Starting phenix.real_space_refine on Mon Mar 18 04:00:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fhh_29085/03_2024/8fhh_29085_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fhh_29085/03_2024/8fhh_29085.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fhh_29085/03_2024/8fhh_29085.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fhh_29085/03_2024/8fhh_29085.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fhh_29085/03_2024/8fhh_29085_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fhh_29085/03_2024/8fhh_29085_neut_updated.pdb" } resolution = 3.09 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.002 sd= 0.044 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 P 4 5.49 5 S 140 5.16 5 C 12912 2.51 5 N 3288 2.21 5 O 3480 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 19824 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4853 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 24, 'TRANS': 581} Chain breaks: 1 Chain: "B" Number of atoms: 4853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4853 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 24, 'TRANS': 581} Chain breaks: 1 Chain: "C" Number of atoms: 4853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4853 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 24, 'TRANS': 581} Chain breaks: 1 Chain: "D" Number of atoms: 4853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4853 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 24, 'TRANS': 581} Chain breaks: 1 Chain: "A" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 103 Unusual residues: {'ERG': 2, 'POV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "B" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 103 Unusual residues: {'ERG': 2, 'POV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "C" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 103 Unusual residues: {'ERG': 2, 'POV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "D" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 103 Unusual residues: {'ERG': 2, 'POV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Time building chain proxies: 10.47, per 1000 atoms: 0.53 Number of scatterers: 19824 At special positions: 0 Unit cell: (141.93, 141.93, 121.18, 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 140 16.00 P 4 15.00 O 3480 8.00 N 3288 7.00 C 12912 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 - 3.50 Amino acid : False - 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: 7.44 Conformation dependent library (CDL) restraints added in 3.3 seconds 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: 4576 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 132 helices and 8 sheets defined 60.2% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.96 Creating SS restraints... Processing helix chain 'A' and resid 30 through 46 Processing helix chain 'A' and resid 48 through 55 Processing helix chain 'A' and resid 58 through 66 Processing helix chain 'A' and resid 82 through 88 Processing helix chain 'A' and resid 92 through 101 Processing helix chain 'A' and resid 103 through 107 Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 120 through 126 Processing helix chain 'A' and resid 130 through 139 Processing helix chain 'A' and resid 166 through 173 Processing helix chain 'A' and resid 176 through 184 Processing helix chain 'A' and resid 199 through 204 Processing helix chain 'A' and resid 211 through 220 Processing helix chain 'A' and resid 232 through 234 No H-bonds generated for 'chain 'A' and resid 232 through 234' Processing helix chain 'A' and resid 243 through 250 Processing helix chain 'A' and resid 253 through 263 removed outlier: 3.861A pdb=" N LYS A 262 " --> pdb=" O HIS A 258 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG A 263 " --> pdb=" O LEU A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 284 No H-bonds generated for 'chain 'A' and resid 281 through 284' Processing helix chain 'A' and resid 292 through 297 Processing helix chain 'A' and resid 303 through 306 Processing helix chain 'A' and resid 311 through 323 removed outlier: 3.886A pdb=" N GLU A 315 " --> pdb=" O THR A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 348 Processing helix chain 'A' and resid 373 through 376 No H-bonds generated for 'chain 'A' and resid 373 through 376' Processing helix chain 'A' and resid 380 through 410 Proline residue: A 405 - end of helix removed outlier: 3.748A pdb=" N PHE A 408 " --> pdb=" O ILE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 417 Processing helix chain 'A' and resid 423 through 444 removed outlier: 3.684A pdb=" N VAL A 427 " --> pdb=" O GLY A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 466 removed outlier: 3.761A pdb=" N PHE A 456 " --> pdb=" O VAL A 452 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL A 465 " --> pdb=" O GLY A 461 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N MET A 466 " --> pdb=" O TRP A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 471 Processing helix chain 'A' and resid 473 through 486 Proline residue: A 477 - end of helix Processing helix chain 'A' and resid 489 through 511 removed outlier: 3.959A pdb=" N LEU A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL A 499 " --> pdb=" O TRP A 495 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER A 506 " --> pdb=" O LEU A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 537 Processing helix chain 'A' and resid 553 through 565 Processing helix chain 'A' and resid 570 through 584 removed outlier: 3.805A pdb=" N ILE A 575 " --> pdb=" O LEU A 571 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N TRP A 583 " --> pdb=" O GLY A 579 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG A 584 " --> pdb=" O ASP A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 607 removed outlier: 3.716A pdb=" N VAL A 598 " --> pdb=" O ARG A 594 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N THR A 601 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG A 606 " --> pdb=" O VAL A 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 46 Processing helix chain 'B' and resid 48 through 55 Processing helix chain 'B' and resid 58 through 66 Processing helix chain 'B' and resid 82 through 88 Processing helix chain 'B' and resid 92 through 101 Processing helix chain 'B' and resid 103 through 107 Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 120 through 126 Processing helix chain 'B' and resid 130 through 139 Processing helix chain 'B' and resid 166 through 173 Processing helix chain 'B' and resid 176 through 184 Processing helix chain 'B' and resid 199 through 204 Processing helix chain 'B' and resid 211 through 220 Processing helix chain 'B' and resid 232 through 234 No H-bonds generated for 'chain 'B' and resid 232 through 234' Processing helix chain 'B' and resid 243 through 250 Processing helix chain 'B' and resid 253 through 263 removed outlier: 3.860A pdb=" N LYS B 262 " --> pdb=" O HIS B 258 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG B 263 " --> pdb=" O LEU B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 284 No H-bonds generated for 'chain 'B' and resid 281 through 284' Processing helix chain 'B' and resid 292 through 297 Processing helix chain 'B' and resid 303 through 306 Processing helix chain 'B' and resid 311 through 323 removed outlier: 3.886A pdb=" N GLU B 315 " --> pdb=" O THR B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 348 Processing helix chain 'B' and resid 373 through 376 No H-bonds generated for 'chain 'B' and resid 373 through 376' Processing helix chain 'B' and resid 380 through 410 Proline residue: B 405 - end of helix removed outlier: 3.748A pdb=" N PHE B 408 " --> pdb=" O ILE B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 417 Processing helix chain 'B' and resid 423 through 444 removed outlier: 3.684A pdb=" N VAL B 427 " --> pdb=" O GLY B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 466 removed outlier: 3.760A pdb=" N PHE B 456 " --> pdb=" O VAL B 452 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL B 465 " --> pdb=" O GLY B 461 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N MET B 466 " --> pdb=" O TRP B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 471 Processing helix chain 'B' and resid 473 through 486 Proline residue: B 477 - end of helix Processing helix chain 'B' and resid 489 through 511 removed outlier: 3.959A pdb=" N LEU B 496 " --> pdb=" O ARG B 492 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL B 499 " --> pdb=" O TRP B 495 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER B 506 " --> pdb=" O LEU B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 537 Processing helix chain 'B' and resid 553 through 565 Processing helix chain 'B' and resid 570 through 584 removed outlier: 3.805A pdb=" N ILE B 575 " --> pdb=" O LEU B 571 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N TRP B 583 " --> pdb=" O GLY B 579 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG B 584 " --> pdb=" O ASP B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 607 removed outlier: 3.716A pdb=" N VAL B 598 " --> pdb=" O ARG B 594 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N THR B 601 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG B 606 " --> pdb=" O VAL B 602 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 46 Processing helix chain 'C' and resid 48 through 55 Processing helix chain 'C' and resid 58 through 66 Processing helix chain 'C' and resid 82 through 88 Processing helix chain 'C' and resid 92 through 101 Processing helix chain 'C' and resid 103 through 107 Processing helix chain 'C' and resid 113 through 115 No H-bonds generated for 'chain 'C' and resid 113 through 115' Processing helix chain 'C' and resid 120 through 126 Processing helix chain 'C' and resid 130 through 139 Processing helix chain 'C' and resid 166 through 173 Processing helix chain 'C' and resid 176 through 184 Processing helix chain 'C' and resid 199 through 204 Processing helix chain 'C' and resid 211 through 220 Processing helix chain 'C' and resid 232 through 234 No H-bonds generated for 'chain 'C' and resid 232 through 234' Processing helix chain 'C' and resid 243 through 250 Processing helix chain 'C' and resid 253 through 263 removed outlier: 3.861A pdb=" N LYS C 262 " --> pdb=" O HIS C 258 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG C 263 " --> pdb=" O LEU C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 284 No H-bonds generated for 'chain 'C' and resid 281 through 284' Processing helix chain 'C' and resid 292 through 297 Processing helix chain 'C' and resid 303 through 306 Processing helix chain 'C' and resid 311 through 323 removed outlier: 3.886A pdb=" N GLU C 315 " --> pdb=" O THR C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 348 Processing helix chain 'C' and resid 373 through 376 No H-bonds generated for 'chain 'C' and resid 373 through 376' Processing helix chain 'C' and resid 380 through 410 Proline residue: C 405 - end of helix removed outlier: 3.748A pdb=" N PHE C 408 " --> pdb=" O ILE C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 417 Processing helix chain 'C' and resid 423 through 444 removed outlier: 3.684A pdb=" N VAL C 427 " --> pdb=" O GLY C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 466 removed outlier: 3.761A pdb=" N PHE C 456 " --> pdb=" O VAL C 452 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL C 465 " --> pdb=" O GLY C 461 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N MET C 466 " --> pdb=" O TRP C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 471 Processing helix chain 'C' and resid 473 through 486 Proline residue: C 477 - end of helix Processing helix chain 'C' and resid 489 through 511 removed outlier: 3.959A pdb=" N LEU C 496 " --> pdb=" O ARG C 492 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL C 499 " --> pdb=" O TRP C 495 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER C 506 " --> pdb=" O LEU C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 537 Processing helix chain 'C' and resid 553 through 565 Processing helix chain 'C' and resid 570 through 584 removed outlier: 3.805A pdb=" N ILE C 575 " --> pdb=" O LEU C 571 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N TRP C 583 " --> pdb=" O GLY C 579 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG C 584 " --> pdb=" O ASP C 580 " (cutoff:3.500A) Processing helix chain 'C' and resid 586 through 607 removed outlier: 3.716A pdb=" N VAL C 598 " --> pdb=" O ARG C 594 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N THR C 601 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG C 606 " --> pdb=" O VAL C 602 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 46 Processing helix chain 'D' and resid 48 through 55 Processing helix chain 'D' and resid 58 through 66 Processing helix chain 'D' and resid 82 through 88 Processing helix chain 'D' and resid 92 through 101 Processing helix chain 'D' and resid 103 through 107 Processing helix chain 'D' and resid 113 through 115 No H-bonds generated for 'chain 'D' and resid 113 through 115' Processing helix chain 'D' and resid 120 through 126 Processing helix chain 'D' and resid 130 through 139 Processing helix chain 'D' and resid 166 through 173 Processing helix chain 'D' and resid 176 through 184 Processing helix chain 'D' and resid 199 through 204 Processing helix chain 'D' and resid 211 through 220 Processing helix chain 'D' and resid 232 through 234 No H-bonds generated for 'chain 'D' and resid 232 through 234' Processing helix chain 'D' and resid 243 through 250 Processing helix chain 'D' and resid 253 through 263 removed outlier: 3.861A pdb=" N LYS D 262 " --> pdb=" O HIS D 258 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG D 263 " --> pdb=" O LEU D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 284 No H-bonds generated for 'chain 'D' and resid 281 through 284' Processing helix chain 'D' and resid 292 through 297 Processing helix chain 'D' and resid 303 through 306 Processing helix chain 'D' and resid 311 through 323 removed outlier: 3.886A pdb=" N GLU D 315 " --> pdb=" O THR D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 348 Processing helix chain 'D' and resid 373 through 376 No H-bonds generated for 'chain 'D' and resid 373 through 376' Processing helix chain 'D' and resid 380 through 410 Proline residue: D 405 - end of helix removed outlier: 3.747A pdb=" N PHE D 408 " --> pdb=" O ILE D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 417 Processing helix chain 'D' and resid 423 through 444 removed outlier: 3.684A pdb=" N VAL D 427 " --> pdb=" O GLY D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 466 removed outlier: 3.761A pdb=" N PHE D 456 " --> pdb=" O VAL D 452 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL D 465 " --> pdb=" O GLY D 461 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N MET D 466 " --> pdb=" O TRP D 462 " (cutoff:3.500A) Processing helix chain 'D' and resid 468 through 471 Processing helix chain 'D' and resid 473 through 486 Proline residue: D 477 - end of helix Processing helix chain 'D' and resid 489 through 511 removed outlier: 3.959A pdb=" N LEU D 496 " --> pdb=" O ARG D 492 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL D 499 " --> pdb=" O TRP D 495 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER D 506 " --> pdb=" O LEU D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 526 through 537 Processing helix chain 'D' and resid 553 through 565 Processing helix chain 'D' and resid 570 through 584 removed outlier: 3.805A pdb=" N ILE D 575 " --> pdb=" O LEU D 571 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N TRP D 583 " --> pdb=" O GLY D 579 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG D 584 " --> pdb=" O ASP D 580 " (cutoff:3.500A) Processing helix chain 'D' and resid 586 through 607 removed outlier: 3.716A pdb=" N VAL D 598 " --> pdb=" O ARG D 594 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N THR D 601 " --> pdb=" O VAL D 597 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG D 606 " --> pdb=" O VAL D 602 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 273 through 279 Processing sheet with id= B, first strand: chain 'A' and resid 352 through 354 Processing sheet with id= C, first strand: chain 'B' and resid 273 through 279 Processing sheet with id= D, first strand: chain 'B' and resid 352 through 354 Processing sheet with id= E, first strand: chain 'C' and resid 273 through 279 Processing sheet with id= F, first strand: chain 'C' and resid 352 through 354 Processing sheet with id= G, first strand: chain 'D' and resid 273 through 279 Processing sheet with id= H, first strand: chain 'D' and resid 352 through 354 892 hydrogen bonds defined for protein. 2628 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: 5.73 Time building geometry restraints manager: 8.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3291 1.32 - 1.44: 5291 1.44 - 1.57: 11466 1.57 - 1.69: 16 1.69 - 1.81: 228 Bond restraints: 20292 Sorted by residual: bond pdb=" CA ALA D 595 " pdb=" CB ALA D 595 " ideal model delta sigma weight residual 1.529 1.474 0.055 1.58e-02 4.01e+03 1.21e+01 bond pdb=" CA ALA B 595 " pdb=" CB ALA B 595 " ideal model delta sigma weight residual 1.529 1.474 0.055 1.58e-02 4.01e+03 1.21e+01 bond pdb=" CA ALA C 595 " pdb=" CB ALA C 595 " ideal model delta sigma weight residual 1.529 1.474 0.055 1.58e-02 4.01e+03 1.21e+01 bond pdb=" CA ALA A 595 " pdb=" CB ALA A 595 " ideal model delta sigma weight residual 1.529 1.474 0.055 1.58e-02 4.01e+03 1.21e+01 bond pdb=" N VAL D 597 " pdb=" CA VAL D 597 " ideal model delta sigma weight residual 1.459 1.502 -0.043 1.29e-02 6.01e+03 1.10e+01 ... (remaining 20287 not shown) Histogram of bond angle deviations from ideal: 98.39 - 105.55: 448 105.55 - 112.70: 10636 112.70 - 119.85: 7209 119.85 - 127.01: 9027 127.01 - 134.16: 252 Bond angle restraints: 27572 Sorted by residual: angle pdb=" O ARG B 589 " pdb=" C ARG B 589 " pdb=" N ASP B 590 " ideal model delta sigma weight residual 122.22 114.99 7.23 1.17e+00 7.31e-01 3.82e+01 angle pdb=" O ARG C 589 " pdb=" C ARG C 589 " pdb=" N ASP C 590 " ideal model delta sigma weight residual 122.22 114.99 7.23 1.17e+00 7.31e-01 3.82e+01 angle pdb=" O ARG D 589 " pdb=" C ARG D 589 " pdb=" N ASP D 590 " ideal model delta sigma weight residual 122.22 114.99 7.23 1.17e+00 7.31e-01 3.82e+01 angle pdb=" O ARG A 589 " pdb=" C ARG A 589 " pdb=" N ASP A 590 " ideal model delta sigma weight residual 122.22 114.99 7.23 1.17e+00 7.31e-01 3.82e+01 angle pdb=" N GLN D 513 " pdb=" CA GLN D 513 " pdb=" C GLN D 513 " ideal model delta sigma weight residual 113.28 106.63 6.65 1.22e+00 6.72e-01 2.97e+01 ... (remaining 27567 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.77: 12041 24.77 - 49.53: 399 49.53 - 74.30: 40 74.30 - 99.07: 4 99.07 - 123.83: 8 Dihedral angle restraints: 12492 sinusoidal: 5412 harmonic: 7080 Sorted by residual: dihedral pdb=" CA CYS D 112 " pdb=" C CYS D 112 " pdb=" N GLU D 113 " pdb=" CA GLU D 113 " ideal model delta harmonic sigma weight residual -180.00 -158.63 -21.37 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA CYS C 112 " pdb=" C CYS C 112 " pdb=" N GLU C 113 " pdb=" CA GLU C 113 " ideal model delta harmonic sigma weight residual -180.00 -158.65 -21.35 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" CA CYS B 112 " pdb=" C CYS B 112 " pdb=" N GLU B 113 " pdb=" CA GLU B 113 " ideal model delta harmonic sigma weight residual -180.00 -158.65 -21.35 0 5.00e+00 4.00e-02 1.82e+01 ... (remaining 12489 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2510 0.054 - 0.107: 489 0.107 - 0.161: 109 0.161 - 0.214: 28 0.214 - 0.268: 4 Chirality restraints: 3140 Sorted by residual: chirality pdb=" CB VAL D 499 " pdb=" CA VAL D 499 " pdb=" CG1 VAL D 499 " pdb=" CG2 VAL D 499 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CB VAL A 499 " pdb=" CA VAL A 499 " pdb=" CG1 VAL A 499 " pdb=" CG2 VAL A 499 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CB VAL C 499 " pdb=" CA VAL C 499 " pdb=" CG1 VAL C 499 " pdb=" CG2 VAL C 499 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.76e+00 ... (remaining 3137 not shown) Planarity restraints: 3436 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 POV C 801 " -0.077 2.00e-02 2.50e+03 7.60e-02 5.78e+01 pdb=" C29 POV C 801 " 0.084 2.00e-02 2.50e+03 pdb="C210 POV C 801 " 0.067 2.00e-02 2.50e+03 pdb="C211 POV C 801 " -0.074 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV D 801 " -0.077 2.00e-02 2.50e+03 7.60e-02 5.77e+01 pdb=" C29 POV D 801 " 0.084 2.00e-02 2.50e+03 pdb="C210 POV D 801 " 0.067 2.00e-02 2.50e+03 pdb="C211 POV D 801 " -0.074 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV B 801 " 0.077 2.00e-02 2.50e+03 7.59e-02 5.76e+01 pdb=" C29 POV B 801 " -0.084 2.00e-02 2.50e+03 pdb="C210 POV B 801 " -0.067 2.00e-02 2.50e+03 pdb="C211 POV B 801 " 0.074 2.00e-02 2.50e+03 ... (remaining 3433 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 5631 2.81 - 3.34: 18359 3.34 - 3.86: 34634 3.86 - 4.38: 41193 4.38 - 4.90: 69494 Nonbonded interactions: 169311 Sorted by model distance: nonbonded pdb=" OH TYR C 161 " pdb=" OD2 ASP C 193 " model vdw 2.292 2.440 nonbonded pdb=" OH TYR B 161 " pdb=" OD2 ASP B 193 " model vdw 2.292 2.440 nonbonded pdb=" OH TYR D 161 " pdb=" OD2 ASP D 193 " model vdw 2.292 2.440 nonbonded pdb=" OH TYR A 161 " pdb=" OD2 ASP A 193 " model vdw 2.292 2.440 nonbonded pdb=" O PRO D 544 " pdb=" OH TYR D 555 " model vdw 2.313 2.440 ... (remaining 169306 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.980 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: 0.010 Extract box with map and model: 6.090 Check model and map are aligned: 0.290 Set scattering table: 0.170 Process input model: 50.250 Find NCS groups from input model: 1.140 Set up NCS constraints: 0.110 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 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 : 0.006 0.055 20292 Z= 0.354 Angle : 0.831 7.638 27572 Z= 0.524 Chirality : 0.049 0.268 3140 Planarity : 0.007 0.076 3436 Dihedral : 12.506 123.832 7916 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.19 % Allowed : 5.53 % Favored : 94.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.14), residues: 2408 helix: -1.27 (0.11), residues: 1496 sheet: -2.50 (0.37), residues: 124 loop : -1.11 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 268 HIS 0.005 0.001 HIS B 201 PHE 0.014 0.002 PHE B 537 TYR 0.010 0.002 TYR D 467 ARG 0.003 0.000 ARG A 363 *********************** 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 456 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 452 time to evaluate : 2.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7699 (mt0) cc_final: 0.6789 (tt0) REVERT: A 176 GLU cc_start: 0.7833 (mt-10) cc_final: 0.7555 (mp0) REVERT: A 219 LEU cc_start: 0.8665 (mt) cc_final: 0.8454 (mp) REVERT: A 318 SER cc_start: 0.9124 (t) cc_final: 0.8745 (m) REVERT: A 322 LYS cc_start: 0.8822 (mmtt) cc_final: 0.8600 (mttm) REVERT: A 358 ASN cc_start: 0.8132 (m-40) cc_final: 0.7899 (m-40) REVERT: A 419 THR cc_start: 0.8755 (m) cc_final: 0.8428 (m) REVERT: A 444 LEU cc_start: 0.9315 (mt) cc_final: 0.9105 (mt) REVERT: B 31 GLN cc_start: 0.7699 (mt0) cc_final: 0.6786 (tt0) REVERT: B 176 GLU cc_start: 0.7833 (mt-10) cc_final: 0.7555 (mp0) REVERT: B 219 LEU cc_start: 0.8665 (mt) cc_final: 0.8451 (mp) REVERT: B 318 SER cc_start: 0.9123 (t) cc_final: 0.8744 (m) REVERT: B 322 LYS cc_start: 0.8825 (mmtt) cc_final: 0.8604 (mttm) REVERT: B 358 ASN cc_start: 0.8120 (m-40) cc_final: 0.7890 (m-40) REVERT: B 419 THR cc_start: 0.8750 (m) cc_final: 0.8423 (m) REVERT: B 444 LEU cc_start: 0.9314 (mt) cc_final: 0.9102 (mt) REVERT: C 31 GLN cc_start: 0.7700 (mt0) cc_final: 0.6791 (tt0) REVERT: C 176 GLU cc_start: 0.7830 (mt-10) cc_final: 0.7554 (mp0) REVERT: C 219 LEU cc_start: 0.8668 (mt) cc_final: 0.8453 (mp) REVERT: C 318 SER cc_start: 0.9116 (t) cc_final: 0.8736 (m) REVERT: C 322 LYS cc_start: 0.8819 (mmtt) cc_final: 0.8598 (mttm) REVERT: C 358 ASN cc_start: 0.8121 (m-40) cc_final: 0.7890 (m-40) REVERT: C 419 THR cc_start: 0.8750 (m) cc_final: 0.8425 (m) REVERT: C 444 LEU cc_start: 0.9314 (mt) cc_final: 0.9100 (mt) REVERT: D 31 GLN cc_start: 0.7699 (mt0) cc_final: 0.6790 (tt0) REVERT: D 176 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7554 (mp0) REVERT: D 219 LEU cc_start: 0.8666 (mt) cc_final: 0.8457 (mp) REVERT: D 318 SER cc_start: 0.9118 (t) cc_final: 0.8739 (m) REVERT: D 322 LYS cc_start: 0.8822 (mmtt) cc_final: 0.8601 (mttm) REVERT: D 358 ASN cc_start: 0.8118 (m-40) cc_final: 0.7878 (m-40) REVERT: D 419 THR cc_start: 0.8754 (m) cc_final: 0.8426 (m) REVERT: D 444 LEU cc_start: 0.9315 (mt) cc_final: 0.9101 (mt) outliers start: 4 outliers final: 0 residues processed: 456 average time/residue: 0.3580 time to fit residues: 235.6595 Evaluate side-chains 302 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 302 time to evaluate : 2.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 4.9990 chunk 181 optimal weight: 8.9990 chunk 100 optimal weight: 0.8980 chunk 62 optimal weight: 10.0000 chunk 122 optimal weight: 9.9990 chunk 97 optimal weight: 1.9990 chunk 188 optimal weight: 7.9990 chunk 72 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 chunk 140 optimal weight: 6.9990 chunk 217 optimal weight: 0.8980 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 122 HIS A 192 GLN A 267 GLN ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 635 ASN B 31 GLN B 122 HIS B 192 GLN B 267 GLN ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 635 ASN C 31 GLN C 122 HIS C 192 GLN C 267 GLN ** C 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 635 ASN D 31 GLN D 122 HIS D 192 GLN D 267 GLN ** D 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 635 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 20292 Z= 0.336 Angle : 0.524 5.436 27572 Z= 0.269 Chirality : 0.040 0.169 3140 Planarity : 0.004 0.042 3436 Dihedral : 8.856 113.611 3324 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.39 % Allowed : 6.92 % Favored : 90.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.16), residues: 2408 helix: 0.30 (0.13), residues: 1500 sheet: -1.73 (0.49), residues: 84 loop : -0.61 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 593 HIS 0.005 0.001 HIS D 201 PHE 0.015 0.002 PHE A 468 TYR 0.013 0.002 TYR A 526 ARG 0.004 0.001 ARG D 139 *********************** 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 372 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 322 time to evaluate : 2.365 Fit side-chains REVERT: A 31 GLN cc_start: 0.7723 (mt0) cc_final: 0.6818 (tt0) REVERT: A 176 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7585 (mp0) REVERT: A 233 GLU cc_start: 0.8392 (mt-10) cc_final: 0.8112 (mt-10) REVERT: A 314 LYS cc_start: 0.8752 (tttt) cc_final: 0.8535 (tttp) REVERT: A 318 SER cc_start: 0.9182 (t) cc_final: 0.8673 (m) REVERT: A 322 LYS cc_start: 0.8779 (mmtt) cc_final: 0.8530 (mttm) REVERT: A 414 ARG cc_start: 0.7969 (mtm-85) cc_final: 0.7673 (ttt180) REVERT: B 31 GLN cc_start: 0.7727 (mt0) cc_final: 0.6822 (tt0) REVERT: B 176 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7585 (mp0) REVERT: B 233 GLU cc_start: 0.8353 (mt-10) cc_final: 0.8104 (mt-10) REVERT: B 314 LYS cc_start: 0.8752 (tttt) cc_final: 0.8535 (tttp) REVERT: B 318 SER cc_start: 0.9176 (t) cc_final: 0.8664 (m) REVERT: B 322 LYS cc_start: 0.8781 (mmtt) cc_final: 0.8533 (mttm) REVERT: B 414 ARG cc_start: 0.7966 (mtm-85) cc_final: 0.7674 (ttt180) REVERT: C 31 GLN cc_start: 0.7726 (mt0) cc_final: 0.6825 (tt0) REVERT: C 176 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7586 (mp0) REVERT: C 233 GLU cc_start: 0.8356 (mt-10) cc_final: 0.8104 (mt-10) REVERT: C 314 LYS cc_start: 0.8752 (tttt) cc_final: 0.8534 (tttp) REVERT: C 318 SER cc_start: 0.9176 (t) cc_final: 0.8664 (m) REVERT: C 322 LYS cc_start: 0.8776 (mmtt) cc_final: 0.8525 (mttm) REVERT: C 414 ARG cc_start: 0.7968 (mtm-85) cc_final: 0.7676 (ttt180) REVERT: D 31 GLN cc_start: 0.7722 (mt0) cc_final: 0.6820 (tt0) REVERT: D 176 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7585 (mp0) REVERT: D 233 GLU cc_start: 0.8356 (mt-10) cc_final: 0.8105 (mt-10) REVERT: D 314 LYS cc_start: 0.8755 (tttt) cc_final: 0.8537 (tttp) REVERT: D 318 SER cc_start: 0.9177 (t) cc_final: 0.8663 (m) REVERT: D 322 LYS cc_start: 0.8774 (mmtt) cc_final: 0.8525 (mttm) REVERT: D 414 ARG cc_start: 0.7969 (mtm-85) cc_final: 0.7674 (ttt180) outliers start: 50 outliers final: 36 residues processed: 354 average time/residue: 0.3344 time to fit residues: 181.2801 Evaluate side-chains 316 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 280 time to evaluate : 2.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 616 SER Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain C residue 616 SER Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 413 SER Chi-restraints excluded: chain D residue 616 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 1.9990 chunk 67 optimal weight: 0.0470 chunk 181 optimal weight: 0.9990 chunk 148 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 218 optimal weight: 0.0770 chunk 235 optimal weight: 4.9990 chunk 194 optimal weight: 3.9990 chunk 216 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 175 optimal weight: 0.9980 overall best weight: 0.6240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 596 GLN ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 596 GLN C 185 HIS ** C 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 596 GLN D 185 HIS ** D 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 596 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 20292 Z= 0.130 Angle : 0.426 5.168 27572 Z= 0.222 Chirality : 0.036 0.181 3140 Planarity : 0.004 0.042 3436 Dihedral : 8.277 100.358 3324 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.10 % Allowed : 10.16 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.17), residues: 2408 helix: 1.13 (0.13), residues: 1476 sheet: -2.46 (0.37), residues: 124 loop : -0.36 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 593 HIS 0.002 0.000 HIS A 201 PHE 0.011 0.001 PHE B 574 TYR 0.007 0.001 TYR B 216 ARG 0.005 0.000 ARG C 302 *********************** 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 321 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 298 time to evaluate : 2.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7647 (mt0) cc_final: 0.6787 (tt0) REVERT: A 176 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7600 (mp0) REVERT: A 233 GLU cc_start: 0.8381 (mt-10) cc_final: 0.8104 (mt-10) REVERT: A 314 LYS cc_start: 0.8787 (tttt) cc_final: 0.8508 (tttp) REVERT: A 318 SER cc_start: 0.9161 (t) cc_final: 0.8731 (m) REVERT: A 322 LYS cc_start: 0.8738 (mmtt) cc_final: 0.8483 (mttm) REVERT: A 414 ARG cc_start: 0.7953 (mtm-85) cc_final: 0.7693 (mtt90) REVERT: B 31 GLN cc_start: 0.7650 (mt0) cc_final: 0.6788 (tt0) REVERT: B 176 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7600 (mp0) REVERT: B 233 GLU cc_start: 0.8334 (mt-10) cc_final: 0.8101 (mt-10) REVERT: B 314 LYS cc_start: 0.8787 (tttt) cc_final: 0.8508 (tttp) REVERT: B 318 SER cc_start: 0.9162 (t) cc_final: 0.8733 (m) REVERT: B 322 LYS cc_start: 0.8739 (mmtt) cc_final: 0.8483 (mttm) REVERT: B 414 ARG cc_start: 0.7963 (mtm-85) cc_final: 0.7698 (mtt90) REVERT: C 31 GLN cc_start: 0.7651 (mt0) cc_final: 0.6792 (tt0) REVERT: C 176 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7603 (mp0) REVERT: C 233 GLU cc_start: 0.8334 (mt-10) cc_final: 0.8098 (mt-10) REVERT: C 314 LYS cc_start: 0.8787 (tttt) cc_final: 0.8509 (tttp) REVERT: C 318 SER cc_start: 0.9162 (t) cc_final: 0.8731 (m) REVERT: C 322 LYS cc_start: 0.8739 (mmtt) cc_final: 0.8484 (mttm) REVERT: C 414 ARG cc_start: 0.7965 (mtm-85) cc_final: 0.7700 (mtt90) REVERT: D 31 GLN cc_start: 0.7649 (mt0) cc_final: 0.6790 (tt0) REVERT: D 176 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7608 (mp0) REVERT: D 233 GLU cc_start: 0.8332 (mt-10) cc_final: 0.8096 (mt-10) REVERT: D 314 LYS cc_start: 0.8790 (tttt) cc_final: 0.8512 (tttp) REVERT: D 318 SER cc_start: 0.9163 (t) cc_final: 0.8732 (m) REVERT: D 322 LYS cc_start: 0.8739 (mmtt) cc_final: 0.8484 (mttm) REVERT: D 414 ARG cc_start: 0.7965 (mtm-85) cc_final: 0.7701 (mtt90) outliers start: 23 outliers final: 23 residues processed: 313 average time/residue: 0.3209 time to fit residues: 150.7146 Evaluate side-chains 316 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 293 time to evaluate : 2.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain C residue 506 SER Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 413 SER Chi-restraints excluded: chain D residue 506 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 5.9990 chunk 164 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 chunk 24 optimal weight: 7.9990 chunk 104 optimal weight: 3.9990 chunk 146 optimal weight: 0.9990 chunk 219 optimal weight: 2.9990 chunk 231 optimal weight: 0.0040 chunk 114 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 overall best weight: 2.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20292 Z= 0.270 Angle : 0.466 5.229 27572 Z= 0.241 Chirality : 0.039 0.172 3140 Planarity : 0.004 0.040 3436 Dihedral : 8.177 93.402 3324 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.34 % Allowed : 10.02 % Favored : 88.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.17), residues: 2408 helix: 1.39 (0.13), residues: 1476 sheet: -1.53 (0.51), residues: 84 loop : -0.33 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 593 HIS 0.003 0.001 HIS B 201 PHE 0.014 0.001 PHE D 468 TYR 0.011 0.001 TYR B 526 ARG 0.005 0.000 ARG A 302 *********************** 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 333 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 305 time to evaluate : 2.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7671 (mt0) cc_final: 0.6828 (tt0) REVERT: A 176 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7587 (mp0) REVERT: A 233 GLU cc_start: 0.8440 (mt-10) cc_final: 0.8143 (mt-10) REVERT: A 318 SER cc_start: 0.9182 (t) cc_final: 0.8671 (m) REVERT: A 340 MET cc_start: 0.9195 (mmm) cc_final: 0.8904 (mmp) REVERT: A 409 ARG cc_start: 0.8015 (ttt90) cc_final: 0.7524 (ttt90) REVERT: A 414 ARG cc_start: 0.7972 (mtm-85) cc_final: 0.7704 (ttt180) REVERT: B 31 GLN cc_start: 0.7672 (mt0) cc_final: 0.6828 (tt0) REVERT: B 176 GLU cc_start: 0.7834 (mt-10) cc_final: 0.7586 (mp0) REVERT: B 233 GLU cc_start: 0.8397 (mt-10) cc_final: 0.8193 (mt-10) REVERT: B 318 SER cc_start: 0.9181 (t) cc_final: 0.8670 (m) REVERT: B 340 MET cc_start: 0.9194 (mmm) cc_final: 0.8905 (mmp) REVERT: B 409 ARG cc_start: 0.8012 (ttt90) cc_final: 0.7521 (ttt90) REVERT: B 414 ARG cc_start: 0.7966 (mtm-85) cc_final: 0.7705 (ttt180) REVERT: C 31 GLN cc_start: 0.7673 (mt0) cc_final: 0.6833 (tt0) REVERT: C 176 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7584 (mp0) REVERT: C 233 GLU cc_start: 0.8397 (mt-10) cc_final: 0.8191 (mt-10) REVERT: C 318 SER cc_start: 0.9183 (t) cc_final: 0.8678 (m) REVERT: C 340 MET cc_start: 0.9199 (mmm) cc_final: 0.8912 (mmp) REVERT: C 409 ARG cc_start: 0.8013 (ttt90) cc_final: 0.7522 (ttt90) REVERT: C 414 ARG cc_start: 0.7969 (mtm-85) cc_final: 0.7707 (ttt180) REVERT: D 31 GLN cc_start: 0.7672 (mt0) cc_final: 0.6829 (tt0) REVERT: D 176 GLU cc_start: 0.7844 (mt-10) cc_final: 0.7591 (mp0) REVERT: D 233 GLU cc_start: 0.8400 (mt-10) cc_final: 0.8194 (mt-10) REVERT: D 318 SER cc_start: 0.9181 (t) cc_final: 0.8669 (m) REVERT: D 340 MET cc_start: 0.9201 (mmm) cc_final: 0.8912 (mmp) REVERT: D 409 ARG cc_start: 0.8015 (ttt90) cc_final: 0.7527 (ttt90) REVERT: D 414 ARG cc_start: 0.7971 (mtm-85) cc_final: 0.7758 (ttt90) outliers start: 28 outliers final: 25 residues processed: 332 average time/residue: 0.3222 time to fit residues: 162.2895 Evaluate side-chains 317 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 292 time to evaluate : 2.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain C residue 506 SER Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 413 SER Chi-restraints excluded: chain D residue 506 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 0.8980 chunk 131 optimal weight: 9.9990 chunk 3 optimal weight: 9.9990 chunk 172 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 197 optimal weight: 0.8980 chunk 160 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 118 optimal weight: 9.9990 chunk 208 optimal weight: 0.9990 chunk 58 optimal weight: 9.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 HIS ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 20292 Z= 0.154 Angle : 0.416 5.096 27572 Z= 0.218 Chirality : 0.036 0.140 3140 Planarity : 0.004 0.043 3436 Dihedral : 7.739 70.496 3324 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.48 % Allowed : 11.45 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.17), residues: 2408 helix: 1.74 (0.13), residues: 1472 sheet: -2.31 (0.38), residues: 124 loop : -0.18 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 593 HIS 0.008 0.001 HIS D 637 PHE 0.017 0.001 PHE A 574 TYR 0.007 0.001 TYR C 526 ARG 0.006 0.000 ARG A 302 *********************** 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 340 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 309 time to evaluate : 2.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7571 (mt0) cc_final: 0.6744 (tt0) REVERT: A 176 GLU cc_start: 0.7855 (mt-10) cc_final: 0.7588 (mp0) REVERT: A 207 PRO cc_start: 0.9081 (Cg_endo) cc_final: 0.8861 (Cg_exo) REVERT: A 233 GLU cc_start: 0.8444 (mt-10) cc_final: 0.8189 (mt-10) REVERT: A 318 SER cc_start: 0.9185 (t) cc_final: 0.8733 (m) REVERT: A 340 MET cc_start: 0.9190 (mmm) cc_final: 0.8824 (mmp) REVERT: A 414 ARG cc_start: 0.7977 (mtm-85) cc_final: 0.7769 (mtt90) REVERT: B 31 GLN cc_start: 0.7572 (mt0) cc_final: 0.6746 (tt0) REVERT: B 176 GLU cc_start: 0.7855 (mt-10) cc_final: 0.7588 (mp0) REVERT: B 207 PRO cc_start: 0.9084 (Cg_endo) cc_final: 0.8862 (Cg_exo) REVERT: B 233 GLU cc_start: 0.8371 (mt-10) cc_final: 0.8171 (mt-10) REVERT: B 318 SER cc_start: 0.9185 (t) cc_final: 0.8734 (m) REVERT: B 340 MET cc_start: 0.9191 (mmm) cc_final: 0.8827 (mmp) REVERT: B 414 ARG cc_start: 0.7966 (mtm-85) cc_final: 0.7757 (mtt90) REVERT: C 31 GLN cc_start: 0.7571 (mt0) cc_final: 0.6748 (tt0) REVERT: C 176 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7586 (mp0) REVERT: C 207 PRO cc_start: 0.9098 (Cg_endo) cc_final: 0.8888 (Cg_exo) REVERT: C 233 GLU cc_start: 0.8372 (mt-10) cc_final: 0.8172 (mt-10) REVERT: C 318 SER cc_start: 0.9184 (t) cc_final: 0.8732 (m) REVERT: C 340 MET cc_start: 0.9191 (mmm) cc_final: 0.8827 (mmp) REVERT: C 414 ARG cc_start: 0.7970 (mtm-85) cc_final: 0.7750 (mtt90) REVERT: D 31 GLN cc_start: 0.7582 (mt0) cc_final: 0.6765 (tt0) REVERT: D 176 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7621 (mp0) REVERT: D 207 PRO cc_start: 0.9084 (Cg_endo) cc_final: 0.8861 (Cg_exo) REVERT: D 233 GLU cc_start: 0.8375 (mt-10) cc_final: 0.8174 (mt-10) REVERT: D 318 SER cc_start: 0.9186 (t) cc_final: 0.8733 (m) REVERT: D 340 MET cc_start: 0.9192 (mmm) cc_final: 0.8827 (mmp) REVERT: D 414 ARG cc_start: 0.7974 (mtm-85) cc_final: 0.7773 (mtt90) outliers start: 31 outliers final: 27 residues processed: 325 average time/residue: 0.3230 time to fit residues: 160.7761 Evaluate side-chains 324 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 297 time to evaluate : 2.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain C residue 506 SER Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 413 SER Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 506 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 1.9990 chunk 208 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 136 optimal weight: 10.0000 chunk 57 optimal weight: 1.9990 chunk 232 optimal weight: 1.9990 chunk 192 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 76 optimal weight: 7.9990 chunk 121 optimal weight: 4.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 20292 Z= 0.245 Angle : 0.455 6.823 27572 Z= 0.235 Chirality : 0.038 0.139 3140 Planarity : 0.004 0.042 3436 Dihedral : 7.754 65.220 3324 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.57 % Allowed : 11.40 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.17), residues: 2408 helix: 1.70 (0.13), residues: 1480 sheet: -1.44 (0.53), residues: 84 loop : -0.12 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 593 HIS 0.007 0.001 HIS C 637 PHE 0.018 0.001 PHE A 574 TYR 0.011 0.001 TYR B 526 ARG 0.006 0.000 ARG C 302 *********************** 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 328 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 295 time to evaluate : 2.314 Fit side-chains REVERT: A 31 GLN cc_start: 0.7617 (mt0) cc_final: 0.6798 (tt0) REVERT: A 176 GLU cc_start: 0.7847 (mt-10) cc_final: 0.7517 (mp0) REVERT: A 233 GLU cc_start: 0.8468 (mt-10) cc_final: 0.8201 (mt-10) REVERT: A 318 SER cc_start: 0.9198 (t) cc_final: 0.8694 (m) REVERT: A 340 MET cc_start: 0.9221 (mmm) cc_final: 0.8932 (mmp) REVERT: A 409 ARG cc_start: 0.7887 (ttt90) cc_final: 0.7469 (ttt90) REVERT: A 414 ARG cc_start: 0.7951 (mtm-85) cc_final: 0.7739 (mtt90) REVERT: B 31 GLN cc_start: 0.7617 (mt0) cc_final: 0.6799 (tt0) REVERT: B 176 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7516 (mp0) REVERT: B 233 GLU cc_start: 0.8414 (mt-10) cc_final: 0.8182 (mt-10) REVERT: B 318 SER cc_start: 0.9197 (t) cc_final: 0.8693 (m) REVERT: B 340 MET cc_start: 0.9222 (mmm) cc_final: 0.8934 (mmp) REVERT: B 409 ARG cc_start: 0.7885 (ttt90) cc_final: 0.7466 (ttt90) REVERT: B 414 ARG cc_start: 0.7955 (mtm-85) cc_final: 0.7741 (mtt90) REVERT: C 31 GLN cc_start: 0.7620 (mt0) cc_final: 0.6803 (tt0) REVERT: C 176 GLU cc_start: 0.7829 (mt-10) cc_final: 0.7493 (mp0) REVERT: C 233 GLU cc_start: 0.8438 (mt-10) cc_final: 0.8203 (mt-10) REVERT: C 318 SER cc_start: 0.9183 (t) cc_final: 0.8674 (m) REVERT: C 340 MET cc_start: 0.9223 (mmm) cc_final: 0.8936 (mmp) REVERT: C 409 ARG cc_start: 0.7885 (ttt90) cc_final: 0.7466 (ttt90) REVERT: C 414 ARG cc_start: 0.7961 (mtm-85) cc_final: 0.7742 (mtt90) REVERT: D 31 GLN cc_start: 0.7622 (mt0) cc_final: 0.6801 (tt0) REVERT: D 176 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7555 (mp0) REVERT: D 233 GLU cc_start: 0.8422 (mt-10) cc_final: 0.8188 (mt-10) REVERT: D 318 SER cc_start: 0.9197 (t) cc_final: 0.8694 (m) REVERT: D 340 MET cc_start: 0.9223 (mmm) cc_final: 0.8934 (mmp) REVERT: D 409 ARG cc_start: 0.7889 (ttt90) cc_final: 0.7469 (ttt90) REVERT: D 414 ARG cc_start: 0.7960 (mtm-85) cc_final: 0.7741 (mtt90) outliers start: 33 outliers final: 25 residues processed: 319 average time/residue: 0.3063 time to fit residues: 149.2645 Evaluate side-chains 312 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 287 time to evaluate : 2.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 506 SER Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 413 SER Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 506 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 132 optimal weight: 0.1980 chunk 169 optimal weight: 2.9990 chunk 131 optimal weight: 6.9990 chunk 195 optimal weight: 4.9990 chunk 129 optimal weight: 1.9990 chunk 231 optimal weight: 0.0970 chunk 144 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 20292 Z= 0.232 Angle : 0.445 5.138 27572 Z= 0.233 Chirality : 0.038 0.144 3140 Planarity : 0.004 0.043 3436 Dihedral : 7.610 64.963 3324 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.81 % Allowed : 11.83 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.17), residues: 2408 helix: 1.71 (0.13), residues: 1472 sheet: -1.42 (0.52), residues: 84 loop : -0.15 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 593 HIS 0.007 0.001 HIS C 637 PHE 0.014 0.001 PHE A 574 TYR 0.010 0.001 TYR A 526 ARG 0.007 0.000 ARG B 302 *********************** 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 325 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 287 time to evaluate : 2.238 Fit side-chains REVERT: A 31 GLN cc_start: 0.7617 (mt0) cc_final: 0.6800 (tt0) REVERT: A 176 GLU cc_start: 0.7816 (mt-10) cc_final: 0.7493 (mp0) REVERT: A 207 PRO cc_start: 0.9099 (Cg_endo) cc_final: 0.8897 (Cg_exo) REVERT: A 233 GLU cc_start: 0.8468 (mt-10) cc_final: 0.8199 (mt-10) REVERT: A 318 SER cc_start: 0.9178 (t) cc_final: 0.8668 (m) REVERT: A 340 MET cc_start: 0.9215 (mmm) cc_final: 0.8925 (mmp) REVERT: A 409 ARG cc_start: 0.7891 (ttt90) cc_final: 0.7466 (ttt90) REVERT: A 414 ARG cc_start: 0.7918 (mtm-85) cc_final: 0.7709 (mtt90) REVERT: B 31 GLN cc_start: 0.7615 (mt0) cc_final: 0.6799 (tt0) REVERT: B 176 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7492 (mp0) REVERT: B 207 PRO cc_start: 0.9099 (Cg_endo) cc_final: 0.8898 (Cg_exo) REVERT: B 318 SER cc_start: 0.9178 (t) cc_final: 0.8668 (m) REVERT: B 340 MET cc_start: 0.9216 (mmm) cc_final: 0.8927 (mmp) REVERT: B 409 ARG cc_start: 0.7889 (ttt90) cc_final: 0.7462 (ttt90) REVERT: B 414 ARG cc_start: 0.7912 (mtm-85) cc_final: 0.7708 (mtt90) REVERT: C 31 GLN cc_start: 0.7616 (mt0) cc_final: 0.6804 (tt0) REVERT: C 176 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7490 (mp0) REVERT: C 318 SER cc_start: 0.9177 (t) cc_final: 0.8665 (m) REVERT: C 340 MET cc_start: 0.9216 (mmm) cc_final: 0.8928 (mmp) REVERT: C 409 ARG cc_start: 0.7892 (ttt90) cc_final: 0.7463 (ttt90) REVERT: C 414 ARG cc_start: 0.7917 (mtm-85) cc_final: 0.7709 (mtt90) REVERT: D 31 GLN cc_start: 0.7617 (mt0) cc_final: 0.6808 (tt0) REVERT: D 176 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7534 (mp0) REVERT: D 207 PRO cc_start: 0.9093 (Cg_endo) cc_final: 0.8891 (Cg_exo) REVERT: D 318 SER cc_start: 0.9176 (t) cc_final: 0.8665 (m) REVERT: D 340 MET cc_start: 0.9217 (mmm) cc_final: 0.8927 (mmp) REVERT: D 409 ARG cc_start: 0.7893 (ttt90) cc_final: 0.7465 (ttt90) REVERT: D 414 ARG cc_start: 0.7916 (mtm-85) cc_final: 0.7708 (mtt90) outliers start: 38 outliers final: 31 residues processed: 306 average time/residue: 0.3181 time to fit residues: 147.9421 Evaluate side-chains 318 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 287 time to evaluate : 1.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 497 MET Chi-restraints excluded: chain C residue 506 SER Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 413 SER Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 497 MET Chi-restraints excluded: chain D residue 506 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 8.9990 chunk 92 optimal weight: 8.9990 chunk 138 optimal weight: 0.0020 chunk 69 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 147 optimal weight: 0.0670 chunk 157 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 181 optimal weight: 7.9990 overall best weight: 0.5326 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 20292 Z= 0.120 Angle : 0.403 5.013 27572 Z= 0.211 Chirality : 0.035 0.124 3140 Planarity : 0.003 0.044 3436 Dihedral : 6.943 66.197 3324 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.10 % Allowed : 12.12 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.17), residues: 2408 helix: 1.97 (0.13), residues: 1456 sheet: -2.07 (0.38), residues: 124 loop : -0.06 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 593 HIS 0.006 0.001 HIS C 637 PHE 0.013 0.001 PHE A 574 TYR 0.007 0.001 TYR B 555 ARG 0.007 0.000 ARG A 302 *********************** 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 322 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 299 time to evaluate : 1.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7507 (mt0) cc_final: 0.6734 (tt0) REVERT: A 75 ARG cc_start: 0.8334 (mmt-90) cc_final: 0.8091 (mmt-90) REVERT: A 176 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7480 (mp0) REVERT: A 233 GLU cc_start: 0.8460 (mt-10) cc_final: 0.8189 (mt-10) REVERT: A 318 SER cc_start: 0.9173 (t) cc_final: 0.8727 (m) REVERT: A 340 MET cc_start: 0.9181 (mmm) cc_final: 0.8875 (mmt) REVERT: A 409 ARG cc_start: 0.7947 (ttt90) cc_final: 0.7606 (ttt90) REVERT: B 31 GLN cc_start: 0.7503 (mt0) cc_final: 0.6733 (tt0) REVERT: B 75 ARG cc_start: 0.8336 (mmt-90) cc_final: 0.8090 (mmt-90) REVERT: B 176 GLU cc_start: 0.7816 (mt-10) cc_final: 0.7480 (mp0) REVERT: B 233 GLU cc_start: 0.8415 (mt-10) cc_final: 0.8209 (mt-10) REVERT: B 318 SER cc_start: 0.9173 (t) cc_final: 0.8728 (m) REVERT: B 340 MET cc_start: 0.9183 (mmm) cc_final: 0.8875 (mmt) REVERT: B 409 ARG cc_start: 0.7945 (ttt90) cc_final: 0.7601 (ttt90) REVERT: C 31 GLN cc_start: 0.7503 (mt0) cc_final: 0.6736 (tt0) REVERT: C 75 ARG cc_start: 0.8338 (mmt-90) cc_final: 0.8095 (mmt-90) REVERT: C 176 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7479 (mp0) REVERT: C 233 GLU cc_start: 0.8414 (mt-10) cc_final: 0.8208 (mt-10) REVERT: C 318 SER cc_start: 0.9173 (t) cc_final: 0.8728 (m) REVERT: C 340 MET cc_start: 0.9183 (mmm) cc_final: 0.8876 (mmt) REVERT: C 409 ARG cc_start: 0.7948 (ttt90) cc_final: 0.7602 (ttt90) REVERT: D 31 GLN cc_start: 0.7511 (mt0) cc_final: 0.6725 (tt0) REVERT: D 176 GLU cc_start: 0.7858 (mt-10) cc_final: 0.7530 (mp0) REVERT: D 233 GLU cc_start: 0.8416 (mt-10) cc_final: 0.8208 (mt-10) REVERT: D 318 SER cc_start: 0.9173 (t) cc_final: 0.8728 (m) REVERT: D 340 MET cc_start: 0.9184 (mmm) cc_final: 0.8875 (mmt) REVERT: D 409 ARG cc_start: 0.7948 (ttt90) cc_final: 0.7602 (ttt90) outliers start: 23 outliers final: 19 residues processed: 308 average time/residue: 0.3369 time to fit residues: 156.1046 Evaluate side-chains 316 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 297 time to evaluate : 2.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 413 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 0.8980 chunk 221 optimal weight: 0.9980 chunk 202 optimal weight: 2.9990 chunk 215 optimal weight: 7.9990 chunk 129 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 169 optimal weight: 0.9980 chunk 66 optimal weight: 6.9990 chunk 194 optimal weight: 2.9990 chunk 203 optimal weight: 5.9990 chunk 214 optimal weight: 2.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20292 Z= 0.224 Angle : 0.439 5.161 27572 Z= 0.229 Chirality : 0.038 0.137 3140 Planarity : 0.004 0.043 3436 Dihedral : 7.078 64.712 3324 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.24 % Allowed : 12.50 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.17), residues: 2408 helix: 1.90 (0.13), residues: 1472 sheet: -1.37 (0.52), residues: 84 loop : -0.07 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 593 HIS 0.007 0.001 HIS C 637 PHE 0.011 0.001 PHE D 574 TYR 0.010 0.001 TYR A 526 ARG 0.009 0.000 ARG C 302 *********************** 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 311 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 285 time to evaluate : 2.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7577 (mt0) cc_final: 0.6779 (tt0) REVERT: A 176 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7474 (mp0) REVERT: A 233 GLU cc_start: 0.8460 (mt-10) cc_final: 0.8175 (mt-10) REVERT: A 318 SER cc_start: 0.9184 (t) cc_final: 0.8694 (m) REVERT: A 340 MET cc_start: 0.9207 (mmm) cc_final: 0.8921 (mmp) REVERT: A 409 ARG cc_start: 0.7958 (ttt90) cc_final: 0.7598 (ttt90) REVERT: B 31 GLN cc_start: 0.7579 (mt0) cc_final: 0.6779 (tt0) REVERT: B 176 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7472 (mp0) REVERT: B 233 GLU cc_start: 0.8445 (mt-10) cc_final: 0.8214 (mt-10) REVERT: B 318 SER cc_start: 0.9183 (t) cc_final: 0.8695 (m) REVERT: B 340 MET cc_start: 0.9209 (mmm) cc_final: 0.8922 (mmp) REVERT: B 409 ARG cc_start: 0.7955 (ttt90) cc_final: 0.7594 (ttt90) REVERT: C 31 GLN cc_start: 0.7576 (mt0) cc_final: 0.6784 (tt0) REVERT: C 176 GLU cc_start: 0.7820 (mt-10) cc_final: 0.7471 (mp0) REVERT: C 233 GLU cc_start: 0.8451 (mt-10) cc_final: 0.8217 (mt-10) REVERT: C 318 SER cc_start: 0.9174 (t) cc_final: 0.8682 (m) REVERT: C 340 MET cc_start: 0.9210 (mmm) cc_final: 0.8924 (mmp) REVERT: C 409 ARG cc_start: 0.7957 (ttt90) cc_final: 0.7594 (ttt90) REVERT: D 31 GLN cc_start: 0.7580 (mt0) cc_final: 0.6777 (tt0) REVERT: D 176 GLU cc_start: 0.7859 (mt-10) cc_final: 0.7515 (mp0) REVERT: D 233 GLU cc_start: 0.8452 (mt-10) cc_final: 0.8220 (mt-10) REVERT: D 318 SER cc_start: 0.9184 (t) cc_final: 0.8694 (m) REVERT: D 340 MET cc_start: 0.9210 (mmm) cc_final: 0.8924 (mmp) REVERT: D 409 ARG cc_start: 0.7959 (ttt90) cc_final: 0.7596 (ttt90) outliers start: 26 outliers final: 25 residues processed: 302 average time/residue: 0.3086 time to fit residues: 142.6398 Evaluate side-chains 310 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 285 time to evaluate : 2.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain C residue 62 LYS Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 506 SER Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 413 SER Chi-restraints excluded: chain D residue 506 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 3.9990 chunk 227 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 158 optimal weight: 0.7980 chunk 239 optimal weight: 4.9990 chunk 220 optimal weight: 0.9990 chunk 190 optimal weight: 8.9990 chunk 19 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 116 optimal weight: 4.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 20292 Z= 0.243 Angle : 0.449 5.135 27572 Z= 0.234 Chirality : 0.038 0.137 3140 Planarity : 0.004 0.043 3436 Dihedral : 7.210 63.954 3324 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.29 % Allowed : 12.69 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.17), residues: 2408 helix: 1.81 (0.13), residues: 1472 sheet: -1.36 (0.52), residues: 84 loop : -0.09 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 593 HIS 0.006 0.001 HIS A 637 PHE 0.012 0.001 PHE B 574 TYR 0.011 0.001 TYR C 526 ARG 0.009 0.000 ARG D 302 ********************** 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 313 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 286 time to evaluate : 2.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7603 (mt0) cc_final: 0.6791 (tt0) REVERT: A 176 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7476 (mp0) REVERT: A 233 GLU cc_start: 0.8479 (mt-10) cc_final: 0.8191 (mt-10) REVERT: A 318 SER cc_start: 0.9187 (t) cc_final: 0.8675 (m) REVERT: A 340 MET cc_start: 0.9212 (mmm) cc_final: 0.8923 (mmp) REVERT: B 31 GLN cc_start: 0.7602 (mt0) cc_final: 0.6792 (tt0) REVERT: B 176 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7477 (mp0) REVERT: B 233 GLU cc_start: 0.8450 (mt-10) cc_final: 0.8216 (mt-10) REVERT: B 318 SER cc_start: 0.9187 (t) cc_final: 0.8676 (m) REVERT: B 340 MET cc_start: 0.9213 (mmm) cc_final: 0.8924 (mmp) REVERT: C 31 GLN cc_start: 0.7609 (mt0) cc_final: 0.6797 (tt0) REVERT: C 176 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7475 (mp0) REVERT: C 233 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8217 (mt-10) REVERT: C 318 SER cc_start: 0.9179 (t) cc_final: 0.8663 (m) REVERT: C 340 MET cc_start: 0.9213 (mmm) cc_final: 0.8925 (mmp) REVERT: D 31 GLN cc_start: 0.7600 (mt0) cc_final: 0.6790 (tt0) REVERT: D 176 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7514 (mp0) REVERT: D 233 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8221 (mt-10) REVERT: D 318 SER cc_start: 0.9188 (t) cc_final: 0.8676 (m) REVERT: D 340 MET cc_start: 0.9214 (mmm) cc_final: 0.8924 (mmp) outliers start: 27 outliers final: 26 residues processed: 302 average time/residue: 0.3185 time to fit residues: 146.8078 Evaluate side-chains 315 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 289 time to evaluate : 2.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 506 SER Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 413 SER Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 506 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 0.7980 chunk 202 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 175 optimal weight: 5.9990 chunk 28 optimal weight: 0.6980 chunk 52 optimal weight: 0.7980 chunk 190 optimal weight: 0.7980 chunk 79 optimal weight: 7.9990 chunk 195 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.120241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.089970 restraints weight = 24598.670| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 1.50 r_work: 0.2811 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2679 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 20292 Z= 0.166 Angle : 0.422 5.089 27572 Z= 0.221 Chirality : 0.036 0.128 3140 Planarity : 0.004 0.043 3436 Dihedral : 7.080 64.622 3324 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.24 % Allowed : 12.69 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.17), residues: 2408 helix: 1.93 (0.13), residues: 1468 sheet: -2.07 (0.38), residues: 124 loop : -0.09 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 593 HIS 0.006 0.001 HIS C 637 PHE 0.018 0.001 PHE C 574 TYR 0.008 0.001 TYR A 526 ARG 0.009 0.000 ARG D 302 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4249.46 seconds wall clock time: 77 minutes 8.63 seconds (4628.63 seconds total)