 ( 913) hydrogen bonds : angle 3.84545 ( 2715) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Evaluate side-chains 175 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 168 time to evaluate : 0.856 Fit side-chains revert: symmetry clash REVERT: A 339 LEU cc_start: 0.8198 (tt) cc_final: 0.7970 (tp) REVERT: B 369 PHE cc_start: 0.7818 (m-10) cc_final: 0.7586 (m-10) REVERT: C 259 ASN cc_start: 0.5537 (t0) cc_final: 0.4997 (m-40) REVERT: D 523 MET cc_start: 0.7731 (ttp) cc_final: 0.7280 (ttp) outliers start: 7 outliers final: 6 residues processed: 174 average time/residue: 0.2512 time to fit residues: 69.1481 Evaluate side-chains 170 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 164 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 687 ASN Chi-restraints excluded: chain B residue 320 HIS Chi-restraints excluded: chain B residue 378 HIS Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain C residue 378 HIS Chi-restraints excluded: chain D residue 378 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 105 optimal weight: 6.9990 chunk 131 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 94 optimal weight: 5.9990 chunk 194 optimal weight: 0.9990 chunk 155 optimal weight: 20.0000 chunk 109 optimal weight: 6.9990 chunk 103 optimal weight: 9.9990 chunk 5 optimal weight: 20.0000 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 498 GLN C 498 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.218664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 103)---------------| | r_work = 0.3899 r_free = 0.3899 target = 0.166960 restraints weight = 47430.948| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 1.39 r_work: 0.3416 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3142 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3142 r_free = 0.3142 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3142 r_free = 0.3142 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3142 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 17064 Z= 0.157 Angle : 0.492 6.834 23212 Z= 0.253 Chirality : 0.034 0.117 2656 Planarity : 0.003 0.045 2844 Dihedral : 13.812 177.244 2952 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.31 % Allowed : 10.96 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (0.18), residues: 2076 helix: 1.70 (0.15), residues: 1300 sheet: -3.30 (0.47), residues: 56 loop : -1.10 (0.20), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 409 TYR 0.010 0.001 TYR C 309 PHE 0.010 0.001 PHE D 448 TRP 0.005 0.001 TRP C 549 HIS 0.006 0.001 HIS C 378 Details of bonding type rmsd covalent geometry : bond 0.00361 (17060) covalent geometry : angle 0.49203 (23204) SS BOND : bond 0.00257 ( 4) SS BOND : angle 0.78567 ( 8) hydrogen bonds : bond 0.03435 ( 913) hydrogen bonds : angle 3.87771 ( 2715) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7894.54 seconds wall clock time: 134 minutes 27.53 seconds (8067.53 seconds total)