Starting phenix.real_space_refine on Sat Jul 4 12:50:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7b05_11957/07_2026/7b05_11957.cif Found real_map, /net/cci-nas-00/data/ceres_data/7b05_11957/07_2026/7b05_11957.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7b05_11957/07_2026/7b05_11957.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7b05_11957/07_2026/7b05_11957.map" model { file = "/net/cci-nas-00/data/ceres_data/7b05_11957/07_2026/7b05_11957.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7b05_11957/07_2026/7b05_11957.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7b05_11957/07_2026/7b05_11957.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7b05_11957/07_2026/7b05_11957.cif" } resolution = 3.8 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= 0.000 sd= 0.002 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: 8 Type Number sf(0) Gaussians Ca 4 9.91 5 P 4 5.49 5 S 108 5.16 5 Cl 4 4.86 5 C 13760 2.51 5 N 3452 2.21 5 O 3716 1.98 5 F 8 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 224 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21056 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 645, 5215 Classifications: {'peptide': 645} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 21, 'TRANS': 623} Chain breaks: 5 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'GLU:plan': 7, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "A" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 49 Unusual residues: {' CA': 1, '44E': 1} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Restraints were copied for chains: B, C, D Time building chain proxies: 5.75, per 1000 atoms: 0.27 Number of scatterers: 21056 At special positions: 0 Unit cell: (141.05, 141.05, 138.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Ca 4 19.99 Cl 4 17.00 S 108 16.00 P 4 15.00 F 8 9.00 O 3716 8.00 N 3452 7.00 C 13760 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.85 Conformation dependent library (CDL) restraints added in 916.1 milliseconds 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4960 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 0 sheets defined 76.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 32 through 43 removed outlier: 3.906A pdb=" N TYR A 36 " --> pdb=" O GLN A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 59 removed outlier: 4.062A pdb=" N ILE A 57 " --> pdb=" O GLU A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 80 Processing helix chain 'A' and resid 82 through 92 removed outlier: 3.507A pdb=" N SER A 91 " --> pdb=" O GLU A 87 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE A 92 " --> pdb=" O LEU A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 107 removed outlier: 3.528A pdb=" N HIS A 102 " --> pdb=" O ASP A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 117 removed outlier: 3.828A pdb=" N VAL A 112 " --> pdb=" O VAL A 108 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ASN A 117 " --> pdb=" O GLU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 152 removed outlier: 3.543A pdb=" N THR A 152 " --> pdb=" O LEU A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 165 removed outlier: 3.800A pdb=" N ILE A 158 " --> pdb=" O ASN A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 204 Processing helix chain 'A' and resid 205 through 212 Processing helix chain 'A' and resid 215 through 234 removed outlier: 3.660A pdb=" N LEU A 223 " --> pdb=" O THR A 219 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LYS A 232 " --> pdb=" O GLN A 228 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL A 233 " --> pdb=" O GLU A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 258 removed outlier: 3.640A pdb=" N GLN A 258 " --> pdb=" O ASP A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 271 Processing helix chain 'A' and resid 286 through 295 Processing helix chain 'A' and resid 303 through 316 removed outlier: 3.522A pdb=" N ASP A 316 " --> pdb=" O SER A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 338 removed outlier: 3.619A pdb=" N ILE A 336 " --> pdb=" O THR A 332 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLY A 337 " --> pdb=" O CYS A 333 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU A 338 " --> pdb=" O VAL A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 350 Processing helix chain 'A' and resid 355 through 361 removed outlier: 3.674A pdb=" N ILE A 359 " --> pdb=" O TYR A 355 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG A 360 " --> pdb=" O GLY A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 383 Processing helix chain 'A' and resid 400 through 425 removed outlier: 4.042A pdb=" N LEU A 407 " --> pdb=" O GLU A 403 " (cutoff:3.500A) Proline residue: A 408 - end of helix Processing helix chain 'A' and resid 432 through 459 removed outlier: 3.633A pdb=" N LEU A 444 " --> pdb=" O VAL A 440 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N TYR A 445 " --> pdb=" O MET A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 491 removed outlier: 3.702A pdb=" N ARG A 491 " --> pdb=" O PHE A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 499 removed outlier: 3.859A pdb=" N THR A 497 " --> pdb=" O SER A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 512 removed outlier: 3.538A pdb=" N MET A 512 " --> pdb=" O SER A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 539 removed outlier: 3.850A pdb=" N LYS A 518 " --> pdb=" O LEU A 514 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N PHE A 519 " --> pdb=" O ASP A 515 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE A 521 " --> pdb=" O LEU A 517 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N ILE A 522 " --> pdb=" O LYS A 518 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLN A 536 " --> pdb=" O ASN A 532 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU A 537 " --> pdb=" O GLY A 533 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TYR A 538 " --> pdb=" O LEU A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 542 No H-bonds generated for 'chain 'A' and resid 540 through 542' Processing helix chain 'A' and resid 563 through 574 Processing helix chain 'A' and resid 575 through 577 No H-bonds generated for 'chain 'A' and resid 575 through 577' Processing helix chain 'A' and resid 580 through 584 removed outlier: 3.704A pdb=" N VAL A 583 " --> pdb=" O SER A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 611 removed outlier: 3.559A pdb=" N ALA A 598 " --> pdb=" O GLU A 594 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL A 611 " --> pdb=" O ILE A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 629 removed outlier: 3.779A pdb=" N ASN A 622 " --> pdb=" O ALA A 618 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLN A 625 " --> pdb=" O ASN A 621 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N HIS A 626 " --> pdb=" O ASN A 622 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASP A 629 " --> pdb=" O GLN A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 645 removed outlier: 3.980A pdb=" N PHE A 637 " --> pdb=" O ILE A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 720 removed outlier: 3.582A pdb=" N GLU A 707 " --> pdb=" O HIS A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 728 removed outlier: 3.594A pdb=" N GLU A 728 " --> pdb=" O LYS A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 754 removed outlier: 3.698A pdb=" N PHE A 735 " --> pdb=" O THR A 731 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LYS A 754 " --> pdb=" O ILE A 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 43 removed outlier: 3.906A pdb=" N TYR B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 59 removed outlier: 4.062A pdb=" N ILE B 57 " --> pdb=" O GLU B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 80 Processing helix chain 'B' and resid 82 through 92 removed outlier: 3.507A pdb=" N SER B 91 " --> pdb=" O GLU B 87 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE B 92 " --> pdb=" O LEU B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 107 removed outlier: 3.528A pdb=" N HIS B 102 " --> pdb=" O ASP B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 117 removed outlier: 3.828A pdb=" N VAL B 112 " --> pdb=" O VAL B 108 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ASN B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 152 removed outlier: 3.543A pdb=" N THR B 152 " --> pdb=" O LEU B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 165 removed outlier: 3.800A pdb=" N ILE B 158 " --> pdb=" O ASN B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 204 Processing helix chain 'B' and resid 205 through 212 Processing helix chain 'B' and resid 215 through 234 removed outlier: 3.660A pdb=" N LEU B 223 " --> pdb=" O THR B 219 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LYS B 232 " --> pdb=" O GLN B 228 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL B 233 " --> pdb=" O GLU B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 258 removed outlier: 3.640A pdb=" N GLN B 258 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 271 Processing helix chain 'B' and resid 286 through 295 Processing helix chain 'B' and resid 303 through 316 removed outlier: 3.522A pdb=" N ASP B 316 " --> pdb=" O SER B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 338 removed outlier: 3.619A pdb=" N ILE B 336 " --> pdb=" O THR B 332 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLY B 337 " --> pdb=" O CYS B 333 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU B 338 " --> pdb=" O VAL B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 350 Processing helix chain 'B' and resid 355 through 361 removed outlier: 3.674A pdb=" N ILE B 359 " --> pdb=" O TYR B 355 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG B 360 " --> pdb=" O GLY B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 383 Processing helix chain 'B' and resid 400 through 425 removed outlier: 4.042A pdb=" N LEU B 407 " --> pdb=" O GLU B 403 " (cutoff:3.500A) Proline residue: B 408 - end of helix Processing helix chain 'B' and resid 432 through 459 removed outlier: 3.633A pdb=" N LEU B 444 " --> pdb=" O VAL B 440 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N TYR B 445 " --> pdb=" O MET B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 491 removed outlier: 3.702A pdb=" N ARG B 491 " --> pdb=" O PHE B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 499 removed outlier: 3.859A pdb=" N THR B 497 " --> pdb=" O SER B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 512 removed outlier: 3.538A pdb=" N MET B 512 " --> pdb=" O SER B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 539 removed outlier: 3.850A pdb=" N LYS B 518 " --> pdb=" O LEU B 514 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N PHE B 519 " --> pdb=" O ASP B 515 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE B 521 " --> pdb=" O LEU B 517 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N ILE B 522 " --> pdb=" O LYS B 518 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLN B 536 " --> pdb=" O ASN B 532 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU B 537 " --> pdb=" O GLY B 533 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TYR B 538 " --> pdb=" O LEU B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 542 No H-bonds generated for 'chain 'B' and resid 540 through 542' Processing helix chain 'B' and resid 563 through 574 Processing helix chain 'B' and resid 575 through 577 No H-bonds generated for 'chain 'B' and resid 575 through 577' Processing helix chain 'B' and resid 580 through 584 removed outlier: 3.704A pdb=" N VAL B 583 " --> pdb=" O SER B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 611 removed outlier: 3.559A pdb=" N ALA B 598 " --> pdb=" O GLU B 594 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL B 611 " --> pdb=" O ILE B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 629 removed outlier: 3.779A pdb=" N ASN B 622 " --> pdb=" O ALA B 618 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLN B 625 " --> pdb=" O ASN B 621 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N HIS B 626 " --> pdb=" O ASN B 622 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASP B 629 " --> pdb=" O GLN B 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 645 removed outlier: 3.980A pdb=" N PHE B 637 " --> pdb=" O ILE B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 698 through 720 removed outlier: 3.582A pdb=" N GLU B 707 " --> pdb=" O HIS B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 728 removed outlier: 3.594A pdb=" N GLU B 728 " --> pdb=" O LYS B 725 " (cutoff:3.500A) Processing helix chain 'B' and resid 731 through 754 removed outlier: 3.698A pdb=" N PHE B 735 " --> pdb=" O THR B 731 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LYS B 754 " --> pdb=" O ILE B 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 43 removed outlier: 3.906A pdb=" N TYR C 36 " --> pdb=" O GLN C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 59 removed outlier: 4.062A pdb=" N ILE C 57 " --> pdb=" O GLU C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 80 Processing helix chain 'C' and resid 82 through 92 removed outlier: 3.507A pdb=" N SER C 91 " --> pdb=" O GLU C 87 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE C 92 " --> pdb=" O LEU C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 107 removed outlier: 3.528A pdb=" N HIS C 102 " --> pdb=" O ASP C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 117 removed outlier: 3.828A pdb=" N VAL C 112 " --> pdb=" O VAL C 108 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ASN C 117 " --> pdb=" O GLU C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 152 removed outlier: 3.543A pdb=" N THR C 152 " --> pdb=" O LEU C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 165 removed outlier: 3.800A pdb=" N ILE C 158 " --> pdb=" O ASN C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 204 Processing helix chain 'C' and resid 205 through 212 Processing helix chain 'C' and resid 215 through 234 removed outlier: 3.660A pdb=" N LEU C 223 " --> pdb=" O THR C 219 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LYS C 232 " --> pdb=" O GLN C 228 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL C 233 " --> pdb=" O GLU C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 258 removed outlier: 3.640A pdb=" N GLN C 258 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 271 Processing helix chain 'C' and resid 286 through 295 Processing helix chain 'C' and resid 303 through 316 removed outlier: 3.522A pdb=" N ASP C 316 " --> pdb=" O SER C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 338 removed outlier: 3.619A pdb=" N ILE C 336 " --> pdb=" O THR C 332 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLY C 337 " --> pdb=" O CYS C 333 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU C 338 " --> pdb=" O VAL C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 350 Processing helix chain 'C' and resid 355 through 361 removed outlier: 3.674A pdb=" N ILE C 359 " --> pdb=" O TYR C 355 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG C 360 " --> pdb=" O GLY C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 383 Processing helix chain 'C' and resid 400 through 425 removed outlier: 4.042A pdb=" N LEU C 407 " --> pdb=" O GLU C 403 " (cutoff:3.500A) Proline residue: C 408 - end of helix Processing helix chain 'C' and resid 432 through 459 removed outlier: 3.633A pdb=" N LEU C 444 " --> pdb=" O VAL C 440 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N TYR C 445 " --> pdb=" O MET C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 491 removed outlier: 3.702A pdb=" N ARG C 491 " --> pdb=" O PHE C 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 492 through 499 removed outlier: 3.859A pdb=" N THR C 497 " --> pdb=" O SER C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 512 removed outlier: 3.538A pdb=" N MET C 512 " --> pdb=" O SER C 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 539 removed outlier: 3.850A pdb=" N LYS C 518 " --> pdb=" O LEU C 514 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N PHE C 519 " --> pdb=" O ASP C 515 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE C 521 " --> pdb=" O LEU C 517 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N ILE C 522 " --> pdb=" O LYS C 518 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLN C 536 " --> pdb=" O ASN C 532 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU C 537 " --> pdb=" O GLY C 533 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TYR C 538 " --> pdb=" O LEU C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 540 through 542 No H-bonds generated for 'chain 'C' and resid 540 through 542' Processing helix chain 'C' and resid 563 through 574 Processing helix chain 'C' and resid 575 through 577 No H-bonds generated for 'chain 'C' and resid 575 through 577' Processing helix chain 'C' and resid 580 through 584 removed outlier: 3.704A pdb=" N VAL C 583 " --> pdb=" O SER C 580 " (cutoff:3.500A) Processing helix chain 'C' and resid 592 through 611 removed outlier: 3.559A pdb=" N ALA C 598 " --> pdb=" O GLU C 594 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL C 611 " --> pdb=" O ILE C 607 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 629 removed outlier: 3.779A pdb=" N ASN C 622 " --> pdb=" O ALA C 618 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLN C 625 " --> pdb=" O ASN C 621 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N HIS C 626 " --> pdb=" O ASN C 622 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASP C 629 " --> pdb=" O GLN C 625 " (cutoff:3.500A) Processing helix chain 'C' and resid 631 through 645 removed outlier: 3.980A pdb=" N PHE C 637 " --> pdb=" O ILE C 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 698 through 720 removed outlier: 3.582A pdb=" N GLU C 707 " --> pdb=" O HIS C 703 " (cutoff:3.500A) Processing helix chain 'C' and resid 724 through 728 removed outlier: 3.594A pdb=" N GLU C 728 " --> pdb=" O LYS C 725 " (cutoff:3.500A) Processing helix chain 'C' and resid 731 through 754 removed outlier: 3.698A pdb=" N PHE C 735 " --> pdb=" O THR C 731 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LYS C 754 " --> pdb=" O ILE C 750 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 43 removed outlier: 3.906A pdb=" N TYR D 36 " --> pdb=" O GLN D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 59 removed outlier: 4.062A pdb=" N ILE D 57 " --> pdb=" O GLU D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 80 Processing helix chain 'D' and resid 82 through 92 removed outlier: 3.507A pdb=" N SER D 91 " --> pdb=" O GLU D 87 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE D 92 " --> pdb=" O LEU D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 107 removed outlier: 3.528A pdb=" N HIS D 102 " --> pdb=" O ASP D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 117 removed outlier: 3.828A pdb=" N VAL D 112 " --> pdb=" O VAL D 108 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ASN D 117 " --> pdb=" O GLU D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 152 removed outlier: 3.543A pdb=" N THR D 152 " --> pdb=" O LEU D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 165 removed outlier: 3.800A pdb=" N ILE D 158 " --> pdb=" O ASN D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 204 Processing helix chain 'D' and resid 205 through 212 Processing helix chain 'D' and resid 215 through 234 removed outlier: 3.660A pdb=" N LEU D 223 " --> pdb=" O THR D 219 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LYS D 232 " --> pdb=" O GLN D 228 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL D 233 " --> pdb=" O GLU D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 258 removed outlier: 3.640A pdb=" N GLN D 258 " --> pdb=" O ASP D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 271 Processing helix chain 'D' and resid 286 through 295 Processing helix chain 'D' and resid 303 through 316 removed outlier: 3.522A pdb=" N ASP D 316 " --> pdb=" O SER D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 338 removed outlier: 3.619A pdb=" N ILE D 336 " --> pdb=" O THR D 332 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLY D 337 " --> pdb=" O CYS D 333 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU D 338 " --> pdb=" O VAL D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 350 Processing helix chain 'D' and resid 355 through 361 removed outlier: 3.674A pdb=" N ILE D 359 " --> pdb=" O TYR D 355 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG D 360 " --> pdb=" O GLY D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 383 Processing helix chain 'D' and resid 400 through 425 removed outlier: 4.042A pdb=" N LEU D 407 " --> pdb=" O GLU D 403 " (cutoff:3.500A) Proline residue: D 408 - end of helix Processing helix chain 'D' and resid 432 through 459 removed outlier: 3.633A pdb=" N LEU D 444 " --> pdb=" O VAL D 440 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N TYR D 445 " --> pdb=" O MET D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 491 removed outlier: 3.702A pdb=" N ARG D 491 " --> pdb=" O PHE D 487 " (cutoff:3.500A) Processing helix chain 'D' and resid 492 through 499 removed outlier: 3.859A pdb=" N THR D 497 " --> pdb=" O SER D 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 502 through 512 removed outlier: 3.538A pdb=" N MET D 512 " --> pdb=" O SER D 508 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 539 removed outlier: 3.850A pdb=" N LYS D 518 " --> pdb=" O LEU D 514 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N PHE D 519 " --> pdb=" O ASP D 515 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE D 521 " --> pdb=" O LEU D 517 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N ILE D 522 " --> pdb=" O LYS D 518 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLN D 536 " --> pdb=" O ASN D 532 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU D 537 " --> pdb=" O GLY D 533 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TYR D 538 " --> pdb=" O LEU D 534 " (cutoff:3.500A) Processing helix chain 'D' and resid 540 through 542 No H-bonds generated for 'chain 'D' and resid 540 through 542' Processing helix chain 'D' and resid 563 through 574 Processing helix chain 'D' and resid 575 through 577 No H-bonds generated for 'chain 'D' and resid 575 through 577' Processing helix chain 'D' and resid 580 through 584 removed outlier: 3.704A pdb=" N VAL D 583 " --> pdb=" O SER D 580 " (cutoff:3.500A) Processing helix chain 'D' and resid 592 through 611 removed outlier: 3.559A pdb=" N ALA D 598 " --> pdb=" O GLU D 594 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL D 611 " --> pdb=" O ILE D 607 " (cutoff:3.500A) Processing helix chain 'D' and resid 612 through 629 removed outlier: 3.779A pdb=" N ASN D 622 " --> pdb=" O ALA D 618 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLN D 625 " --> pdb=" O ASN D 621 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N HIS D 626 " --> pdb=" O ASN D 622 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASP D 629 " --> pdb=" O GLN D 625 " (cutoff:3.500A) Processing helix chain 'D' and resid 631 through 645 removed outlier: 3.980A pdb=" N PHE D 637 " --> pdb=" O ILE D 633 " (cutoff:3.500A) Processing helix chain 'D' and resid 698 through 720 removed outlier: 3.582A pdb=" N GLU D 707 " --> pdb=" O HIS D 703 " (cutoff:3.500A) Processing helix chain 'D' and resid 724 through 728 removed outlier: 3.594A pdb=" N GLU D 728 " --> pdb=" O LYS D 725 " (cutoff:3.500A) Processing helix chain 'D' and resid 731 through 754 removed outlier: 3.698A pdb=" N PHE D 735 " --> pdb=" O THR D 731 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LYS D 754 " --> pdb=" O ILE D 750 " (cutoff:3.500A) 1248 hydrogen bonds defined for protein. 3672 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: 3.54 Time building geometry restraints manager: 2.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 3308 1.30 - 1.43: 5944 1.43 - 1.56: 12124 1.56 - 1.68: 4 1.68 - 1.81: 180 Bond restraints: 21560 Sorted by residual: bond pdb=" O13 44E C1003 " pdb=" P 44E C1003 " ideal model delta sigma weight residual 1.684 1.504 0.180 2.00e-02 2.50e+03 8.12e+01 bond pdb=" O13 44E A1003 " pdb=" P 44E A1003 " ideal model delta sigma weight residual 1.684 1.504 0.180 2.00e-02 2.50e+03 8.12e+01 bond pdb=" O13 44E D1003 " pdb=" P 44E D1003 " ideal model delta sigma weight residual 1.684 1.504 0.180 2.00e-02 2.50e+03 8.12e+01 bond pdb=" O13 44E B1003 " pdb=" P 44E B1003 " ideal model delta sigma weight residual 1.684 1.504 0.180 2.00e-02 2.50e+03 8.12e+01 bond pdb=" CAV SJQ C1001 " pdb=" OAW SJQ C1001 " ideal model delta sigma weight residual 1.221 1.396 -0.175 2.00e-02 2.50e+03 7.61e+01 ... (remaining 21555 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.92: 29200 10.92 - 21.84: 24 21.84 - 32.77: 0 32.77 - 43.69: 0 43.69 - 54.61: 4 Bond angle restraints: 29228 Sorted by residual: angle pdb=" O13 44E C1003 " pdb=" P 44E C1003 " pdb=" O14 44E C1003 " ideal model delta sigma weight residual 54.79 109.40 -54.61 3.00e+00 1.11e-01 3.31e+02 angle pdb=" O13 44E D1003 " pdb=" P 44E D1003 " pdb=" O14 44E D1003 " ideal model delta sigma weight residual 54.79 109.40 -54.61 3.00e+00 1.11e-01 3.31e+02 angle pdb=" O13 44E A1003 " pdb=" P 44E A1003 " pdb=" O14 44E A1003 " ideal model delta sigma weight residual 54.79 109.40 -54.61 3.00e+00 1.11e-01 3.31e+02 angle pdb=" O13 44E B1003 " pdb=" P 44E B1003 " pdb=" O14 44E B1003 " ideal model delta sigma weight residual 54.79 109.40 -54.61 3.00e+00 1.11e-01 3.31e+02 angle pdb=" O12 44E C1003 " pdb=" P 44E C1003 " pdb=" O14 44E C1003 " ideal model delta sigma weight residual 127.76 109.80 17.96 3.00e+00 1.11e-01 3.58e+01 ... (remaining 29223 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.43: 11968 24.43 - 48.85: 828 48.85 - 73.27: 80 73.27 - 97.70: 24 97.70 - 122.12: 4 Dihedral angle restraints: 12904 sinusoidal: 5280 harmonic: 7624 Sorted by residual: dihedral pdb=" C2 44E A1003 " pdb=" C1 44E A1003 " pdb=" O11 44E A1003 " pdb=" P 44E A1003 " ideal model delta sinusoidal sigma weight residual 117.56 -120.32 -122.12 1 3.00e+01 1.11e-03 1.63e+01 dihedral pdb=" C2 44E B1003 " pdb=" C1 44E B1003 " pdb=" O11 44E B1003 " pdb=" P 44E B1003 " ideal model delta sinusoidal sigma weight residual 117.56 -120.32 -122.12 1 3.00e+01 1.11e-03 1.63e+01 dihedral pdb=" C2 44E D1003 " pdb=" C1 44E D1003 " pdb=" O11 44E D1003 " pdb=" P 44E D1003 " ideal model delta sinusoidal sigma weight residual 117.56 -120.32 -122.12 1 3.00e+01 1.11e-03 1.63e+01 ... (remaining 12901 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2508 0.052 - 0.105: 712 0.105 - 0.157: 56 0.157 - 0.209: 8 0.209 - 0.262: 4 Chirality restraints: 3288 Sorted by residual: chirality pdb=" CAH SJQ C1001 " pdb=" CAD SJQ C1001 " pdb=" CAG SJQ C1001 " pdb=" CAI SJQ C1001 " both_signs ideal model delta sigma weight residual False -2.55 -2.81 0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CAH SJQ D1001 " pdb=" CAD SJQ D1001 " pdb=" CAG SJQ D1001 " pdb=" CAI SJQ D1001 " both_signs ideal model delta sigma weight residual False -2.55 -2.81 0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CAH SJQ B1001 " pdb=" CAD SJQ B1001 " pdb=" CAG SJQ B1001 " pdb=" CAI SJQ B1001 " both_signs ideal model delta sigma weight residual False -2.55 -2.81 0.26 2.00e-01 2.50e+01 1.71e+00 ... (remaining 3285 not shown) Planarity restraints: 3616 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N SJQ C1001 " -0.082 2.00e-02 2.50e+03 4.72e-02 2.23e+01 pdb=" CA SJQ C1001 " 0.028 2.00e-02 2.50e+03 pdb=" CAL SJQ C1001 " 0.027 2.00e-02 2.50e+03 pdb=" CAP SJQ C1001 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N SJQ D1001 " -0.082 2.00e-02 2.50e+03 4.72e-02 2.23e+01 pdb=" CA SJQ D1001 " 0.028 2.00e-02 2.50e+03 pdb=" CAL SJQ D1001 " 0.027 2.00e-02 2.50e+03 pdb=" CAP SJQ D1001 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N SJQ B1001 " 0.082 2.00e-02 2.50e+03 4.72e-02 2.23e+01 pdb=" CA SJQ B1001 " -0.028 2.00e-02 2.50e+03 pdb=" CAL SJQ B1001 " -0.027 2.00e-02 2.50e+03 pdb=" CAP SJQ B1001 " -0.028 2.00e-02 2.50e+03 ... (remaining 3613 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 5672 2.79 - 3.32: 22124 3.32 - 3.85: 32858 3.85 - 4.37: 36232 4.37 - 4.90: 62528 Nonbonded interactions: 159414 Sorted by model distance: nonbonded pdb=" O LEU A 88 " pdb=" OG SER A 91 " model vdw 2.267 3.040 nonbonded pdb=" O LEU B 88 " pdb=" OG SER B 91 " model vdw 2.267 3.040 nonbonded pdb=" O LEU D 88 " pdb=" OG SER D 91 " model vdw 2.267 3.040 nonbonded pdb=" O LEU C 88 " pdb=" OG SER C 91 " model vdw 2.267 3.040 nonbonded pdb=" O ASN D 117 " pdb=" ND1 HIS D 118 " model vdw 2.285 3.120 ... (remaining 159409 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.050 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: 0.020 Extract box with map and model: 0.400 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.460 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 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: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 24.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 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 : 0.009 0.180 21560 Z= 0.436 Angle : 1.125 54.612 29228 Z= 0.499 Chirality : 0.045 0.262 3288 Planarity : 0.004 0.047 3616 Dihedral : 15.759 122.124 7944 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.12 (0.17), residues: 2532 helix: 0.72 (0.12), residues: 1824 sheet: None (None), residues: 0 loop : -2.15 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 491 TYR 0.022 0.002 TYR D 36 PHE 0.020 0.002 PHE D 539 TRP 0.008 0.001 TRP C 415 HIS 0.005 0.001 HIS C 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00946 / 0.44 (21560) covalent geometry : angle 1.12541 / 0.50 (29228) hydrogen bonds : bond 0.13574 / 9.40 ( 1248) hydrogen bonds : angle 5.63269 / 4.03 ( 3672) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 268 time to evaluate : 0.590 Fit side-chains REVERT: A 543 ASN cc_start: 0.8217 (t0) cc_final: 0.7970 (t0) REVERT: B 543 ASN cc_start: 0.8213 (t0) cc_final: 0.7967 (t0) REVERT: C 543 ASN cc_start: 0.8215 (t0) cc_final: 0.7969 (t0) REVERT: D 543 ASN cc_start: 0.8212 (t0) cc_final: 0.7970 (t0) outliers start: 0 outliers final: 0 residues processed: 268 average time/residue: 0.1333 time to fit residues: 58.2497 Evaluate side-chains 216 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 4.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 7.9990 chunk 71 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 622 ASN ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 622 ASN ** C 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 622 ASN ** D 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 622 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.102597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.081505 restraints weight = 50963.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.081503 restraints weight = 30358.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.082184 restraints weight = 26491.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.083232 restraints weight = 21109.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.083132 restraints weight = 18060.662| |-----------------------------------------------------------------------------| r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21560 Z= 0.136 Angle : 0.635 8.746 29228 Z= 0.316 Chirality : 0.038 0.151 3288 Planarity : 0.004 0.034 3616 Dihedral : 9.053 129.844 3028 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 0.36 % Allowed : 10.83 % Favored : 88.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.53 (0.17), residues: 2532 helix: 1.20 (0.12), residues: 1848 sheet: None (None), residues: 0 loop : -1.99 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 491 TYR 0.014 0.001 TYR A 36 PHE 0.016 0.001 PHE B 735 TRP 0.011 0.001 TRP C 635 HIS 0.004 0.001 HIS A 472 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.14 (21560) covalent geometry : angle 0.63473 / 0.32 (29228) hydrogen bonds : bond 0.05230 / 3.59 ( 1248) hydrogen bonds : angle 4.20702 / 2.99 ( 3672) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 296 time to evaluate : 0.887 Fit side-chains REVERT: A 346 CYS cc_start: 0.8672 (m) cc_final: 0.7819 (t) REVERT: B 346 CYS cc_start: 0.8677 (m) cc_final: 0.7819 (t) REVERT: C 346 CYS cc_start: 0.8673 (m) cc_final: 0.7817 (t) REVERT: D 346 CYS cc_start: 0.8675 (m) cc_final: 0.7814 (t) outliers start: 8 outliers final: 8 residues processed: 300 average time/residue: 0.1294 time to fit residues: 64.7064 Evaluate side-chains 250 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 242 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 753 MET Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 753 MET Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 753 MET Chi-restraints excluded: chain D residue 505 LEU Chi-restraints excluded: chain D residue 753 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 36 optimal weight: 4.9990 chunk 186 optimal weight: 0.7980 chunk 28 optimal weight: 8.9990 chunk 252 optimal weight: 0.8980 chunk 192 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 51 optimal weight: 0.4980 chunk 173 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.103569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.082307 restraints weight = 50996.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.082385 restraints weight = 29529.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.083061 restraints weight = 24946.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.083456 restraints weight = 20732.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.083654 restraints weight = 18880.107| |-----------------------------------------------------------------------------| r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 21560 Z= 0.121 Angle : 0.555 8.477 29228 Z= 0.282 Chirality : 0.037 0.156 3288 Planarity : 0.004 0.033 3616 Dihedral : 8.560 129.008 3028 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 1.42 % Allowed : 13.68 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.83 (0.17), residues: 2532 helix: 1.46 (0.12), residues: 1828 sheet: None (None), residues: 0 loop : -1.92 (0.24), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 491 TYR 0.014 0.001 TYR A 36 PHE 0.020 0.001 PHE B 735 TRP 0.007 0.001 TRP B 314 HIS 0.003 0.001 HIS D 325 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (21560) covalent geometry : angle 0.55476 / 0.28 (29228) hydrogen bonds : bond 0.04417 / 3.02 ( 1248) hydrogen bonds : angle 3.80191 / 2.70 ( 3672) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 280 time to evaluate : 0.880 Fit side-chains REVERT: A 335 PHE cc_start: 0.8706 (t80) cc_final: 0.8444 (t80) REVERT: A 378 PHE cc_start: 0.9026 (t80) cc_final: 0.8672 (t80) REVERT: B 335 PHE cc_start: 0.8706 (t80) cc_final: 0.8446 (t80) REVERT: C 335 PHE cc_start: 0.8710 (t80) cc_final: 0.8449 (t80) REVERT: C 378 PHE cc_start: 0.9026 (t80) cc_final: 0.8673 (t80) REVERT: D 335 PHE cc_start: 0.8711 (t80) cc_final: 0.8448 (t80) outliers start: 32 outliers final: 20 residues processed: 292 average time/residue: 0.1271 time to fit residues: 62.7284 Evaluate side-chains 262 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 242 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 753 MET Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 753 MET Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 753 MET Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 753 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 92 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 207 optimal weight: 0.2980 chunk 156 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 chunk 244 optimal weight: 3.9990 chunk 217 optimal weight: 10.0000 chunk 75 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 34 optimal weight: 10.0000 chunk 57 optimal weight: 3.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.102968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.081582 restraints weight = 51209.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.081459 restraints weight = 29948.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.082284 restraints weight = 25603.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.082645 restraints weight = 20895.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.082790 restraints weight = 19179.444| |-----------------------------------------------------------------------------| r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 21560 Z= 0.135 Angle : 0.550 9.104 29228 Z= 0.279 Chirality : 0.037 0.143 3288 Planarity : 0.004 0.034 3616 Dihedral : 8.313 129.015 3028 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.87 % Allowed : 16.16 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.06 (0.18), residues: 2532 helix: 1.66 (0.12), residues: 1824 sheet: None (None), residues: 0 loop : -1.91 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 491 TYR 0.014 0.001 TYR A 36 PHE 0.018 0.001 PHE B 735 TRP 0.008 0.001 TRP D 314 HIS 0.004 0.001 HIS B 325 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (21560) covalent geometry : angle 0.54963 / 0.28 (29228) hydrogen bonds : bond 0.04283 / 2.92 ( 1248) hydrogen bonds : angle 3.69716 / 2.62 ( 3672) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 272 time to evaluate : 0.859 Fit side-chains REVERT: A 335 PHE cc_start: 0.8735 (t80) cc_final: 0.8418 (t80) REVERT: A 378 PHE cc_start: 0.9057 (t80) cc_final: 0.8687 (t80) REVERT: B 335 PHE cc_start: 0.8735 (t80) cc_final: 0.8418 (t80) REVERT: C 335 PHE cc_start: 0.8738 (t80) cc_final: 0.8421 (t80) REVERT: C 378 PHE cc_start: 0.9054 (t80) cc_final: 0.8685 (t80) REVERT: D 335 PHE cc_start: 0.8739 (t80) cc_final: 0.8420 (t80) outliers start: 42 outliers final: 16 residues processed: 290 average time/residue: 0.1175 time to fit residues: 58.9331 Evaluate side-chains 268 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 252 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 611 VAL Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 611 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 78 optimal weight: 4.9990 chunk 38 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 24 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 173 optimal weight: 0.8980 chunk 186 optimal weight: 0.0010 chunk 219 optimal weight: 8.9990 chunk 202 optimal weight: 1.9990 chunk 193 optimal weight: 5.9990 chunk 166 optimal weight: 8.9990 overall best weight: 1.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.103191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.081686 restraints weight = 51234.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.081528 restraints weight = 31358.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.082212 restraints weight = 27994.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.082951 restraints weight = 22529.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.082990 restraints weight = 19858.432| |-----------------------------------------------------------------------------| r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 21560 Z= 0.143 Angle : 0.561 9.230 29228 Z= 0.282 Chirality : 0.037 0.138 3288 Planarity : 0.004 0.034 3616 Dihedral : 8.222 129.094 3028 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.42 % Favored : 95.42 % Rotamer: Outliers : 3.02 % Allowed : 16.03 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.12 (0.18), residues: 2532 helix: 1.73 (0.13), residues: 1824 sheet: None (None), residues: 0 loop : -1.97 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 491 TYR 0.014 0.001 TYR A 36 PHE 0.017 0.001 PHE B 735 TRP 0.009 0.001 TRP B 314 HIS 0.004 0.001 HIS B 325 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (21560) covalent geometry : angle 0.56110 / 0.28 (29228) hydrogen bonds : bond 0.04204 / 2.86 ( 1248) hydrogen bonds : angle 3.65601 / 2.60 ( 3672) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 256 time to evaluate : 0.834 Fit side-chains REVERT: A 335 PHE cc_start: 0.8714 (t80) cc_final: 0.8405 (t80) REVERT: A 378 PHE cc_start: 0.9065 (t80) cc_final: 0.8710 (t80) REVERT: A 451 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.8927 (tt) REVERT: B 335 PHE cc_start: 0.8716 (t80) cc_final: 0.8407 (t80) REVERT: B 451 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.8925 (tt) REVERT: C 335 PHE cc_start: 0.8718 (t80) cc_final: 0.8410 (t80) REVERT: C 378 PHE cc_start: 0.9065 (t80) cc_final: 0.8710 (t80) REVERT: C 451 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.8927 (tt) REVERT: D 335 PHE cc_start: 0.8720 (t80) cc_final: 0.8410 (t80) REVERT: D 451 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.8928 (tt) outliers start: 68 outliers final: 30 residues processed: 294 average time/residue: 0.1193 time to fit residues: 61.0771 Evaluate side-chains 282 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 248 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 118 HIS Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 753 MET Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 118 HIS Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 753 MET Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 118 HIS Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 611 VAL Chi-restraints excluded: chain C residue 753 MET Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 118 HIS Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 611 VAL Chi-restraints excluded: chain D residue 753 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 5 optimal weight: 0.9990 chunk 243 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 169 optimal weight: 0.6980 chunk 75 optimal weight: 0.7980 chunk 208 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 224 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 241 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.104661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.082940 restraints weight = 50393.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.083643 restraints weight = 28270.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.083899 restraints weight = 22968.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.084342 restraints weight = 20513.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.084476 restraints weight = 18879.923| |-----------------------------------------------------------------------------| r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 21560 Z= 0.112 Angle : 0.540 9.461 29228 Z= 0.271 Chirality : 0.036 0.142 3288 Planarity : 0.004 0.033 3616 Dihedral : 8.046 128.302 3028 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.02 % Allowed : 15.85 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.32 (0.18), residues: 2532 helix: 1.88 (0.13), residues: 1820 sheet: None (None), residues: 0 loop : -1.89 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 491 TYR 0.014 0.001 TYR A 355 PHE 0.016 0.001 PHE D 378 TRP 0.008 0.001 TRP B 635 HIS 0.004 0.001 HIS B 325 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (21560) covalent geometry : angle 0.54042 / 0.27 (29228) hydrogen bonds : bond 0.03782 / 2.58 ( 1248) hydrogen bonds : angle 3.49266 / 2.48 ( 3672) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 273 time to evaluate : 0.803 Fit side-chains REVERT: A 335 PHE cc_start: 0.8675 (t80) cc_final: 0.8391 (t80) REVERT: A 378 PHE cc_start: 0.9034 (t80) cc_final: 0.8678 (t80) REVERT: A 451 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8939 (tt) REVERT: B 335 PHE cc_start: 0.8671 (t80) cc_final: 0.8390 (t80) REVERT: B 451 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.8939 (tt) REVERT: C 335 PHE cc_start: 0.8679 (t80) cc_final: 0.8396 (t80) REVERT: C 378 PHE cc_start: 0.9032 (t80) cc_final: 0.8678 (t80) REVERT: C 451 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8941 (tt) REVERT: D 335 PHE cc_start: 0.8679 (t80) cc_final: 0.8395 (t80) REVERT: D 451 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8941 (tt) outliers start: 68 outliers final: 48 residues processed: 317 average time/residue: 0.1147 time to fit residues: 63.4575 Evaluate side-chains 285 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 233 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 118 HIS Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 563 THR Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 734 ASN Chi-restraints excluded: chain A residue 753 MET Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 118 HIS Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 563 THR Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 734 ASN Chi-restraints excluded: chain B residue 753 MET Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 118 HIS Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 609 LEU Chi-restraints excluded: chain C residue 734 ASN Chi-restraints excluded: chain C residue 753 MET Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 118 HIS Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 563 THR Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 734 ASN Chi-restraints excluded: chain D residue 753 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 184 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 154 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 chunk 253 optimal weight: 10.0000 chunk 231 optimal weight: 1.9990 chunk 98 optimal weight: 7.9990 chunk 182 optimal weight: 0.6980 chunk 10 optimal weight: 7.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.104798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.083287 restraints weight = 50820.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.083180 restraints weight = 30001.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.083939 restraints weight = 25548.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.084284 restraints weight = 20939.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.084587 restraints weight = 19284.215| |-----------------------------------------------------------------------------| r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 21560 Z= 0.112 Angle : 0.562 10.685 29228 Z= 0.275 Chirality : 0.036 0.164 3288 Planarity : 0.004 0.033 3616 Dihedral : 7.954 128.263 3028 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.44 % Allowed : 17.23 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.40 (0.18), residues: 2532 helix: 1.93 (0.13), residues: 1824 sheet: None (None), residues: 0 loop : -1.84 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 511 TYR 0.014 0.001 TYR C 355 PHE 0.015 0.001 PHE A 735 TRP 0.008 0.001 TRP B 314 HIS 0.004 0.001 HIS B 325 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (21560) covalent geometry : angle 0.56181 / 0.28 (29228) hydrogen bonds : bond 0.03720 / 2.54 ( 1248) hydrogen bonds : angle 3.44067 / 2.44 ( 3672) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 239 time to evaluate : 0.902 Fit side-chains REVERT: A 335 PHE cc_start: 0.8671 (t80) cc_final: 0.8359 (t80) REVERT: A 451 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.8959 (tt) REVERT: B 335 PHE cc_start: 0.8666 (t80) cc_final: 0.8356 (t80) REVERT: B 451 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8960 (tt) REVERT: C 335 PHE cc_start: 0.8674 (t80) cc_final: 0.8364 (t80) REVERT: C 451 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8960 (tt) REVERT: D 335 PHE cc_start: 0.8673 (t80) cc_final: 0.8360 (t80) REVERT: D 451 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.8964 (tt) outliers start: 55 outliers final: 48 residues processed: 274 average time/residue: 0.1198 time to fit residues: 56.7831 Evaluate side-chains 285 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 233 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 118 HIS Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 563 THR Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 734 ASN Chi-restraints excluded: chain A residue 753 MET Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 118 HIS Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 563 THR Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 734 ASN Chi-restraints excluded: chain B residue 753 MET Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 118 HIS Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 609 LEU Chi-restraints excluded: chain C residue 734 ASN Chi-restraints excluded: chain C residue 753 MET Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 118 HIS Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 563 THR Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 734 ASN Chi-restraints excluded: chain D residue 753 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 165 optimal weight: 8.9990 chunk 188 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 199 optimal weight: 1.9990 chunk 193 optimal weight: 5.9990 chunk 118 optimal weight: 0.7980 chunk 242 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 25 optimal weight: 10.0000 chunk 109 optimal weight: 2.9990 chunk 153 optimal weight: 8.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 704 GLN ** A 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.104194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.082716 restraints weight = 50660.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.083011 restraints weight = 29079.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.083308 restraints weight = 24621.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.083708 restraints weight = 22343.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.083822 restraints weight = 20569.130| |-----------------------------------------------------------------------------| r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 21560 Z= 0.129 Angle : 0.564 10.738 29228 Z= 0.278 Chirality : 0.037 0.180 3288 Planarity : 0.004 0.034 3616 Dihedral : 7.960 129.135 3028 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.98 % Allowed : 16.92 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.43 (0.18), residues: 2532 helix: 1.93 (0.13), residues: 1824 sheet: None (None), residues: 0 loop : -1.79 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 511 TYR 0.013 0.001 TYR A 36 PHE 0.018 0.001 PHE B 378 TRP 0.009 0.001 TRP B 314 HIS 0.004 0.001 HIS B 325 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (21560) covalent geometry : angle 0.56384 / 0.28 (29228) hydrogen bonds : bond 0.03817 / 2.60 ( 1248) hydrogen bonds : angle 3.43383 / 2.43 ( 3672) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 244 time to evaluate : 1.050 Fit side-chains REVERT: A 335 PHE cc_start: 0.8653 (t80) cc_final: 0.8385 (t80) REVERT: A 451 LEU cc_start: 0.9275 (OUTLIER) cc_final: 0.8979 (tt) REVERT: B 335 PHE cc_start: 0.8648 (t80) cc_final: 0.8387 (t80) REVERT: B 451 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.8977 (tt) REVERT: C 335 PHE cc_start: 0.8656 (t80) cc_final: 0.8392 (t80) REVERT: C 451 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.8979 (tt) REVERT: D 335 PHE cc_start: 0.8656 (t80) cc_final: 0.8392 (t80) REVERT: D 451 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.8980 (tt) outliers start: 67 outliers final: 58 residues processed: 286 average time/residue: 0.1214 time to fit residues: 60.2660 Evaluate side-chains 302 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 240 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 118 HIS Chi-restraints excluded: chain A residue 136 PHE Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 431 HIS Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 563 THR Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 734 ASN Chi-restraints excluded: chain A residue 753 MET Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 118 HIS Chi-restraints excluded: chain B residue 136 PHE Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 431 HIS Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 563 THR Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 734 ASN Chi-restraints excluded: chain B residue 753 MET Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 118 HIS Chi-restraints excluded: chain C residue 136 PHE Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 431 HIS Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 609 LEU Chi-restraints excluded: chain C residue 734 ASN Chi-restraints excluded: chain C residue 753 MET Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 118 HIS Chi-restraints excluded: chain D residue 136 PHE Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 372 SER Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 431 HIS Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 563 THR Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 734 ASN Chi-restraints excluded: chain D residue 753 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 112 optimal weight: 7.9990 chunk 85 optimal weight: 0.0570 chunk 119 optimal weight: 0.6980 chunk 17 optimal weight: 7.9990 chunk 235 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 203 optimal weight: 0.7980 chunk 4 optimal weight: 0.2980 chunk 169 optimal weight: 0.7980 chunk 50 optimal weight: 0.0980 chunk 19 optimal weight: 7.9990 overall best weight: 0.3898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 704 GLN ** A 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.106849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.085471 restraints weight = 50405.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.086065 restraints weight = 30406.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.086365 restraints weight = 23990.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.086694 restraints weight = 21880.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.086877 restraints weight = 20710.225| |-----------------------------------------------------------------------------| r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 21560 Z= 0.102 Angle : 0.556 11.222 29228 Z= 0.273 Chirality : 0.036 0.163 3288 Planarity : 0.004 0.033 3616 Dihedral : 7.834 127.184 3028 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.40 % Allowed : 17.10 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.43 (0.18), residues: 2532 helix: 1.92 (0.13), residues: 1844 sheet: None (None), residues: 0 loop : -1.85 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 511 TYR 0.015 0.001 TYR D 355 PHE 0.013 0.001 PHE D 340 TRP 0.006 0.001 TRP D 314 HIS 0.004 0.000 HIS C 325 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.10 (21560) covalent geometry : angle 0.55584 / 0.27 (29228) hydrogen bonds : bond 0.03290 / 2.25 ( 1248) hydrogen bonds : angle 3.32210 / 2.35 ( 3672) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 251 time to evaluate : 0.913 Fit side-chains REVERT: A 378 PHE cc_start: 0.8984 (t80) cc_final: 0.8681 (t80) REVERT: A 451 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.8969 (tt) REVERT: B 451 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.8968 (tt) REVERT: C 378 PHE cc_start: 0.8980 (t80) cc_final: 0.8678 (t80) REVERT: C 451 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8970 (tt) REVERT: D 451 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.8975 (tt) outliers start: 54 outliers final: 46 residues processed: 287 average time/residue: 0.1208 time to fit residues: 59.7457 Evaluate side-chains 291 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 241 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 118 HIS Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 563 THR Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 734 ASN Chi-restraints excluded: chain A residue 753 MET Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 118 HIS Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 563 THR Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 734 ASN Chi-restraints excluded: chain B residue 753 MET Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 118 HIS Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 372 SER Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 734 ASN Chi-restraints excluded: chain C residue 753 MET Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 118 HIS Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 372 SER Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 563 THR Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 734 ASN Chi-restraints excluded: chain D residue 753 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 48 optimal weight: 0.0570 chunk 223 optimal weight: 10.0000 chunk 24 optimal weight: 0.9980 chunk 141 optimal weight: 0.9980 chunk 122 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 249 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 107 optimal weight: 0.7980 chunk 221 optimal weight: 4.9990 chunk 38 optimal weight: 10.0000 overall best weight: 1.1700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 704 GLN ** A 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 704 GLN ** C 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 704 GLN ** D 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.105708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.084324 restraints weight = 51554.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.083706 restraints weight = 32061.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.084634 restraints weight = 28135.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.085444 restraints weight = 22327.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.085437 restraints weight = 19897.770| |-----------------------------------------------------------------------------| r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21560 Z= 0.117 Angle : 0.561 11.058 29228 Z= 0.280 Chirality : 0.037 0.171 3288 Planarity : 0.004 0.033 3616 Dihedral : 7.812 128.812 3028 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.44 % Allowed : 17.10 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.53 (0.18), residues: 2532 helix: 2.02 (0.13), residues: 1824 sheet: None (None), residues: 0 loop : -1.76 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 71 TYR 0.012 0.001 TYR C 355 PHE 0.021 0.001 PHE B 378 TRP 0.008 0.001 TRP B 314 HIS 0.004 0.001 HIS B 325 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (21560) covalent geometry : angle 0.56077 / 0.28 (29228) hydrogen bonds : bond 0.03473 / 2.37 ( 1248) hydrogen bonds : angle 3.30244 / 2.34 ( 3672) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 243 time to evaluate : 0.855 Fit side-chains REVERT: A 451 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.8987 (tt) REVERT: B 451 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.8986 (tt) REVERT: C 451 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.8988 (tt) REVERT: D 451 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.8989 (tt) REVERT: D 615 MET cc_start: 0.7281 (ptp) cc_final: 0.7030 (ptp) outliers start: 55 outliers final: 51 residues processed: 279 average time/residue: 0.1195 time to fit residues: 58.0015 Evaluate side-chains 300 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 245 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 118 HIS Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 431 HIS Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 563 THR Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 734 ASN Chi-restraints excluded: chain A residue 753 MET Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 118 HIS Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 431 HIS Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 563 THR Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 734 ASN Chi-restraints excluded: chain B residue 753 MET Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 118 HIS Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 372 SER Chi-restraints excluded: chain C residue 431 HIS Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 734 ASN Chi-restraints excluded: chain C residue 753 MET Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 118 HIS Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 372 SER Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 431 HIS Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 563 THR Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 620 MET Chi-restraints excluded: chain D residue 734 ASN Chi-restraints excluded: chain D residue 753 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 157 optimal weight: 0.9990 chunk 134 optimal weight: 8.9990 chunk 15 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 182 optimal weight: 0.8980 chunk 35 optimal weight: 8.9990 chunk 31 optimal weight: 0.8980 chunk 242 optimal weight: 0.5980 chunk 56 optimal weight: 0.6980 chunk 39 optimal weight: 8.9990 chunk 71 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 704 GLN ** B 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 704 GLN ** C 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.106332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.085057 restraints weight = 50697.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.085094 restraints weight = 30647.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.085845 restraints weight = 25040.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.086260 restraints weight = 20015.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.086375 restraints weight = 18306.522| |-----------------------------------------------------------------------------| r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 21560 Z= 0.106 Angle : 0.550 11.389 29228 Z= 0.274 Chirality : 0.036 0.152 3288 Planarity : 0.004 0.033 3616 Dihedral : 7.810 128.474 3028 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.58 % Allowed : 18.16 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.50 (0.18), residues: 2532 helix: 1.96 (0.13), residues: 1848 sheet: None (None), residues: 0 loop : -1.82 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 71 TYR 0.011 0.001 TYR A 36 PHE 0.013 0.001 PHE D 340 TRP 0.007 0.001 TRP B 314 HIS 0.004 0.000 HIS B 325 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (21560) covalent geometry : angle 0.54960 / 0.27 (29228) hydrogen bonds : bond 0.03353 / 2.29 ( 1248) hydrogen bonds : angle 3.24587 / 2.30 ( 3672) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2877.48 seconds wall clock time: 51 minutes 7.42 seconds (3067.42 seconds total)