Starting phenix.real_space_refine on Thu Mar 5 04:11:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xj1_33216/03_2026/7xj1_33216.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xj1_33216/03_2026/7xj1_33216.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7xj1_33216/03_2026/7xj1_33216.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xj1_33216/03_2026/7xj1_33216.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xj1_33216/03_2026/7xj1_33216.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xj1_33216/03_2026/7xj1_33216.map" } resolution = 2.93 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= 0.001 sd= 0.103 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: 5 Type Number sf(0) Gaussians S 120 5.16 5 C 12467 2.51 5 N 3129 2.21 5 O 3164 1.98 5 F 30 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 121 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18910 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 4593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4593 Classifications: {'peptide': 606} Incomplete info: {'truncation_to_alanine': 89} Link IDs: {'PTRANS': 13, 'TRANS': 592} Chain breaks: 4 Unresolved non-hydrogen bonds: 343 Unresolved non-hydrogen angles: 422 Unresolved non-hydrogen dihedrals: 275 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'ARG:plan': 7, 'GLU:plan': 29, 'GLN:plan1': 3, 'ASN:plan1': 6, 'ASP:plan': 12, 'TYR:plan': 1, 'HIS:plan': 2, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 242 Chain: "C" Number of atoms: 4647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 616, 4647 Classifications: {'peptide': 616} Incomplete info: {'truncation_to_alanine': 95} Link IDs: {'PTRANS': 14, 'TRANS': 601} Chain breaks: 3 Unresolved non-hydrogen bonds: 375 Unresolved non-hydrogen angles: 463 Unresolved non-hydrogen dihedrals: 305 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'ARG:plan': 9, 'GLU:plan': 28, 'GLN:plan1': 4, 'ASN:plan1': 7, 'ASP:plan': 11, 'TYR:plan': 1, 'HIS:plan': 2, 'TRP:plan': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 261 Chain: "A" Number of atoms: 4641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 616, 4641 Classifications: {'peptide': 616} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PTRANS': 14, 'TRANS': 601} Chain breaks: 3 Unresolved non-hydrogen bonds: 381 Unresolved non-hydrogen angles: 470 Unresolved non-hydrogen dihedrals: 310 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'ARG:plan': 9, 'GLU:plan': 28, 'GLN:plan1': 4, 'ASN:plan1': 8, 'ASP:plan': 11, 'TYR:plan': 1, 'HIS:plan': 2, 'TRP:plan': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 264 Chain: "D" Number of atoms: 4570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4570 Classifications: {'peptide': 606} Incomplete info: {'truncation_to_alanine': 95} Link IDs: {'PTRANS': 13, 'TRANS': 592} Chain breaks: 4 Unresolved non-hydrogen bonds: 366 Unresolved non-hydrogen angles: 449 Unresolved non-hydrogen dihedrals: 294 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'ARG:plan': 8, 'GLU:plan': 29, 'GLN:plan1': 3, 'ASN:plan1': 8, 'ASP:plan': 11, 'TYR:plan': 1, 'HIS:plan': 2, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 250 Chain: "B" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 104 Unusual residues: {'6OU': 3, 'EQK': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'6OU:plan-2': 3, '6OU:plan-3': 3} Unresolved non-hydrogen planarities: 24 Chain: "C" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 139 Unusual residues: {'6OU': 3, 'EQK': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 125 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'6OU:plan-2': 3, '6OU:plan-3': 3} Unresolved non-hydrogen planarities: 24 Chain: "A" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 124 Unusual residues: {'6OU': 2, 'EQK': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'6OU:plan-2': 2, '6OU:plan-3': 2} Unresolved non-hydrogen planarities: 16 Chain: "D" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 92 Unusual residues: {'6OU': 2, 'EQK': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'6OU:plan-2': 2, '6OU:plan-3': 2} Unresolved non-hydrogen planarities: 16 Time building chain proxies: 5.21, per 1000 atoms: 0.28 Number of scatterers: 18910 At special positions: 0 Unit cell: (149.76, 146.64, 125.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 120 16.00 F 30 9.00 O 3164 8.00 N 3129 7.00 C 12467 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: 1.61 Conformation dependent library (CDL) restraints added in 674.6 milliseconds 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4676 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 4 sheets defined 64.6% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'B' and resid 118 through 130 removed outlier: 3.809A pdb=" N ARG B 122 " --> pdb=" O ARG B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 148 removed outlier: 4.271A pdb=" N VAL B 136 " --> pdb=" O VAL B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 161 Processing helix chain 'B' and resid 170 through 178 Processing helix chain 'B' and resid 182 through 196 removed outlier: 3.579A pdb=" N ILE B 186 " --> pdb=" O ASN B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 205 removed outlier: 3.685A pdb=" N ASN B 205 " --> pdb=" O GLY B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 225 Processing helix chain 'B' and resid 227 through 237 Processing helix chain 'B' and resid 264 through 272 Processing helix chain 'B' and resid 274 through 283 Processing helix chain 'B' and resid 298 through 307 Processing helix chain 'B' and resid 315 through 328 removed outlier: 3.588A pdb=" N ARG B 319 " --> pdb=" O ASP B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 351 Processing helix chain 'B' and resid 353 through 362 Processing helix chain 'B' and resid 370 through 374 Processing helix chain 'B' and resid 402 through 410 Processing helix chain 'B' and resid 415 through 420 Processing helix chain 'B' and resid 422 through 436 removed outlier: 4.248A pdb=" N THR B 427 " --> pdb=" O GLU B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 461 Processing helix chain 'B' and resid 488 through 507 removed outlier: 3.592A pdb=" N LEU B 507 " --> pdb=" O ILE B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 542 removed outlier: 3.573A pdb=" N VAL B 525 " --> pdb=" O TRP B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 562 removed outlier: 4.080A pdb=" N CYS B 550 " --> pdb=" O GLU B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 579 Processing helix chain 'B' and resid 585 through 608 removed outlier: 3.690A pdb=" N LEU B 608 " --> pdb=" O ALA B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 637 Processing helix chain 'B' and resid 650 through 678 Processing helix chain 'B' and resid 680 through 707 removed outlier: 3.644A pdb=" N LEU B 707 " --> pdb=" O PHE B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 716 Processing helix chain 'C' and resid 119 through 130 removed outlier: 3.812A pdb=" N GLY C 130 " --> pdb=" O ALA C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 148 removed outlier: 3.943A pdb=" N VAL C 136 " --> pdb=" O VAL C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 161 Processing helix chain 'C' and resid 170 through 178 removed outlier: 3.664A pdb=" N ASN C 178 " --> pdb=" O LYS C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 196 removed outlier: 3.510A pdb=" N ILE C 186 " --> pdb=" O ASN C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 205 removed outlier: 3.572A pdb=" N ASN C 205 " --> pdb=" O GLY C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 225 Processing helix chain 'C' and resid 227 through 237 Processing helix chain 'C' and resid 264 through 272 Processing helix chain 'C' and resid 274 through 283 Processing helix chain 'C' and resid 298 through 307 Processing helix chain 'C' and resid 309 through 314 removed outlier: 3.676A pdb=" N GLN C 313 " --> pdb=" O ASP C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 328 Processing helix chain 'C' and resid 343 through 351 Processing helix chain 'C' and resid 353 through 362 Processing helix chain 'C' and resid 369 through 374 removed outlier: 4.402A pdb=" N SER C 372 " --> pdb=" O ARG C 369 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU C 373 " --> pdb=" O LEU C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 410 Processing helix chain 'C' and resid 415 through 420 Processing helix chain 'C' and resid 422 through 436 Processing helix chain 'C' and resid 436 through 461 Processing helix chain 'C' and resid 482 through 507 Processing helix chain 'C' and resid 518 through 520 No H-bonds generated for 'chain 'C' and resid 518 through 520' Processing helix chain 'C' and resid 521 through 542 removed outlier: 3.627A pdb=" N VAL C 525 " --> pdb=" O TRP C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 567 removed outlier: 3.723A pdb=" N CYS C 550 " --> pdb=" O GLU C 546 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LEU C 563 " --> pdb=" O TRP C 559 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N TYR C 564 " --> pdb=" O ALA C 560 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N TYR C 565 " --> pdb=" O ASN C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 608 removed outlier: 3.500A pdb=" N MET C 574 " --> pdb=" O GLN C 570 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LEU C 588 " --> pdb=" O LEU C 584 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS C 589 " --> pdb=" O HIS C 585 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 637 Processing helix chain 'C' and resid 650 through 680 Processing helix chain 'C' and resid 682 through 707 removed outlier: 4.227A pdb=" N LYS C 686 " --> pdb=" O GLU C 682 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLU C 689 " --> pdb=" O SER C 685 " (cutoff:3.500A) Processing helix chain 'C' and resid 708 through 716 Processing helix chain 'A' and resid 119 through 130 removed outlier: 3.734A pdb=" N GLY A 130 " --> pdb=" O ALA A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 149 removed outlier: 3.949A pdb=" N VAL A 136 " --> pdb=" O VAL A 132 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ARG A 149 " --> pdb=" O LEU A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 162 Processing helix chain 'A' and resid 170 through 178 removed outlier: 3.688A pdb=" N ASN A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 196 removed outlier: 3.529A pdb=" N ILE A 186 " --> pdb=" O ASN A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 205 removed outlier: 3.594A pdb=" N ASN A 205 " --> pdb=" O GLY A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 225 Processing helix chain 'A' and resid 227 through 237 Processing helix chain 'A' and resid 264 through 272 Processing helix chain 'A' and resid 274 through 283 Processing helix chain 'A' and resid 298 through 307 Processing helix chain 'A' and resid 316 through 328 Processing helix chain 'A' and resid 343 through 351 Processing helix chain 'A' and resid 353 through 362 Processing helix chain 'A' and resid 369 through 374 removed outlier: 4.401A pdb=" N SER A 372 " --> pdb=" O ARG A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 410 Processing helix chain 'A' and resid 415 through 420 Processing helix chain 'A' and resid 422 through 436 Processing helix chain 'A' and resid 436 through 461 Processing helix chain 'A' and resid 482 through 507 Processing helix chain 'A' and resid 520 through 542 removed outlier: 4.416A pdb=" N PHE A 524 " --> pdb=" O ALA A 520 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL A 525 " --> pdb=" O TRP A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 567 removed outlier: 3.770A pdb=" N CYS A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N LEU A 563 " --> pdb=" O TRP A 559 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N TYR A 564 " --> pdb=" O ALA A 560 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N TYR A 565 " --> pdb=" O ASN A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 608 removed outlier: 4.532A pdb=" N MET A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N TYR A 575 " --> pdb=" O SER A 571 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N LEU A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS A 589 " --> pdb=" O HIS A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 637 Processing helix chain 'A' and resid 650 through 680 Processing helix chain 'A' and resid 682 through 707 removed outlier: 3.926A pdb=" N LYS A 686 " --> pdb=" O GLU A 682 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLU A 689 " --> pdb=" O SER A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 716 Processing helix chain 'D' and resid 119 through 130 Processing helix chain 'D' and resid 132 through 149 removed outlier: 4.374A pdb=" N VAL D 136 " --> pdb=" O VAL D 132 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG D 149 " --> pdb=" O LEU D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 161 Processing helix chain 'D' and resid 170 through 178 Processing helix chain 'D' and resid 183 through 196 Processing helix chain 'D' and resid 199 through 205 removed outlier: 3.715A pdb=" N ASN D 205 " --> pdb=" O GLY D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 225 Processing helix chain 'D' and resid 227 through 237 Processing helix chain 'D' and resid 264 through 272 Processing helix chain 'D' and resid 274 through 283 Processing helix chain 'D' and resid 298 through 307 Processing helix chain 'D' and resid 315 through 328 removed outlier: 4.325A pdb=" N ARG D 319 " --> pdb=" O ASP D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 351 Processing helix chain 'D' and resid 353 through 362 Processing helix chain 'D' and resid 370 through 374 Processing helix chain 'D' and resid 402 through 410 Processing helix chain 'D' and resid 415 through 420 Processing helix chain 'D' and resid 422 through 436 removed outlier: 4.242A pdb=" N THR D 427 " --> pdb=" O GLU D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 461 Processing helix chain 'D' and resid 486 through 507 removed outlier: 4.094A pdb=" N VAL D 490 " --> pdb=" O GLY D 486 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LEU D 491 " --> pdb=" O ARG D 487 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 542 Processing helix chain 'D' and resid 546 through 562 removed outlier: 4.010A pdb=" N CYS D 550 " --> pdb=" O GLU D 546 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 582 removed outlier: 5.063A pdb=" N GLN D 580 " --> pdb=" O SER D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 585 through 608 removed outlier: 3.557A pdb=" N LYS D 589 " --> pdb=" O HIS D 585 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N PHE D 590 " --> pdb=" O ASP D 586 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU D 608 " --> pdb=" O ALA D 604 " (cutoff:3.500A) Processing helix chain 'D' and resid 624 through 637 Processing helix chain 'D' and resid 650 through 678 Processing helix chain 'D' and resid 680 through 707 removed outlier: 3.574A pdb=" N LEU D 707 " --> pdb=" O PHE D 703 " (cutoff:3.500A) Processing helix chain 'D' and resid 708 through 716 Processing sheet with id=AA1, first strand: chain 'B' and resid 376 through 378 Processing sheet with id=AA2, first strand: chain 'C' and resid 385 through 391 Processing sheet with id=AA3, first strand: chain 'A' and resid 385 through 391 Processing sheet with id=AA4, first strand: chain 'D' and resid 376 through 378 1120 hydrogen bonds defined for protein. 3315 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: 3.10 Time building geometry restraints manager: 2.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.26: 2831 1.26 - 1.40: 4984 1.40 - 1.54: 10981 1.54 - 1.67: 334 1.67 - 1.81: 186 Bond restraints: 19316 Sorted by residual: bond pdb=" C20 EQK D1103 " pdb=" S01 EQK D1103 " ideal model delta sigma weight residual 1.732 1.505 0.227 2.00e-02 2.50e+03 1.29e+02 bond pdb=" C20 EQK B1602 " pdb=" S01 EQK B1602 " ideal model delta sigma weight residual 1.732 1.506 0.226 2.00e-02 2.50e+03 1.28e+02 bond pdb=" C20 EQK A1801 " pdb=" S01 EQK A1801 " ideal model delta sigma weight residual 1.732 1.508 0.224 2.00e-02 2.50e+03 1.26e+02 bond pdb=" C20 EQK C1106 " pdb=" S01 EQK C1106 " ideal model delta sigma weight residual 1.732 1.508 0.224 2.00e-02 2.50e+03 1.25e+02 bond pdb=" C20 EQK A1802 " pdb=" S01 EQK A1802 " ideal model delta sigma weight residual 1.732 1.510 0.222 2.00e-02 2.50e+03 1.24e+02 ... (remaining 19311 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.85: 26032 3.85 - 7.69: 205 7.69 - 11.54: 34 11.54 - 15.39: 0 15.39 - 19.24: 10 Bond angle restraints: 26281 Sorted by residual: angle pdb=" C20 EQK A1805 " pdb=" S01 EQK A1805 " pdb=" C25 EQK A1805 " ideal model delta sigma weight residual 88.77 108.01 -19.24 3.00e+00 1.11e-01 4.11e+01 angle pdb=" C20 EQK C1101 " pdb=" S01 EQK C1101 " pdb=" C25 EQK C1101 " ideal model delta sigma weight residual 88.77 107.75 -18.98 3.00e+00 1.11e-01 4.00e+01 angle pdb=" C20 EQK B1603 " pdb=" S01 EQK B1603 " pdb=" C25 EQK B1603 " ideal model delta sigma weight residual 88.77 107.68 -18.91 3.00e+00 1.11e-01 3.97e+01 angle pdb=" C20 EQK D1101 " pdb=" S01 EQK D1101 " pdb=" C25 EQK D1101 " ideal model delta sigma weight residual 88.77 107.39 -18.62 3.00e+00 1.11e-01 3.85e+01 angle pdb=" C20 EQK D1103 " pdb=" S01 EQK D1103 " pdb=" C25 EQK D1103 " ideal model delta sigma weight residual 88.77 106.95 -18.18 3.00e+00 1.11e-01 3.67e+01 ... (remaining 26276 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.46: 9932 18.46 - 36.91: 1080 36.91 - 55.37: 279 55.37 - 73.82: 67 73.82 - 92.28: 31 Dihedral angle restraints: 11389 sinusoidal: 4199 harmonic: 7190 Sorted by residual: dihedral pdb=" CA THR B 680 " pdb=" C THR B 680 " pdb=" N VAL B 681 " pdb=" CA VAL B 681 " ideal model delta harmonic sigma weight residual -180.00 -152.11 -27.89 0 5.00e+00 4.00e-02 3.11e+01 dihedral pdb=" CA GLY D 678 " pdb=" C GLY D 678 " pdb=" N GLU D 679 " pdb=" CA GLU D 679 " ideal model delta harmonic sigma weight residual -180.00 -152.82 -27.18 0 5.00e+00 4.00e-02 2.95e+01 dihedral pdb=" CA THR D 680 " pdb=" C THR D 680 " pdb=" N VAL D 681 " pdb=" CA VAL D 681 " ideal model delta harmonic sigma weight residual -180.00 -153.47 -26.53 0 5.00e+00 4.00e-02 2.82e+01 ... (remaining 11386 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 2883 0.072 - 0.143: 196 0.143 - 0.215: 9 0.215 - 0.287: 2 0.287 - 0.358: 2 Chirality restraints: 3092 Sorted by residual: chirality pdb=" CA TRP C 739 " pdb=" N TRP C 739 " pdb=" C TRP C 739 " pdb=" CB TRP C 739 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.21e+00 chirality pdb=" CA PHE C 522 " pdb=" N PHE C 522 " pdb=" C PHE C 522 " pdb=" CB PHE C 522 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" CA ILE C 516 " pdb=" N ILE C 516 " pdb=" C ILE C 516 " pdb=" CB ILE C 516 " both_signs ideal model delta sigma weight residual False 2.43 2.18 0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 3089 not shown) Planarity restraints: 3199 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 403 " 0.014 2.00e-02 2.50e+03 2.99e-02 8.96e+00 pdb=" C VAL B 403 " -0.052 2.00e-02 2.50e+03 pdb=" O VAL B 403 " 0.019 2.00e-02 2.50e+03 pdb=" N LEU B 404 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 403 " -0.014 2.00e-02 2.50e+03 2.98e-02 8.86e+00 pdb=" C VAL D 403 " 0.051 2.00e-02 2.50e+03 pdb=" O VAL D 403 " -0.019 2.00e-02 2.50e+03 pdb=" N LEU D 404 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 583 " 0.012 2.00e-02 2.50e+03 2.35e-02 5.51e+00 pdb=" C ILE A 583 " -0.041 2.00e-02 2.50e+03 pdb=" O ILE A 583 " 0.015 2.00e-02 2.50e+03 pdb=" N LEU A 584 " 0.014 2.00e-02 2.50e+03 ... (remaining 3196 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1929 2.74 - 3.28: 19077 3.28 - 3.82: 31748 3.82 - 4.36: 38439 4.36 - 4.90: 66401 Nonbonded interactions: 157594 Sorted by model distance: nonbonded pdb=" O GLU A 682 " pdb=" OG SER A 685 " model vdw 2.200 3.040 nonbonded pdb=" NH1 ARG D 567 " pdb=" OE1 GLN D 695 " model vdw 2.208 3.120 nonbonded pdb=" NH1 ARG D 363 " pdb=" O LEU D 373 " model vdw 2.212 3.120 nonbonded pdb=" O LYS C 545 " pdb=" OH TYR D 650 " model vdw 2.218 3.040 nonbonded pdb=" NH1 ARG B 363 " pdb=" O LEU B 373 " model vdw 2.220 3.120 ... (remaining 157589 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 118 through 464 or resid 484 through 508 or resid 515 thro \ ugh 518 or (resid 519 through 520 and (name N or name CA or name C or name O or \ name CB )) or resid 521 through 582 or (resid 583 and (name N or name CA or name \ C or name O or name CB )) or resid 584 through 648 or (resid 649 and (name N or \ name CA or name C or name O or name CB )) or resid 650 through 681 or (resid 68 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 683 through \ 716 or (resid 717 and (name N or name CA or name C or name O or name CB or name \ CG or name SD )) or resid 718 through 754 or resid 1804)) selection = (chain 'B' and ((resid 118 through 123 and (name N or name CA or name C or name \ O or name CB )) or resid 124 through 410 or (resid 411 through 412 and (name N o \ r name CA or name C or name O or name CB )) or resid 413 through 644 or (resid 6 \ 45 and (name N or name CA or name C or name O or name CB )) or resid 646 through \ 676 or (resid 677 and (name N or name CA or name C or name O or name CB )) or r \ esid 678 through 716 or (resid 717 and (name N or name CA or name C or name O or \ name CB or name CG or name SD )) or resid 718 through 734 or (resid 735 through \ 736 and (name N or name CA or name C or name O or name CB )) or resid 737 throu \ gh 754 or resid 1604)) selection = (chain 'C' and (resid 118 through 464 or resid 484 through 508 or resid 515 thro \ ugh 518 or (resid 519 through 520 and (name N or name CA or name C or name O or \ name CB )) or resid 521 through 582 or (resid 583 and (name N or name CA or name \ C or name O or name CB )) or resid 584 through 648 or (resid 649 and (name N or \ name CA or name C or name O or name CB )) or resid 650 through 681 or (resid 68 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 683 through \ 734 or (resid 735 through 736 and (name N or name CA or name C or name O or name \ CB )) or resid 737 or (resid 738 and (name N or name CA or name C or name O or \ name CB )) or resid 739 through 754 or resid 1104)) selection = (chain 'D' and (resid 118 through 518 or (resid 519 through 520 and (name N or n \ ame CA or name C or name O or name CB )) or resid 521 through 644 or (resid 645 \ and (name N or name CA or name C or name O or name CB )) or resid 646 through 67 \ 6 or (resid 677 and (name N or name CA or name C or name O or name CB )) or resi \ d 678 through 754 or resid 1104)) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.200 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: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.900 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.030 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:7.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 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 : 0.015 0.227 19316 Z= 0.742 Angle : 0.955 19.237 26281 Z= 0.457 Chirality : 0.041 0.358 3092 Planarity : 0.004 0.041 3199 Dihedral : 17.487 92.280 6713 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 4.02 % Allowed : 19.78 % Favored : 76.19 % Cbeta Deviations : 0.04 % 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: -3.39 (0.14), residues: 2408 helix: -1.72 (0.11), residues: 1582 sheet: -2.22 (0.59), residues: 64 loop : -3.12 (0.18), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 371 TYR 0.021 0.002 TYR C 451 PHE 0.014 0.001 PHE B 316 TRP 0.038 0.002 TRP D 380 HIS 0.009 0.001 HIS D 301 Details of bonding type rmsd covalent geometry : bond 0.01485 (19316) covalent geometry : angle 0.95511 (26281) hydrogen bonds : bond 0.12377 ( 1120) hydrogen bonds : angle 5.76951 ( 3315) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 2166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 397 time to evaluate : 0.715 Fit side-chains REVERT: B 160 HIS cc_start: 0.6798 (m-70) cc_final: 0.6584 (m90) REVERT: B 358 LYS cc_start: 0.8456 (ttpt) cc_final: 0.8205 (tttm) REVERT: B 371 ARG cc_start: 0.8219 (tpp80) cc_final: 0.7889 (tpp80) REVERT: B 447 PHE cc_start: 0.8074 (m-80) cc_final: 0.7824 (m-10) REVERT: B 485 LEU cc_start: 0.7264 (OUTLIER) cc_final: 0.6944 (mm) REVERT: B 487 ARG cc_start: 0.7880 (mtt90) cc_final: 0.5857 (ttt180) REVERT: B 492 ILE cc_start: 0.8896 (mp) cc_final: 0.8600 (mp) REVERT: B 516 ILE cc_start: 0.7890 (mt) cc_final: 0.7470 (pp) REVERT: B 521 TRP cc_start: 0.8281 (t-100) cc_final: 0.8039 (t-100) REVERT: B 631 GLU cc_start: 0.7375 (mm-30) cc_final: 0.7172 (mm-30) REVERT: B 668 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8343 (mp) REVERT: B 672 MET cc_start: 0.7880 (tmm) cc_final: 0.7524 (ttt) REVERT: B 712 ARG cc_start: 0.8021 (mtp180) cc_final: 0.7548 (mtm180) REVERT: C 214 GLU cc_start: 0.8033 (tt0) cc_final: 0.7815 (tt0) REVERT: C 240 ASP cc_start: 0.7773 (p0) cc_final: 0.7495 (p0) REVERT: C 288 ASP cc_start: 0.8293 (t0) cc_final: 0.8015 (t0) REVERT: C 378 THR cc_start: 0.8116 (m) cc_final: 0.7710 (m) REVERT: C 483 GLN cc_start: 0.6212 (tm-30) cc_final: 0.5816 (tm130) REVERT: A 213 TYR cc_start: 0.8306 (m-80) cc_final: 0.8003 (m-80) REVERT: A 214 GLU cc_start: 0.8073 (tt0) cc_final: 0.7860 (tt0) REVERT: A 240 ASP cc_start: 0.7820 (p0) cc_final: 0.7414 (p0) REVERT: A 378 THR cc_start: 0.8217 (m) cc_final: 0.7845 (m) REVERT: A 690 ARG cc_start: 0.7726 (ttm110) cc_final: 0.7230 (ttp-110) REVERT: D 358 LYS cc_start: 0.8498 (ttpt) cc_final: 0.8233 (tttm) REVERT: D 371 ARG cc_start: 0.8242 (tpp80) cc_final: 0.7939 (tpp80) REVERT: D 447 PHE cc_start: 0.8014 (m-80) cc_final: 0.7752 (m-10) REVERT: D 516 ILE cc_start: 0.7950 (mt) cc_final: 0.7487 (pp) REVERT: D 546 GLU cc_start: 0.7704 (mt-10) cc_final: 0.7361 (tp30) REVERT: D 631 GLU cc_start: 0.7402 (mm-30) cc_final: 0.7183 (mm-30) REVERT: D 712 ARG cc_start: 0.7993 (mtp180) cc_final: 0.7563 (mtm180) outliers start: 71 outliers final: 30 residues processed: 454 average time/residue: 0.5465 time to fit residues: 282.9178 Evaluate side-chains 327 residues out of total 2166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 295 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 680 THR Chi-restraints excluded: chain B residue 747 SER Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain C residue 680 THR Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain C residue 747 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 621 SER Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 328 SER Chi-restraints excluded: chain D residue 536 SER Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 641 ASP Chi-restraints excluded: chain D residue 740 THR Chi-restraints excluded: chain D residue 747 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 216 optimal weight: 0.0980 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 0.7980 chunk 107 optimal weight: 0.0570 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.0470 chunk 103 optimal weight: 0.7980 chunk 235 optimal weight: 0.0020 overall best weight: 0.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 242 ASN B 284 HIS ** B 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 647 ASN B 671 ASN C 197 ASN C 205 ASN C 279 GLN C 301 HIS C 330 ASN C 483 GLN C 580 GLN C 745 HIS A 197 ASN A 279 GLN A 301 HIS A 330 ASN A 570 GLN A 580 GLN A 647 ASN ** A 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 284 HIS ** D 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 580 GLN D 647 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.153453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.122610 restraints weight = 23175.437| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.00 r_work: 0.3208 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 19316 Z= 0.108 Angle : 0.549 8.522 26281 Z= 0.281 Chirality : 0.037 0.128 3092 Planarity : 0.004 0.041 3199 Dihedral : 12.247 89.840 3010 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 4.65 % Allowed : 21.49 % Favored : 73.87 % 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 (0.16), residues: 2408 helix: 0.14 (0.13), residues: 1580 sheet: -1.80 (0.53), residues: 78 loop : -2.46 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 369 TYR 0.012 0.001 TYR C 451 PHE 0.022 0.001 PHE D 445 TRP 0.023 0.001 TRP D 380 HIS 0.004 0.001 HIS C 160 Details of bonding type rmsd covalent geometry : bond 0.00215 (19316) covalent geometry : angle 0.54892 (26281) hydrogen bonds : bond 0.03632 ( 1120) hydrogen bonds : angle 3.96242 ( 3315) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 2166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 342 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 160 HIS cc_start: 0.7231 (m-70) cc_final: 0.6914 (m90) REVERT: B 330 ASN cc_start: 0.8215 (t0) cc_final: 0.7628 (p0) REVERT: B 358 LYS cc_start: 0.8312 (ttpt) cc_final: 0.8015 (tttm) REVERT: B 442 PHE cc_start: 0.7597 (t80) cc_final: 0.6307 (m-10) REVERT: B 447 PHE cc_start: 0.8470 (m-80) cc_final: 0.8120 (m-10) REVERT: B 487 ARG cc_start: 0.7910 (mtt90) cc_final: 0.5798 (ttt180) REVERT: B 488 MET cc_start: 0.7407 (OUTLIER) cc_final: 0.6312 (pmm) REVERT: B 492 ILE cc_start: 0.8897 (OUTLIER) cc_final: 0.8598 (mp) REVERT: B 516 ILE cc_start: 0.7937 (mt) cc_final: 0.7462 (pp) REVERT: B 631 GLU cc_start: 0.8132 (mm-30) cc_final: 0.7908 (mm-30) REVERT: B 687 GLU cc_start: 0.7156 (tp30) cc_final: 0.6890 (tp30) REVERT: B 712 ARG cc_start: 0.7981 (mtp180) cc_final: 0.7371 (mtm180) REVERT: B 717 MET cc_start: 0.7619 (mpp) cc_final: 0.6872 (mpp) REVERT: C 214 GLU cc_start: 0.8291 (tt0) cc_final: 0.8087 (tt0) REVERT: C 240 ASP cc_start: 0.7855 (p0) cc_final: 0.7443 (p0) REVERT: C 288 ASP cc_start: 0.8473 (t0) cc_final: 0.8094 (t0) REVERT: C 483 GLN cc_start: 0.5757 (tm130) cc_final: 0.5217 (tm130) REVERT: C 689 GLU cc_start: 0.7807 (tm-30) cc_final: 0.7458 (tp30) REVERT: A 214 GLU cc_start: 0.8364 (tt0) cc_final: 0.8135 (tt0) REVERT: A 240 ASP cc_start: 0.7889 (p0) cc_final: 0.7457 (p0) REVERT: A 431 MET cc_start: 0.8114 (mmp) cc_final: 0.7854 (mmm) REVERT: A 484 LEU cc_start: 0.6568 (mt) cc_final: 0.6266 (mm) REVERT: A 505 ILE cc_start: 0.8815 (mt) cc_final: 0.8526 (mp) REVERT: A 694 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8705 (mp) REVERT: A 714 ARG cc_start: 0.8289 (tpp80) cc_final: 0.7778 (ttt90) REVERT: D 186 ILE cc_start: 0.7970 (OUTLIER) cc_final: 0.7611 (pt) REVERT: D 358 LYS cc_start: 0.8323 (ttpt) cc_final: 0.8024 (tttm) REVERT: D 371 ARG cc_start: 0.8227 (tpp80) cc_final: 0.7914 (tpp80) REVERT: D 442 PHE cc_start: 0.7657 (t80) cc_final: 0.6319 (m-10) REVERT: D 447 PHE cc_start: 0.8490 (m-80) cc_final: 0.8142 (m-10) REVERT: D 579 ILE cc_start: 0.7031 (OUTLIER) cc_final: 0.6468 (mm) REVERT: D 611 LYS cc_start: 0.7977 (ttmt) cc_final: 0.7759 (mttm) REVERT: D 631 GLU cc_start: 0.8127 (mm-30) cc_final: 0.7886 (mm-30) REVERT: D 690 ARG cc_start: 0.7907 (ttm170) cc_final: 0.7638 (mtm110) REVERT: D 693 ARG cc_start: 0.7706 (mtt90) cc_final: 0.7506 (mpt90) REVERT: D 712 ARG cc_start: 0.7999 (mtp180) cc_final: 0.7404 (mtm180) outliers start: 82 outliers final: 30 residues processed: 388 average time/residue: 0.4946 time to fit residues: 220.0741 Evaluate side-chains 341 residues out of total 2166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 306 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 445 PHE Chi-restraints excluded: chain B residue 446 CYS Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 496 CYS Chi-restraints excluded: chain C residue 555 MET Chi-restraints excluded: chain C residue 643 ASN Chi-restraints excluded: chain C residue 732 LEU Chi-restraints excluded: chain C residue 747 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 358 LYS Chi-restraints excluded: chain A residue 496 CYS Chi-restraints excluded: chain A residue 555 MET Chi-restraints excluded: chain A residue 612 CYS Chi-restraints excluded: chain A residue 643 ASN Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 378 THR Chi-restraints excluded: chain D residue 387 SER Chi-restraints excluded: chain D residue 445 PHE Chi-restraints excluded: chain D residue 446 CYS Chi-restraints excluded: chain D residue 579 ILE Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain D residue 677 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 27 optimal weight: 3.9990 chunk 106 optimal weight: 0.5980 chunk 228 optimal weight: 1.9990 chunk 118 optimal weight: 9.9990 chunk 203 optimal weight: 0.6980 chunk 113 optimal weight: 0.7980 chunk 21 optimal weight: 0.0470 chunk 102 optimal weight: 0.0570 chunk 59 optimal weight: 0.0770 chunk 175 optimal weight: 0.0040 chunk 11 optimal weight: 0.7980 overall best weight: 0.1566 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 279 GLN C 284 HIS C 330 ASN A 279 GLN A 330 ASN A 570 GLN A 647 ASN ** A 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 216 GLN D 220 ASN ** D 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 426 HIS D 580 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.155036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.124184 restraints weight = 23335.339| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 1.98 r_work: 0.3241 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 19316 Z= 0.100 Angle : 0.496 6.143 26281 Z= 0.259 Chirality : 0.035 0.132 3092 Planarity : 0.003 0.037 3199 Dihedral : 11.306 88.000 2978 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 4.54 % Allowed : 22.73 % Favored : 72.73 % 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: -0.21 (0.17), residues: 2408 helix: 0.85 (0.13), residues: 1610 sheet: -1.38 (0.55), residues: 78 loop : -2.28 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 122 TYR 0.019 0.001 TYR D 540 PHE 0.015 0.001 PHE D 445 TRP 0.019 0.001 TRP B 380 HIS 0.005 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00196 (19316) covalent geometry : angle 0.49569 (26281) hydrogen bonds : bond 0.03386 ( 1120) hydrogen bonds : angle 3.70129 ( 3315) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 2166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 345 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 159 MET cc_start: 0.7488 (mmm) cc_final: 0.7164 (mmm) REVERT: B 160 HIS cc_start: 0.7176 (m-70) cc_final: 0.6950 (m90) REVERT: B 330 ASN cc_start: 0.8018 (t0) cc_final: 0.7647 (p0) REVERT: B 340 ASP cc_start: 0.8804 (m-30) cc_final: 0.8491 (m-30) REVERT: B 358 LYS cc_start: 0.8194 (ttpt) cc_final: 0.7890 (tttm) REVERT: B 442 PHE cc_start: 0.7500 (t80) cc_final: 0.6168 (m-10) REVERT: B 446 CYS cc_start: 0.8329 (OUTLIER) cc_final: 0.7999 (m) REVERT: B 447 PHE cc_start: 0.8428 (m-80) cc_final: 0.8098 (m-10) REVERT: B 487 ARG cc_start: 0.7712 (mtt90) cc_final: 0.5841 (ttt90) REVERT: B 488 MET cc_start: 0.7374 (OUTLIER) cc_final: 0.6257 (pmm) REVERT: B 492 ILE cc_start: 0.8882 (OUTLIER) cc_final: 0.8581 (mp) REVERT: B 516 ILE cc_start: 0.7826 (OUTLIER) cc_final: 0.7366 (pp) REVERT: B 527 PHE cc_start: 0.8985 (t80) cc_final: 0.8771 (t80) REVERT: B 611 LYS cc_start: 0.7957 (ttmt) cc_final: 0.7722 (ttmm) REVERT: B 631 GLU cc_start: 0.8074 (mm-30) cc_final: 0.7857 (mm-30) REVERT: B 712 ARG cc_start: 0.7943 (mtp180) cc_final: 0.7342 (mtm180) REVERT: B 717 MET cc_start: 0.7534 (mpp) cc_final: 0.6950 (mpp) REVERT: C 214 GLU cc_start: 0.8294 (tt0) cc_final: 0.8087 (tt0) REVERT: C 240 ASP cc_start: 0.7847 (p0) cc_final: 0.7441 (p0) REVERT: C 288 ASP cc_start: 0.8474 (t0) cc_final: 0.8056 (t0) REVERT: C 483 GLN cc_start: 0.5761 (tm130) cc_final: 0.5138 (tm130) REVERT: C 689 GLU cc_start: 0.7720 (tm-30) cc_final: 0.7476 (tp30) REVERT: C 702 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7829 (mt-10) REVERT: A 214 GLU cc_start: 0.8346 (tt0) cc_final: 0.8114 (tt0) REVERT: A 240 ASP cc_start: 0.7735 (p0) cc_final: 0.7283 (p0) REVERT: A 276 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7414 (mp0) REVERT: A 310 PHE cc_start: 0.7939 (t80) cc_final: 0.7503 (t80) REVERT: A 323 MET cc_start: 0.8978 (OUTLIER) cc_final: 0.8704 (ttm) REVERT: A 431 MET cc_start: 0.8123 (mmp) cc_final: 0.7884 (mmm) REVERT: A 484 LEU cc_start: 0.6566 (mt) cc_final: 0.6327 (mm) REVERT: A 505 ILE cc_start: 0.8716 (mt) cc_final: 0.8475 (mp) REVERT: A 513 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8322 (mt) REVERT: A 627 ASP cc_start: 0.8381 (m-30) cc_final: 0.8140 (m-30) REVERT: A 702 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7874 (mt-10) REVERT: A 714 ARG cc_start: 0.8267 (tpp80) cc_final: 0.7800 (ttt90) REVERT: D 186 ILE cc_start: 0.7992 (OUTLIER) cc_final: 0.7741 (pt) REVERT: D 330 ASN cc_start: 0.8245 (t0) cc_final: 0.7585 (p0) REVERT: D 340 ASP cc_start: 0.8707 (m-30) cc_final: 0.8402 (m-30) REVERT: D 358 LYS cc_start: 0.8289 (ttpt) cc_final: 0.7988 (tttm) REVERT: D 371 ARG cc_start: 0.8223 (tpp80) cc_final: 0.7967 (tpp80) REVERT: D 426 HIS cc_start: 0.8116 (t-90) cc_final: 0.7843 (t-170) REVERT: D 442 PHE cc_start: 0.7506 (t80) cc_final: 0.6143 (m-10) REVERT: D 446 CYS cc_start: 0.8380 (OUTLIER) cc_final: 0.8085 (m) REVERT: D 447 PHE cc_start: 0.8487 (m-80) cc_final: 0.8109 (m-10) REVERT: D 527 PHE cc_start: 0.8901 (t80) cc_final: 0.8688 (t80) REVERT: D 631 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7861 (mm-30) REVERT: D 687 GLU cc_start: 0.7146 (tp30) cc_final: 0.6813 (tp30) REVERT: D 690 ARG cc_start: 0.7833 (OUTLIER) cc_final: 0.7629 (mtm110) REVERT: D 712 ARG cc_start: 0.8066 (mtp180) cc_final: 0.7440 (mtm180) outliers start: 80 outliers final: 23 residues processed: 383 average time/residue: 0.4826 time to fit residues: 212.9852 Evaluate side-chains 342 residues out of total 2166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 307 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 446 CYS Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 555 MET Chi-restraints excluded: chain C residue 688 SER Chi-restraints excluded: chain C residue 702 GLU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 555 MET Chi-restraints excluded: chain A residue 643 ASN Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 378 THR Chi-restraints excluded: chain D residue 387 SER Chi-restraints excluded: chain D residue 446 CYS Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain D residue 690 ARG Chi-restraints excluded: chain D residue 730 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 91 optimal weight: 2.9990 chunk 223 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 222 optimal weight: 0.7980 chunk 163 optimal weight: 0.9980 chunk 179 optimal weight: 10.0000 chunk 161 optimal weight: 4.9990 chunk 177 optimal weight: 2.9990 chunk 149 optimal weight: 0.6980 chunk 110 optimal weight: 0.1980 chunk 38 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 301 HIS B 410 ASN C 279 GLN C 330 ASN A 279 GLN A 330 ASN A 570 GLN D 273 ASN ** D 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.153316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.122488 restraints weight = 23303.068| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 1.97 r_work: 0.3220 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 19316 Z= 0.120 Angle : 0.517 7.126 26281 Z= 0.266 Chirality : 0.036 0.131 3092 Planarity : 0.003 0.042 3199 Dihedral : 11.135 88.047 2977 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 4.76 % Allowed : 22.79 % Favored : 72.45 % 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: 0.11 (0.17), residues: 2408 helix: 1.11 (0.13), residues: 1612 sheet: -1.29 (0.55), residues: 78 loop : -2.20 (0.22), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 369 TYR 0.014 0.001 TYR C 451 PHE 0.020 0.001 PHE C 489 TRP 0.020 0.001 TRP B 380 HIS 0.008 0.001 HIS D 745 Details of bonding type rmsd covalent geometry : bond 0.00262 (19316) covalent geometry : angle 0.51745 (26281) hydrogen bonds : bond 0.03465 ( 1120) hydrogen bonds : angle 3.65073 ( 3315) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 317 time to evaluate : 0.645 Fit side-chains revert: symmetry clash REVERT: B 159 MET cc_start: 0.7472 (mmm) cc_final: 0.7161 (mmm) REVERT: B 160 HIS cc_start: 0.7269 (m-70) cc_final: 0.7026 (m90) REVERT: B 358 LYS cc_start: 0.8307 (ttpt) cc_final: 0.8018 (tttm) REVERT: B 369 ARG cc_start: 0.8052 (ttp-110) cc_final: 0.7781 (ttm110) REVERT: B 442 PHE cc_start: 0.7693 (t80) cc_final: 0.6264 (m-10) REVERT: B 445 PHE cc_start: 0.8264 (t80) cc_final: 0.8053 (t80) REVERT: B 446 CYS cc_start: 0.8599 (OUTLIER) cc_final: 0.8182 (m) REVERT: B 447 PHE cc_start: 0.8593 (m-80) cc_final: 0.8290 (m-10) REVERT: B 487 ARG cc_start: 0.7714 (mtt90) cc_final: 0.5782 (ttt90) REVERT: B 488 MET cc_start: 0.7488 (OUTLIER) cc_final: 0.6264 (pmm) REVERT: B 492 ILE cc_start: 0.8870 (OUTLIER) cc_final: 0.8533 (mp) REVERT: B 516 ILE cc_start: 0.7725 (OUTLIER) cc_final: 0.7294 (pp) REVERT: B 527 PHE cc_start: 0.9052 (t80) cc_final: 0.8832 (t80) REVERT: B 611 LYS cc_start: 0.8020 (ttmt) cc_final: 0.7769 (ttmm) REVERT: B 631 GLU cc_start: 0.8451 (mm-30) cc_final: 0.8235 (mm-30) REVERT: B 672 MET cc_start: 0.8057 (OUTLIER) cc_final: 0.7812 (ttt) REVERT: B 712 ARG cc_start: 0.8009 (mtp180) cc_final: 0.7352 (mtm180) REVERT: B 717 MET cc_start: 0.7718 (mpp) cc_final: 0.7149 (mpp) REVERT: C 214 GLU cc_start: 0.8542 (tt0) cc_final: 0.8336 (tt0) REVERT: C 240 ASP cc_start: 0.7949 (p0) cc_final: 0.7546 (p0) REVERT: C 288 ASP cc_start: 0.8632 (t0) cc_final: 0.8155 (t0) REVERT: C 483 GLN cc_start: 0.5729 (tm130) cc_final: 0.5088 (tm130) REVERT: C 544 TYR cc_start: 0.6951 (m-80) cc_final: 0.6748 (m-80) REVERT: C 689 GLU cc_start: 0.8024 (tm-30) cc_final: 0.7705 (tp30) REVERT: A 214 GLU cc_start: 0.8561 (tt0) cc_final: 0.8348 (tt0) REVERT: A 240 ASP cc_start: 0.7931 (p0) cc_final: 0.7517 (p0) REVERT: A 276 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7574 (mp0) REVERT: A 323 MET cc_start: 0.9124 (OUTLIER) cc_final: 0.8852 (ttm) REVERT: A 431 MET cc_start: 0.8608 (mmp) cc_final: 0.8081 (mmp) REVERT: A 513 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8159 (mt) REVERT: A 627 ASP cc_start: 0.8634 (m-30) cc_final: 0.8400 (m-30) REVERT: A 714 ARG cc_start: 0.8402 (tpp80) cc_final: 0.7814 (ttt90) REVERT: D 186 ILE cc_start: 0.8133 (OUTLIER) cc_final: 0.7838 (pt) REVERT: D 330 ASN cc_start: 0.8345 (t0) cc_final: 0.7638 (p0) REVERT: D 358 LYS cc_start: 0.8378 (ttpt) cc_final: 0.8081 (tttm) REVERT: D 371 ARG cc_start: 0.8262 (tpp80) cc_final: 0.8001 (tpp80) REVERT: D 442 PHE cc_start: 0.7674 (t80) cc_final: 0.6200 (m-10) REVERT: D 445 PHE cc_start: 0.8211 (t80) cc_final: 0.8002 (t80) REVERT: D 446 CYS cc_start: 0.8654 (OUTLIER) cc_final: 0.8178 (m) REVERT: D 447 PHE cc_start: 0.8647 (m-80) cc_final: 0.8295 (m-10) REVERT: D 516 ILE cc_start: 0.7723 (OUTLIER) cc_final: 0.7209 (pp) REVERT: D 527 PHE cc_start: 0.8979 (t80) cc_final: 0.8760 (t80) REVERT: D 687 GLU cc_start: 0.7217 (tp30) cc_final: 0.6817 (tp30) REVERT: D 690 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.7571 (mtm110) REVERT: D 712 ARG cc_start: 0.8143 (mtp180) cc_final: 0.7437 (mtm180) outliers start: 84 outliers final: 41 residues processed: 359 average time/residue: 0.5209 time to fit residues: 214.3337 Evaluate side-chains 346 residues out of total 2166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 293 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 446 CYS Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 672 MET Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 358 LYS Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 495 MET Chi-restraints excluded: chain C residue 496 CYS Chi-restraints excluded: chain C residue 555 MET Chi-restraints excluded: chain C residue 688 SER Chi-restraints excluded: chain C residue 732 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 496 CYS Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 555 MET Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 643 ASN Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 378 THR Chi-restraints excluded: chain D residue 387 SER Chi-restraints excluded: chain D residue 440 MET Chi-restraints excluded: chain D residue 446 CYS Chi-restraints excluded: chain D residue 516 ILE Chi-restraints excluded: chain D residue 579 ILE Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 641 ASP Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain D residue 690 ARG Chi-restraints excluded: chain D residue 730 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 135 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 216 optimal weight: 4.9990 chunk 227 optimal weight: 0.6980 chunk 162 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 158 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 155 optimal weight: 6.9990 chunk 157 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 279 GLN A 279 GLN A 570 GLN D 301 HIS D 580 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.153011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.122213 restraints weight = 23002.401| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 1.92 r_work: 0.3226 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19316 Z= 0.137 Angle : 0.532 7.959 26281 Z= 0.272 Chirality : 0.037 0.143 3092 Planarity : 0.003 0.031 3199 Dihedral : 11.134 87.600 2977 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 4.82 % Allowed : 23.24 % Favored : 71.94 % 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: 0.17 (0.17), residues: 2408 helix: 1.15 (0.13), residues: 1622 sheet: -1.14 (0.56), residues: 78 loop : -2.20 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 690 TYR 0.019 0.001 TYR B 390 PHE 0.013 0.001 PHE C 666 TRP 0.019 0.001 TRP B 380 HIS 0.011 0.001 HIS D 745 Details of bonding type rmsd covalent geometry : bond 0.00317 (19316) covalent geometry : angle 0.53216 (26281) hydrogen bonds : bond 0.03525 ( 1120) hydrogen bonds : angle 3.63897 ( 3315) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 300 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 159 MET cc_start: 0.7531 (mmm) cc_final: 0.7182 (mmm) REVERT: B 160 HIS cc_start: 0.7247 (m-70) cc_final: 0.7031 (m90) REVERT: B 330 ASN cc_start: 0.8405 (t0) cc_final: 0.7776 (p0) REVERT: B 358 LYS cc_start: 0.8383 (ttpt) cc_final: 0.8096 (tttm) REVERT: B 369 ARG cc_start: 0.8108 (ttp-110) cc_final: 0.7863 (ttm110) REVERT: B 442 PHE cc_start: 0.7735 (t80) cc_final: 0.6341 (m-10) REVERT: B 446 CYS cc_start: 0.8627 (OUTLIER) cc_final: 0.8224 (m) REVERT: B 447 PHE cc_start: 0.8595 (m-80) cc_final: 0.8301 (m-10) REVERT: B 487 ARG cc_start: 0.7750 (mtt90) cc_final: 0.5807 (ttt90) REVERT: B 488 MET cc_start: 0.7547 (OUTLIER) cc_final: 0.6315 (pmm) REVERT: B 492 ILE cc_start: 0.8885 (OUTLIER) cc_final: 0.8546 (mp) REVERT: B 516 ILE cc_start: 0.7783 (OUTLIER) cc_final: 0.7341 (pp) REVERT: B 546 GLU cc_start: 0.8683 (mt-10) cc_final: 0.7641 (tp30) REVERT: B 631 GLU cc_start: 0.8470 (mm-30) cc_final: 0.8247 (mm-30) REVERT: B 712 ARG cc_start: 0.8077 (mtp180) cc_final: 0.7397 (mtm180) REVERT: B 717 MET cc_start: 0.7697 (mpp) cc_final: 0.7142 (mpp) REVERT: C 214 GLU cc_start: 0.8556 (tt0) cc_final: 0.8335 (tt0) REVERT: C 240 ASP cc_start: 0.7986 (p0) cc_final: 0.7557 (p0) REVERT: C 288 ASP cc_start: 0.8621 (t0) cc_final: 0.8205 (t0) REVERT: C 483 GLN cc_start: 0.5681 (tm130) cc_final: 0.5065 (tm130) REVERT: C 544 TYR cc_start: 0.6955 (m-80) cc_final: 0.6748 (m-80) REVERT: C 689 GLU cc_start: 0.8038 (tm-30) cc_final: 0.7769 (tp30) REVERT: A 214 GLU cc_start: 0.8581 (tt0) cc_final: 0.8361 (tt0) REVERT: A 240 ASP cc_start: 0.7946 (p0) cc_final: 0.7489 (p0) REVERT: A 323 MET cc_start: 0.9126 (OUTLIER) cc_final: 0.8863 (ttm) REVERT: A 431 MET cc_start: 0.8642 (mmp) cc_final: 0.8202 (mmm) REVERT: A 513 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8205 (mt) REVERT: A 627 ASP cc_start: 0.8555 (m-30) cc_final: 0.8303 (m-30) REVERT: A 714 ARG cc_start: 0.8386 (tpp80) cc_final: 0.7806 (ttt90) REVERT: A 717 MET cc_start: 0.7612 (OUTLIER) cc_final: 0.7242 (ptp) REVERT: D 186 ILE cc_start: 0.8119 (OUTLIER) cc_final: 0.7812 (pt) REVERT: D 330 ASN cc_start: 0.8358 (t0) cc_final: 0.7660 (p0) REVERT: D 358 LYS cc_start: 0.8387 (ttpt) cc_final: 0.8095 (tttm) REVERT: D 442 PHE cc_start: 0.7727 (t80) cc_final: 0.6301 (m-10) REVERT: D 446 CYS cc_start: 0.8617 (OUTLIER) cc_final: 0.8192 (m) REVERT: D 447 PHE cc_start: 0.8634 (m-80) cc_final: 0.8283 (m-10) REVERT: D 516 ILE cc_start: 0.7864 (OUTLIER) cc_final: 0.7327 (pp) REVERT: D 687 GLU cc_start: 0.7178 (tp30) cc_final: 0.6843 (tp30) REVERT: D 690 ARG cc_start: 0.7963 (OUTLIER) cc_final: 0.7702 (mtm110) REVERT: D 712 ARG cc_start: 0.8176 (mtp180) cc_final: 0.7508 (mtm180) outliers start: 85 outliers final: 42 residues processed: 351 average time/residue: 0.5139 time to fit residues: 206.7334 Evaluate side-chains 352 residues out of total 2166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 299 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 440 MET Chi-restraints excluded: chain B residue 446 CYS Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 358 LYS Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 495 MET Chi-restraints excluded: chain C residue 496 CYS Chi-restraints excluded: chain C residue 555 MET Chi-restraints excluded: chain C residue 688 SER Chi-restraints excluded: chain C residue 732 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 496 CYS Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 555 MET Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 612 CYS Chi-restraints excluded: chain A residue 643 ASN Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 717 MET Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 378 THR Chi-restraints excluded: chain D residue 387 SER Chi-restraints excluded: chain D residue 440 MET Chi-restraints excluded: chain D residue 446 CYS Chi-restraints excluded: chain D residue 516 ILE Chi-restraints excluded: chain D residue 579 ILE Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 637 ILE Chi-restraints excluded: chain D residue 641 ASP Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain D residue 690 ARG Chi-restraints excluded: chain D residue 730 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 36 optimal weight: 4.9990 chunk 85 optimal weight: 0.9980 chunk 240 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 chunk 130 optimal weight: 5.9990 chunk 118 optimal weight: 8.9990 chunk 35 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 154 optimal weight: 0.7980 chunk 152 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 279 GLN A 279 GLN A 570 GLN D 580 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.152879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.122794 restraints weight = 23086.529| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 1.89 r_work: 0.3234 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.098 19316 Z= 0.140 Angle : 0.541 10.086 26281 Z= 0.275 Chirality : 0.037 0.143 3092 Planarity : 0.003 0.046 3199 Dihedral : 11.124 88.596 2977 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 4.14 % Allowed : 23.75 % Favored : 72.11 % 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: 0.22 (0.17), residues: 2408 helix: 1.19 (0.13), residues: 1622 sheet: -1.13 (0.56), residues: 78 loop : -2.20 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 690 TYR 0.016 0.001 TYR C 451 PHE 0.012 0.001 PHE C 666 TRP 0.019 0.001 TRP B 380 HIS 0.008 0.001 HIS D 745 Details of bonding type rmsd covalent geometry : bond 0.00324 (19316) covalent geometry : angle 0.54072 (26281) hydrogen bonds : bond 0.03548 ( 1120) hydrogen bonds : angle 3.65726 ( 3315) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 301 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 159 MET cc_start: 0.7542 (mmm) cc_final: 0.7205 (mmm) REVERT: B 160 HIS cc_start: 0.7246 (m-70) cc_final: 0.7036 (m90) REVERT: B 330 ASN cc_start: 0.8381 (t0) cc_final: 0.7731 (p0) REVERT: B 358 LYS cc_start: 0.8363 (ttpt) cc_final: 0.8073 (tttm) REVERT: B 369 ARG cc_start: 0.8092 (ttp-110) cc_final: 0.7869 (ttm110) REVERT: B 442 PHE cc_start: 0.7711 (t80) cc_final: 0.6314 (m-10) REVERT: B 446 CYS cc_start: 0.8603 (OUTLIER) cc_final: 0.8198 (m) REVERT: B 447 PHE cc_start: 0.8574 (m-80) cc_final: 0.8285 (m-10) REVERT: B 487 ARG cc_start: 0.7737 (mtt90) cc_final: 0.5803 (ttt90) REVERT: B 488 MET cc_start: 0.7542 (OUTLIER) cc_final: 0.6315 (pmm) REVERT: B 492 ILE cc_start: 0.8883 (OUTLIER) cc_final: 0.8546 (mp) REVERT: B 516 ILE cc_start: 0.7788 (OUTLIER) cc_final: 0.7346 (pp) REVERT: B 527 PHE cc_start: 0.9046 (t80) cc_final: 0.8837 (t80) REVERT: B 546 GLU cc_start: 0.8674 (mt-10) cc_final: 0.7634 (tp30) REVERT: B 631 GLU cc_start: 0.8438 (mm-30) cc_final: 0.8213 (mm-30) REVERT: B 712 ARG cc_start: 0.8063 (mtp180) cc_final: 0.7365 (mtm180) REVERT: B 717 MET cc_start: 0.7686 (mpp) cc_final: 0.7127 (mpp) REVERT: C 214 GLU cc_start: 0.8537 (tt0) cc_final: 0.8317 (tt0) REVERT: C 240 ASP cc_start: 0.7962 (p0) cc_final: 0.7533 (p0) REVERT: C 288 ASP cc_start: 0.8603 (t0) cc_final: 0.8185 (t0) REVERT: C 483 GLN cc_start: 0.5697 (tm130) cc_final: 0.5084 (tm130) REVERT: C 689 GLU cc_start: 0.8033 (tm-30) cc_final: 0.7717 (tp30) REVERT: A 214 GLU cc_start: 0.8569 (tt0) cc_final: 0.8356 (tt0) REVERT: A 240 ASP cc_start: 0.7930 (p0) cc_final: 0.7469 (p0) REVERT: A 323 MET cc_start: 0.9117 (OUTLIER) cc_final: 0.8852 (ttm) REVERT: A 431 MET cc_start: 0.8606 (mmp) cc_final: 0.8402 (mmm) REVERT: A 513 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8367 (mt) REVERT: A 627 ASP cc_start: 0.8463 (m-30) cc_final: 0.8221 (m-30) REVERT: A 714 ARG cc_start: 0.8388 (tpp80) cc_final: 0.7807 (ttt90) REVERT: A 717 MET cc_start: 0.7606 (OUTLIER) cc_final: 0.7235 (ptp) REVERT: D 186 ILE cc_start: 0.8118 (OUTLIER) cc_final: 0.7821 (pt) REVERT: D 330 ASN cc_start: 0.8343 (t0) cc_final: 0.7627 (p0) REVERT: D 358 LYS cc_start: 0.8372 (ttpt) cc_final: 0.8075 (tttm) REVERT: D 369 ARG cc_start: 0.7962 (ttp-110) cc_final: 0.7733 (ttm110) REVERT: D 442 PHE cc_start: 0.7718 (t80) cc_final: 0.6299 (m-10) REVERT: D 446 CYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8160 (m) REVERT: D 447 PHE cc_start: 0.8616 (m-80) cc_final: 0.8268 (m-10) REVERT: D 516 ILE cc_start: 0.7827 (OUTLIER) cc_final: 0.7312 (pp) REVERT: D 672 MET cc_start: 0.8182 (OUTLIER) cc_final: 0.7953 (ttt) REVERT: D 687 GLU cc_start: 0.7178 (tp30) cc_final: 0.6837 (tp30) REVERT: D 690 ARG cc_start: 0.7944 (OUTLIER) cc_final: 0.7679 (mtm110) REVERT: D 712 ARG cc_start: 0.8160 (mtp180) cc_final: 0.7503 (mtm180) outliers start: 73 outliers final: 50 residues processed: 338 average time/residue: 0.5194 time to fit residues: 200.8128 Evaluate side-chains 351 residues out of total 2166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 289 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 440 MET Chi-restraints excluded: chain B residue 446 CYS Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 180 ASN Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 358 LYS Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 495 MET Chi-restraints excluded: chain C residue 496 CYS Chi-restraints excluded: chain C residue 555 MET Chi-restraints excluded: chain C residue 688 SER Chi-restraints excluded: chain C residue 732 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 496 CYS Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 555 MET Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 612 CYS Chi-restraints excluded: chain A residue 621 SER Chi-restraints excluded: chain A residue 643 ASN Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 717 MET Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 378 THR Chi-restraints excluded: chain D residue 387 SER Chi-restraints excluded: chain D residue 440 MET Chi-restraints excluded: chain D residue 446 CYS Chi-restraints excluded: chain D residue 516 ILE Chi-restraints excluded: chain D residue 579 ILE Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 637 ILE Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain D residue 672 MET Chi-restraints excluded: chain D residue 690 ARG Chi-restraints excluded: chain D residue 730 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 215 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 129 optimal weight: 6.9990 chunk 229 optimal weight: 3.9990 chunk 175 optimal weight: 6.9990 chunk 190 optimal weight: 5.9990 chunk 99 optimal weight: 0.9980 chunk 76 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 145 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 279 GLN A 279 GLN A 570 GLN D 580 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.152747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.122668 restraints weight = 23193.144| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 1.89 r_work: 0.3235 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.098 19316 Z= 0.140 Angle : 0.541 10.086 26281 Z= 0.275 Chirality : 0.037 0.143 3092 Planarity : 0.003 0.046 3199 Dihedral : 11.123 88.596 2977 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 3.51 % Allowed : 24.60 % Favored : 71.88 % 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: 0.22 (0.17), residues: 2408 helix: 1.19 (0.13), residues: 1622 sheet: -1.13 (0.56), residues: 78 loop : -2.20 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 690 TYR 0.016 0.001 TYR C 451 PHE 0.012 0.001 PHE C 666 TRP 0.019 0.001 TRP B 380 HIS 0.008 0.001 HIS D 745 Details of bonding type rmsd covalent geometry : bond 0.00324 (19316) covalent geometry : angle 0.54072 (26281) hydrogen bonds : bond 0.03548 ( 1120) hydrogen bonds : angle 3.65726 ( 3315) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 289 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 159 MET cc_start: 0.7541 (mmm) cc_final: 0.7201 (mmm) REVERT: B 160 HIS cc_start: 0.7243 (m-70) cc_final: 0.7033 (m90) REVERT: B 330 ASN cc_start: 0.8380 (t0) cc_final: 0.7734 (p0) REVERT: B 358 LYS cc_start: 0.8366 (ttpt) cc_final: 0.8078 (tttm) REVERT: B 369 ARG cc_start: 0.8092 (ttp-110) cc_final: 0.7869 (ttm110) REVERT: B 442 PHE cc_start: 0.7714 (t80) cc_final: 0.6317 (m-10) REVERT: B 446 CYS cc_start: 0.8611 (OUTLIER) cc_final: 0.8202 (m) REVERT: B 447 PHE cc_start: 0.8574 (m-80) cc_final: 0.8286 (m-10) REVERT: B 487 ARG cc_start: 0.7743 (mtt90) cc_final: 0.5810 (ttt90) REVERT: B 488 MET cc_start: 0.7547 (OUTLIER) cc_final: 0.6326 (pmm) REVERT: B 492 ILE cc_start: 0.8886 (OUTLIER) cc_final: 0.8549 (mp) REVERT: B 516 ILE cc_start: 0.7790 (OUTLIER) cc_final: 0.7345 (pp) REVERT: B 527 PHE cc_start: 0.9049 (t80) cc_final: 0.8837 (t80) REVERT: B 546 GLU cc_start: 0.8676 (mt-10) cc_final: 0.7635 (tp30) REVERT: B 631 GLU cc_start: 0.8436 (mm-30) cc_final: 0.8210 (mm-30) REVERT: B 712 ARG cc_start: 0.8068 (mtp180) cc_final: 0.7370 (mtm180) REVERT: B 717 MET cc_start: 0.7688 (mpp) cc_final: 0.7131 (mpp) REVERT: C 214 GLU cc_start: 0.8536 (tt0) cc_final: 0.8315 (tt0) REVERT: C 240 ASP cc_start: 0.7968 (p0) cc_final: 0.7537 (p0) REVERT: C 288 ASP cc_start: 0.8606 (t0) cc_final: 0.8190 (t0) REVERT: C 483 GLN cc_start: 0.5689 (tm130) cc_final: 0.5076 (tm130) REVERT: C 689 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7718 (tp30) REVERT: A 214 GLU cc_start: 0.8570 (tt0) cc_final: 0.8358 (tt0) REVERT: A 240 ASP cc_start: 0.7935 (p0) cc_final: 0.7480 (p0) REVERT: A 323 MET cc_start: 0.9121 (OUTLIER) cc_final: 0.8858 (ttm) REVERT: A 431 MET cc_start: 0.8612 (mmp) cc_final: 0.8408 (mmm) REVERT: A 513 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8365 (mt) REVERT: A 627 ASP cc_start: 0.8458 (m-30) cc_final: 0.8216 (m-30) REVERT: A 714 ARG cc_start: 0.8389 (tpp80) cc_final: 0.7807 (ttt90) REVERT: A 717 MET cc_start: 0.7598 (OUTLIER) cc_final: 0.7228 (ptp) REVERT: D 186 ILE cc_start: 0.8122 (OUTLIER) cc_final: 0.7827 (pt) REVERT: D 330 ASN cc_start: 0.8334 (t0) cc_final: 0.7626 (p0) REVERT: D 358 LYS cc_start: 0.8367 (ttpt) cc_final: 0.8072 (tttm) REVERT: D 369 ARG cc_start: 0.7967 (ttp-110) cc_final: 0.7737 (ttm110) REVERT: D 442 PHE cc_start: 0.7715 (t80) cc_final: 0.6303 (m-10) REVERT: D 446 CYS cc_start: 0.8582 (OUTLIER) cc_final: 0.8162 (m) REVERT: D 447 PHE cc_start: 0.8617 (m-80) cc_final: 0.8272 (m-10) REVERT: D 516 ILE cc_start: 0.7829 (OUTLIER) cc_final: 0.7308 (pp) REVERT: D 672 MET cc_start: 0.8177 (OUTLIER) cc_final: 0.7945 (ttt) REVERT: D 687 GLU cc_start: 0.7174 (tp30) cc_final: 0.6831 (tp30) REVERT: D 690 ARG cc_start: 0.7943 (OUTLIER) cc_final: 0.7680 (mtm110) REVERT: D 712 ARG cc_start: 0.8160 (mtp180) cc_final: 0.7503 (mtm180) outliers start: 62 outliers final: 50 residues processed: 322 average time/residue: 0.5190 time to fit residues: 191.0926 Evaluate side-chains 351 residues out of total 2166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 289 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 440 MET Chi-restraints excluded: chain B residue 446 CYS Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 180 ASN Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 358 LYS Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 495 MET Chi-restraints excluded: chain C residue 496 CYS Chi-restraints excluded: chain C residue 555 MET Chi-restraints excluded: chain C residue 688 SER Chi-restraints excluded: chain C residue 732 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 496 CYS Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 555 MET Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 612 CYS Chi-restraints excluded: chain A residue 621 SER Chi-restraints excluded: chain A residue 643 ASN Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 717 MET Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 378 THR Chi-restraints excluded: chain D residue 387 SER Chi-restraints excluded: chain D residue 440 MET Chi-restraints excluded: chain D residue 446 CYS Chi-restraints excluded: chain D residue 516 ILE Chi-restraints excluded: chain D residue 579 ILE Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 637 ILE Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain D residue 672 MET Chi-restraints excluded: chain D residue 690 ARG Chi-restraints excluded: chain D residue 730 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 90 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 147 optimal weight: 0.8980 chunk 140 optimal weight: 1.9990 chunk 192 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 209 optimal weight: 0.0050 chunk 10 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 279 GLN A 279 GLN A 570 GLN D 580 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.152736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.122669 restraints weight = 23079.964| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 1.89 r_work: 0.3236 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.098 19316 Z= 0.140 Angle : 0.541 10.086 26281 Z= 0.275 Chirality : 0.037 0.143 3092 Planarity : 0.003 0.046 3199 Dihedral : 11.123 88.596 2977 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 3.51 % Allowed : 24.60 % Favored : 71.88 % 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: 0.22 (0.17), residues: 2408 helix: 1.19 (0.13), residues: 1622 sheet: -1.13 (0.56), residues: 78 loop : -2.20 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 690 TYR 0.016 0.001 TYR C 451 PHE 0.012 0.001 PHE C 666 TRP 0.019 0.001 TRP B 380 HIS 0.008 0.001 HIS D 745 Details of bonding type rmsd covalent geometry : bond 0.00324 (19316) covalent geometry : angle 0.54072 (26281) hydrogen bonds : bond 0.03548 ( 1120) hydrogen bonds : angle 3.65726 ( 3315) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 289 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 159 MET cc_start: 0.7542 (mmm) cc_final: 0.7203 (mmm) REVERT: B 160 HIS cc_start: 0.7239 (m-70) cc_final: 0.7029 (m90) REVERT: B 330 ASN cc_start: 0.8377 (t0) cc_final: 0.7732 (p0) REVERT: B 358 LYS cc_start: 0.8366 (ttpt) cc_final: 0.8079 (tttm) REVERT: B 369 ARG cc_start: 0.8093 (ttp-110) cc_final: 0.7870 (ttm110) REVERT: B 442 PHE cc_start: 0.7715 (t80) cc_final: 0.6319 (m-10) REVERT: B 446 CYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8201 (m) REVERT: B 447 PHE cc_start: 0.8573 (m-80) cc_final: 0.8285 (m-10) REVERT: B 487 ARG cc_start: 0.7742 (mtt90) cc_final: 0.5813 (ttt90) REVERT: B 488 MET cc_start: 0.7551 (OUTLIER) cc_final: 0.6329 (pmm) REVERT: B 492 ILE cc_start: 0.8887 (OUTLIER) cc_final: 0.8550 (mp) REVERT: B 516 ILE cc_start: 0.7795 (OUTLIER) cc_final: 0.7348 (pp) REVERT: B 527 PHE cc_start: 0.9048 (t80) cc_final: 0.8837 (t80) REVERT: B 546 GLU cc_start: 0.8669 (mt-10) cc_final: 0.7635 (tp30) REVERT: B 631 GLU cc_start: 0.8429 (mm-30) cc_final: 0.8205 (mm-30) REVERT: B 712 ARG cc_start: 0.8069 (mtp180) cc_final: 0.7372 (mtm180) REVERT: B 717 MET cc_start: 0.7687 (mpp) cc_final: 0.7129 (mpp) REVERT: C 214 GLU cc_start: 0.8534 (tt0) cc_final: 0.8314 (tt0) REVERT: C 240 ASP cc_start: 0.7967 (p0) cc_final: 0.7539 (p0) REVERT: C 288 ASP cc_start: 0.8606 (t0) cc_final: 0.8191 (t0) REVERT: C 483 GLN cc_start: 0.5694 (tm130) cc_final: 0.5082 (tm130) REVERT: C 689 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7720 (tp30) REVERT: A 214 GLU cc_start: 0.8571 (tt0) cc_final: 0.8358 (tt0) REVERT: A 240 ASP cc_start: 0.7932 (p0) cc_final: 0.7476 (p0) REVERT: A 323 MET cc_start: 0.9125 (OUTLIER) cc_final: 0.8862 (ttm) REVERT: A 431 MET cc_start: 0.8611 (mmp) cc_final: 0.8408 (mmm) REVERT: A 513 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8369 (mt) REVERT: A 627 ASP cc_start: 0.8460 (m-30) cc_final: 0.8218 (m-30) REVERT: A 714 ARG cc_start: 0.8386 (tpp80) cc_final: 0.7809 (ttt90) REVERT: A 717 MET cc_start: 0.7602 (OUTLIER) cc_final: 0.7231 (ptp) REVERT: D 186 ILE cc_start: 0.8123 (OUTLIER) cc_final: 0.7829 (pt) REVERT: D 330 ASN cc_start: 0.8335 (t0) cc_final: 0.7627 (p0) REVERT: D 358 LYS cc_start: 0.8366 (ttpt) cc_final: 0.8072 (tttm) REVERT: D 369 ARG cc_start: 0.7965 (ttp-110) cc_final: 0.7736 (ttm110) REVERT: D 442 PHE cc_start: 0.7717 (t80) cc_final: 0.6306 (m-10) REVERT: D 446 CYS cc_start: 0.8574 (OUTLIER) cc_final: 0.8157 (m) REVERT: D 447 PHE cc_start: 0.8614 (m-80) cc_final: 0.8269 (m-10) REVERT: D 516 ILE cc_start: 0.7834 (OUTLIER) cc_final: 0.7314 (pp) REVERT: D 672 MET cc_start: 0.8179 (OUTLIER) cc_final: 0.7946 (ttt) REVERT: D 687 GLU cc_start: 0.7177 (tp30) cc_final: 0.6836 (tp30) REVERT: D 690 ARG cc_start: 0.7944 (OUTLIER) cc_final: 0.7681 (mtm110) REVERT: D 712 ARG cc_start: 0.8163 (mtp180) cc_final: 0.7508 (mtm180) outliers start: 62 outliers final: 50 residues processed: 322 average time/residue: 0.5139 time to fit residues: 189.4908 Evaluate side-chains 351 residues out of total 2166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 289 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 440 MET Chi-restraints excluded: chain B residue 446 CYS Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 180 ASN Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 358 LYS Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 495 MET Chi-restraints excluded: chain C residue 496 CYS Chi-restraints excluded: chain C residue 555 MET Chi-restraints excluded: chain C residue 688 SER Chi-restraints excluded: chain C residue 732 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 496 CYS Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 555 MET Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 612 CYS Chi-restraints excluded: chain A residue 621 SER Chi-restraints excluded: chain A residue 643 ASN Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 717 MET Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 378 THR Chi-restraints excluded: chain D residue 387 SER Chi-restraints excluded: chain D residue 440 MET Chi-restraints excluded: chain D residue 446 CYS Chi-restraints excluded: chain D residue 516 ILE Chi-restraints excluded: chain D residue 579 ILE Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 637 ILE Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain D residue 672 MET Chi-restraints excluded: chain D residue 690 ARG Chi-restraints excluded: chain D residue 730 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 76 optimal weight: 5.9990 chunk 165 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 209 optimal weight: 0.8980 chunk 168 optimal weight: 4.9990 chunk 207 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 279 GLN A 279 GLN A 570 GLN D 580 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.153794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.122777 restraints weight = 23055.194| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 1.94 r_work: 0.3215 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19316 Z= 0.136 Angle : 0.547 10.073 26281 Z= 0.278 Chirality : 0.037 0.173 3092 Planarity : 0.004 0.064 3199 Dihedral : 11.081 88.044 2977 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 4.20 % Allowed : 23.92 % Favored : 71.88 % 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: 0.34 (0.17), residues: 2408 helix: 1.30 (0.13), residues: 1598 sheet: -0.62 (0.62), residues: 64 loop : -2.13 (0.21), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 690 TYR 0.016 0.001 TYR C 382 PHE 0.013 0.001 PHE C 569 TRP 0.019 0.001 TRP B 380 HIS 0.008 0.001 HIS D 745 Details of bonding type rmsd covalent geometry : bond 0.00309 (19316) covalent geometry : angle 0.54739 (26281) hydrogen bonds : bond 0.03554 ( 1120) hydrogen bonds : angle 3.65173 ( 3315) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 299 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 159 MET cc_start: 0.7498 (mmm) cc_final: 0.7281 (mmm) REVERT: B 160 HIS cc_start: 0.7249 (m-70) cc_final: 0.7020 (m90) REVERT: B 330 ASN cc_start: 0.8387 (t0) cc_final: 0.7737 (p0) REVERT: B 358 LYS cc_start: 0.8368 (ttpt) cc_final: 0.8076 (tttm) REVERT: B 369 ARG cc_start: 0.8089 (ttp-110) cc_final: 0.7868 (ttm110) REVERT: B 442 PHE cc_start: 0.7719 (t80) cc_final: 0.6298 (m-10) REVERT: B 446 CYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8237 (m) REVERT: B 447 PHE cc_start: 0.8591 (m-80) cc_final: 0.8305 (m-10) REVERT: B 487 ARG cc_start: 0.7740 (mtt90) cc_final: 0.5795 (ttt90) REVERT: B 488 MET cc_start: 0.7545 (OUTLIER) cc_final: 0.6309 (pmm) REVERT: B 492 ILE cc_start: 0.8885 (OUTLIER) cc_final: 0.8547 (mp) REVERT: B 516 ILE cc_start: 0.7785 (OUTLIER) cc_final: 0.7338 (pp) REVERT: B 527 PHE cc_start: 0.9045 (t80) cc_final: 0.8831 (t80) REVERT: B 546 GLU cc_start: 0.8689 (mt-10) cc_final: 0.7629 (tp30) REVERT: B 631 GLU cc_start: 0.8480 (mm-30) cc_final: 0.8228 (mm-30) REVERT: B 672 MET cc_start: 0.8054 (OUTLIER) cc_final: 0.7778 (ttt) REVERT: B 712 ARG cc_start: 0.8082 (mtp180) cc_final: 0.7371 (mtm180) REVERT: B 717 MET cc_start: 0.7704 (mpp) cc_final: 0.7147 (mpp) REVERT: C 214 GLU cc_start: 0.8575 (tt0) cc_final: 0.8344 (tt0) REVERT: C 240 ASP cc_start: 0.8005 (p0) cc_final: 0.7574 (p0) REVERT: C 288 ASP cc_start: 0.8631 (t0) cc_final: 0.8215 (t0) REVERT: C 483 GLN cc_start: 0.5683 (tm130) cc_final: 0.5069 (tm130) REVERT: A 214 GLU cc_start: 0.8593 (tt0) cc_final: 0.8376 (tt0) REVERT: A 240 ASP cc_start: 0.7949 (p0) cc_final: 0.7497 (p0) REVERT: A 323 MET cc_start: 0.9110 (OUTLIER) cc_final: 0.8841 (ttm) REVERT: A 513 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8363 (mt) REVERT: A 627 ASP cc_start: 0.8477 (m-30) cc_final: 0.8231 (m-30) REVERT: A 714 ARG cc_start: 0.8402 (tpp80) cc_final: 0.7807 (ttt90) REVERT: A 717 MET cc_start: 0.7607 (OUTLIER) cc_final: 0.7216 (ptp) REVERT: D 186 ILE cc_start: 0.8112 (OUTLIER) cc_final: 0.7816 (pt) REVERT: D 330 ASN cc_start: 0.8329 (t0) cc_final: 0.7605 (p0) REVERT: D 358 LYS cc_start: 0.8366 (ttpt) cc_final: 0.8067 (tttm) REVERT: D 369 ARG cc_start: 0.8014 (ttp-110) cc_final: 0.7778 (ttm110) REVERT: D 442 PHE cc_start: 0.7733 (t80) cc_final: 0.6300 (m-10) REVERT: D 446 CYS cc_start: 0.8588 (OUTLIER) cc_final: 0.8198 (m) REVERT: D 447 PHE cc_start: 0.8589 (m-80) cc_final: 0.8294 (m-10) REVERT: D 516 ILE cc_start: 0.7827 (OUTLIER) cc_final: 0.7305 (pp) REVERT: D 672 MET cc_start: 0.8179 (OUTLIER) cc_final: 0.7946 (ttt) REVERT: D 687 GLU cc_start: 0.7176 (tp30) cc_final: 0.6828 (tp30) REVERT: D 690 ARG cc_start: 0.7938 (OUTLIER) cc_final: 0.7680 (mtm110) REVERT: D 712 ARG cc_start: 0.8178 (mtp180) cc_final: 0.7503 (mtm180) outliers start: 74 outliers final: 45 residues processed: 340 average time/residue: 0.4804 time to fit residues: 187.7763 Evaluate side-chains 359 residues out of total 2166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 301 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 440 MET Chi-restraints excluded: chain B residue 446 CYS Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 672 MET Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 180 ASN Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 358 LYS Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 495 MET Chi-restraints excluded: chain C residue 496 CYS Chi-restraints excluded: chain C residue 555 MET Chi-restraints excluded: chain C residue 688 SER Chi-restraints excluded: chain C residue 732 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 496 CYS Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 555 MET Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 612 CYS Chi-restraints excluded: chain A residue 643 ASN Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 717 MET Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 378 THR Chi-restraints excluded: chain D residue 387 SER Chi-restraints excluded: chain D residue 446 CYS Chi-restraints excluded: chain D residue 516 ILE Chi-restraints excluded: chain D residue 579 ILE Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 637 ILE Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain D residue 672 MET Chi-restraints excluded: chain D residue 690 ARG Chi-restraints excluded: chain D residue 730 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 120 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 100 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 98 optimal weight: 0.5980 chunk 205 optimal weight: 0.9990 chunk 118 optimal weight: 9.9990 chunk 114 optimal weight: 5.9990 chunk 111 optimal weight: 0.0770 chunk 192 optimal weight: 2.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 279 GLN A 279 GLN A 570 GLN D 580 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.152641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.122492 restraints weight = 22959.173| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 1.90 r_work: 0.3232 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 19316 Z= 0.133 Angle : 0.549 10.240 26281 Z= 0.278 Chirality : 0.037 0.166 3092 Planarity : 0.003 0.055 3199 Dihedral : 11.070 88.465 2977 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 3.40 % Allowed : 24.43 % Favored : 72.17 % 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: 0.34 (0.17), residues: 2408 helix: 1.29 (0.13), residues: 1610 sheet: -0.59 (0.62), residues: 64 loop : -2.16 (0.22), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 690 TYR 0.016 0.001 TYR C 451 PHE 0.020 0.001 PHE C 489 TRP 0.019 0.001 TRP B 380 HIS 0.008 0.001 HIS D 745 Details of bonding type rmsd covalent geometry : bond 0.00303 (19316) covalent geometry : angle 0.54892 (26281) hydrogen bonds : bond 0.03548 ( 1120) hydrogen bonds : angle 3.67342 ( 3315) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 301 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 159 MET cc_start: 0.7519 (mmm) cc_final: 0.7305 (mmm) REVERT: B 160 HIS cc_start: 0.7231 (m-70) cc_final: 0.7003 (m90) REVERT: B 330 ASN cc_start: 0.8371 (t0) cc_final: 0.7735 (p0) REVERT: B 358 LYS cc_start: 0.8362 (ttpt) cc_final: 0.8074 (tttm) REVERT: B 369 ARG cc_start: 0.8088 (ttp-110) cc_final: 0.7870 (ttm110) REVERT: B 442 PHE cc_start: 0.7713 (t80) cc_final: 0.6310 (m-10) REVERT: B 446 CYS cc_start: 0.8593 (OUTLIER) cc_final: 0.8216 (m) REVERT: B 447 PHE cc_start: 0.8570 (m-80) cc_final: 0.8269 (m-10) REVERT: B 487 ARG cc_start: 0.7737 (mtt90) cc_final: 0.5809 (ttt90) REVERT: B 488 MET cc_start: 0.7530 (OUTLIER) cc_final: 0.6309 (pmm) REVERT: B 492 ILE cc_start: 0.8889 (OUTLIER) cc_final: 0.8552 (mp) REVERT: B 516 ILE cc_start: 0.7802 (OUTLIER) cc_final: 0.7355 (pp) REVERT: B 527 PHE cc_start: 0.9053 (t80) cc_final: 0.8842 (t80) REVERT: B 546 GLU cc_start: 0.8669 (mt-10) cc_final: 0.7633 (tp30) REVERT: B 631 GLU cc_start: 0.8444 (mm-30) cc_final: 0.8193 (mm-30) REVERT: B 672 MET cc_start: 0.8047 (OUTLIER) cc_final: 0.7769 (ttt) REVERT: B 712 ARG cc_start: 0.8075 (mtp180) cc_final: 0.7378 (mtm180) REVERT: B 717 MET cc_start: 0.7689 (mpp) cc_final: 0.7136 (mpp) REVERT: C 214 GLU cc_start: 0.8558 (tt0) cc_final: 0.8324 (tt0) REVERT: C 240 ASP cc_start: 0.7986 (p0) cc_final: 0.7546 (p0) REVERT: C 288 ASP cc_start: 0.8599 (t0) cc_final: 0.8201 (t0) REVERT: C 483 GLN cc_start: 0.5697 (tm130) cc_final: 0.5084 (tm130) REVERT: C 686 LYS cc_start: 0.7488 (pmtt) cc_final: 0.7288 (ptpp) REVERT: A 214 GLU cc_start: 0.8573 (tt0) cc_final: 0.8353 (tt0) REVERT: A 240 ASP cc_start: 0.7944 (p0) cc_final: 0.7493 (p0) REVERT: A 323 MET cc_start: 0.9109 (OUTLIER) cc_final: 0.8841 (ttm) REVERT: A 513 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8384 (mt) REVERT: A 627 ASP cc_start: 0.8457 (m-30) cc_final: 0.8207 (m-30) REVERT: A 714 ARG cc_start: 0.8379 (tpp80) cc_final: 0.7801 (ttt90) REVERT: A 717 MET cc_start: 0.7606 (OUTLIER) cc_final: 0.7210 (ptp) REVERT: D 330 ASN cc_start: 0.8331 (t0) cc_final: 0.7636 (p0) REVERT: D 358 LYS cc_start: 0.8361 (ttpt) cc_final: 0.8065 (tttm) REVERT: D 369 ARG cc_start: 0.7996 (ttp-110) cc_final: 0.7769 (ttm110) REVERT: D 442 PHE cc_start: 0.7714 (t80) cc_final: 0.6308 (m-10) REVERT: D 446 CYS cc_start: 0.8558 (OUTLIER) cc_final: 0.8181 (m) REVERT: D 447 PHE cc_start: 0.8569 (m-80) cc_final: 0.8285 (m-10) REVERT: D 516 ILE cc_start: 0.7845 (OUTLIER) cc_final: 0.7315 (pp) REVERT: D 672 MET cc_start: 0.8174 (OUTLIER) cc_final: 0.7927 (ttt) REVERT: D 687 GLU cc_start: 0.7162 (tp30) cc_final: 0.6824 (tp30) REVERT: D 690 ARG cc_start: 0.7932 (OUTLIER) cc_final: 0.7676 (mtm110) REVERT: D 712 ARG cc_start: 0.8176 (mtp180) cc_final: 0.7511 (mtm180) outliers start: 60 outliers final: 45 residues processed: 332 average time/residue: 0.5210 time to fit residues: 198.3607 Evaluate side-chains 353 residues out of total 2166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 296 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 440 MET Chi-restraints excluded: chain B residue 446 CYS Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 672 MET Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 180 ASN Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 358 LYS Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 495 MET Chi-restraints excluded: chain C residue 496 CYS Chi-restraints excluded: chain C residue 555 MET Chi-restraints excluded: chain C residue 688 SER Chi-restraints excluded: chain C residue 732 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 496 CYS Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 555 MET Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 612 CYS Chi-restraints excluded: chain A residue 643 ASN Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 717 MET Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 378 THR Chi-restraints excluded: chain D residue 387 SER Chi-restraints excluded: chain D residue 440 MET Chi-restraints excluded: chain D residue 446 CYS Chi-restraints excluded: chain D residue 516 ILE Chi-restraints excluded: chain D residue 579 ILE Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 637 ILE Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain D residue 672 MET Chi-restraints excluded: chain D residue 690 ARG Chi-restraints excluded: chain D residue 730 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 193 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 202 optimal weight: 1.9990 chunk 190 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 114 optimal weight: 1.9990 chunk 211 optimal weight: 0.0970 chunk 29 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 279 GLN A 279 GLN A 570 GLN D 580 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.152343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.122179 restraints weight = 23229.169| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.90 r_work: 0.3227 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 19316 Z= 0.147 Angle : 0.552 10.242 26281 Z= 0.280 Chirality : 0.037 0.165 3092 Planarity : 0.003 0.053 3199 Dihedral : 11.045 88.645 2977 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 3.46 % Allowed : 24.38 % Favored : 72.17 % 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: 0.30 (0.17), residues: 2408 helix: 1.23 (0.13), residues: 1624 sheet: -0.56 (0.63), residues: 64 loop : -2.19 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 690 TYR 0.016 0.001 TYR C 451 PHE 0.013 0.001 PHE D 449 TRP 0.020 0.001 TRP B 380 HIS 0.007 0.001 HIS D 745 Details of bonding type rmsd covalent geometry : bond 0.00343 (19316) covalent geometry : angle 0.55242 (26281) hydrogen bonds : bond 0.03588 ( 1120) hydrogen bonds : angle 3.67998 ( 3315) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6773.21 seconds wall clock time: 116 minutes 12.31 seconds (6972.31 seconds total)