Starting phenix.real_space_refine on Mon Feb 19 01:20:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6whu_21676/02_2024/6whu_21676_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6whu_21676/02_2024/6whu_21676.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6whu_21676/02_2024/6whu_21676_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6whu_21676/02_2024/6whu_21676_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6whu_21676/02_2024/6whu_21676_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6whu_21676/02_2024/6whu_21676.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6whu_21676/02_2024/6whu_21676.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6whu_21676/02_2024/6whu_21676_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6whu_21676/02_2024/6whu_21676_updated.pdb" } resolution = 3.93 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= 0.011 sd= 0.781 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 2 5.49 5 S 138 5.16 5 Cl 8 4.86 5 C 14988 2.51 5 N 3780 2.21 5 O 4452 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 181": "OE1" <-> "OE2" Residue "A GLU 213": "OE1" <-> "OE2" Residue "A ARG 489": "NH1" <-> "NH2" Residue "A GLU 549": "OE1" <-> "OE2" Residue "A GLU 642": "OE1" <-> "OE2" Residue "B GLU 106": "OE1" <-> "OE2" Residue "B GLU 162": "OE1" <-> "OE2" Residue "B ARG 337": "NH1" <-> "NH2" Residue "B GLU 578": "OE1" <-> "OE2" Residue "B GLU 790": "OE1" <-> "OE2" Residue "B GLU 791": "OE1" <-> "OE2" Residue "C GLU 181": "OE1" <-> "OE2" Residue "C ARG 489": "NH1" <-> "NH2" Residue "C GLU 543": "OE1" <-> "OE2" Residue "C GLU 642": "OE1" <-> "OE2" Residue "D GLU 106": "OE1" <-> "OE2" Residue "D GLU 162": "OE1" <-> "OE2" Residue "D ARG 337": "NH1" <-> "NH2" Residue "D GLU 578": "OE1" <-> "OE2" Residue "D GLU 790": "OE1" <-> "OE2" Residue "D GLU 791": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 23368 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 5804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 789, 5804 Classifications: {'peptide': 789} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PTRANS': 32, 'TRANS': 756} Chain breaks: 4 Unresolved non-hydrogen bonds: 435 Unresolved non-hydrogen angles: 509 Unresolved non-hydrogen dihedrals: 374 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 18, 'ARG:plan': 25} Unresolved non-hydrogen planarities: 280 Chain: "B" Number of atoms: 5745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 771, 5745 Classifications: {'peptide': 771} Incomplete info: {'truncation_to_alanine': 81} Link IDs: {'PTRANS': 28, 'TRANS': 742} Chain breaks: 5 Unresolved non-hydrogen bonds: 356 Unresolved non-hydrogen angles: 425 Unresolved non-hydrogen dihedrals: 314 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 7, 'ASN:plan1': 1, 'ASP:plan': 7, 'PHE:plan': 2, 'GLU:plan': 12, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 213 Chain: "C" Number of atoms: 5804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 789, 5804 Classifications: {'peptide': 789} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PTRANS': 32, 'TRANS': 756} Chain breaks: 4 Unresolved non-hydrogen bonds: 435 Unresolved non-hydrogen angles: 509 Unresolved non-hydrogen dihedrals: 374 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 18, 'ARG:plan': 25} Unresolved non-hydrogen planarities: 280 Chain: "D" Number of atoms: 5745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 771, 5745 Classifications: {'peptide': 771} Incomplete info: {'truncation_to_alanine': 81} Link IDs: {'PTRANS': 28, 'TRANS': 742} Chain breaks: 5 Unresolved non-hydrogen bonds: 356 Unresolved non-hydrogen angles: 425 Unresolved non-hydrogen dihedrals: 314 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 7, 'ASN:plan1': 1, 'ASP:plan': 7, 'PHE:plan': 2, 'GLU:plan': 12, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 213 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 53 Unusual residues: {'NAG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 54 Unusual residues: {'NAG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 53 Unusual residues: {'NAG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 54 Unusual residues: {'NAG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 12.47, per 1000 atoms: 0.53 Number of scatterers: 23368 At special positions: 0 Unit cell: (141.11, 149.33, 186.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 8 17.00 S 138 16.00 P 2 15.00 O 4452 8.00 N 3780 7.00 C 14988 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 329 " distance=2.03 Simple disulfide: pdb=" SG CYS A 441 " - pdb=" SG CYS A 475 " distance=2.03 Simple disulfide: pdb=" SG CYS A 457 " - pdb=" SG CYS A 476 " distance=2.03 Simple disulfide: pdb=" SG CYS A 765 " - pdb=" SG CYS A 819 " distance=2.02 Simple disulfide: pdb=" SG CYS A 831 " - pdb=" SG CYS D 557 " distance=2.04 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 321 " distance=2.03 Simple disulfide: pdb=" SG CYS B 429 " - pdb=" SG CYS B 456 " distance=2.03 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 457 " distance=2.04 Simple disulfide: pdb=" SG CYS B 557 " - pdb=" SG CYS C 831 " distance=2.02 Simple disulfide: pdb=" SG CYS B 746 " - pdb=" SG CYS B 801 " distance=2.04 Simple disulfide: pdb=" SG CYS C 79 " - pdb=" SG CYS C 329 " distance=2.03 Simple disulfide: pdb=" SG CYS C 441 " - pdb=" SG CYS C 475 " distance=2.03 Simple disulfide: pdb=" SG CYS C 457 " - pdb=" SG CYS C 476 " distance=2.03 Simple disulfide: pdb=" SG CYS C 765 " - pdb=" SG CYS C 819 " distance=2.02 Simple disulfide: pdb=" SG CYS D 86 " - pdb=" SG CYS D 321 " distance=2.03 Simple disulfide: pdb=" SG CYS D 429 " - pdb=" SG CYS D 456 " distance=2.03 Simple disulfide: pdb=" SG CYS D 436 " - pdb=" SG CYS D 457 " distance=2.04 Simple disulfide: pdb=" SG CYS D 746 " - pdb=" SG CYS D 801 " distance=2.04 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 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A1002 " - " ASN A 297 " " NAG A1003 " - " ASN A 224 " " NAG B 902 " - " ASN B 74 " " NAG B 905 " - " ASN B 688 " " NAG C1002 " - " ASN C 297 " " NAG C1003 " - " ASN C 224 " " NAG D 902 " - " ASN D 74 " " NAG D 905 " - " ASN D 688 " " NAG E 1 " - " ASN B 542 " " NAG F 1 " - " ASN D 542 " Time building additional restraints: 9.75 Conformation dependent library (CDL) restraints added in 5.4 seconds 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB QGM A1001 " pdb=" CB QGM C1001 " Number of C-beta restraints generated: 5824 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 103 helices and 28 sheets defined 36.7% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.86 Creating SS restraints... Processing helix chain 'A' and resid 36 through 50 Processing helix chain 'A' and resid 73 through 79 Processing helix chain 'A' and resid 107 through 114 removed outlier: 4.681A pdb=" N TYR A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 157 removed outlier: 4.009A pdb=" N SER A 148 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N SER A 149 " --> pdb=" O SER A 145 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N VAL A 150 " --> pdb=" O HIS A 146 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N TRP A 151 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG A 156 " --> pdb=" O PHE A 152 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL A 157 " --> pdb=" O GLU A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 182 Processing helix chain 'A' and resid 226 through 234 Processing helix chain 'A' and resid 246 through 261 removed outlier: 4.673A pdb=" N MET A 258 " --> pdb=" O ARG A 254 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU A 259 " --> pdb=" O ALA A 255 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N MET A 261 " --> pdb=" O ALA A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 265 No H-bonds generated for 'chain 'A' and resid 263 through 265' Processing helix chain 'A' and resid 277 through 282 removed outlier: 5.154A pdb=" N TYR A 282 " --> pdb=" O ASN A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 316 Processing helix chain 'A' and resid 339 through 346 Processing helix chain 'A' and resid 366 through 368 No H-bonds generated for 'chain 'A' and resid 366 through 368' Processing helix chain 'A' and resid 479 through 490 Processing helix chain 'A' and resid 521 through 527 Processing helix chain 'A' and resid 544 through 547 No H-bonds generated for 'chain 'A' and resid 544 through 547' Processing helix chain 'A' and resid 575 through 578 Proline residue: A 578 - end of helix No H-bonds generated for 'chain 'A' and resid 575 through 578' Processing helix chain 'A' and resid 583 through 602 removed outlier: 3.825A pdb=" N GLY A 588 " --> pdb=" O TRP A 584 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU A 589 " --> pdb=" O LEU A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 636 Processing helix chain 'A' and resid 648 through 679 removed outlier: 4.107A pdb=" N ILE A 652 " --> pdb=" O PHE A 648 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU A 653 " --> pdb=" O SER A 649 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU A 678 " --> pdb=" O ALA A 674 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASP A 679 " --> pdb=" O PHE A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 694 No H-bonds generated for 'chain 'A' and resid 691 through 694' Processing helix chain 'A' and resid 709 through 715 Processing helix chain 'A' and resid 722 through 728 Processing helix chain 'A' and resid 736 through 743 Processing helix chain 'A' and resid 754 through 764 removed outlier: 3.552A pdb=" N LYS A 764 " --> pdb=" O GLU A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 790 through 802 Processing helix chain 'A' and resid 805 through 813 Processing helix chain 'A' and resid 836 through 861 removed outlier: 3.857A pdb=" N PHE A 853 " --> pdb=" O ILE A 849 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 91 removed outlier: 3.644A pdb=" N SER B 90 " --> pdb=" O CYS B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 116 removed outlier: 3.556A pdb=" N ALA B 109 " --> pdb=" O GLU B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 163 Processing helix chain 'B' and resid 180 through 190 Processing helix chain 'B' and resid 214 through 222 removed outlier: 3.516A pdb=" N LYS B 221 " --> pdb=" O GLN B 217 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS B 222 " --> pdb=" O ASN B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 246 removed outlier: 3.545A pdb=" N SER B 246 " --> pdb=" O GLU B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 262 No H-bonds generated for 'chain 'B' and resid 260 through 262' Processing helix chain 'B' and resid 289 through 309 Processing helix chain 'B' and resid 329 through 338 removed outlier: 3.618A pdb=" N TYR B 338 " --> pdb=" O MET B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 471 removed outlier: 3.788A pdb=" N SER B 471 " --> pdb=" O LYS B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 502 Processing helix chain 'B' and resid 517 through 522 Processing helix chain 'B' and resid 558 through 580 removed outlier: 5.006A pdb=" N PHE B 563 " --> pdb=" O TRP B 559 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL B 569 " --> pdb=" O MET B 565 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL B 572 " --> pdb=" O ILE B 568 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE B 575 " --> pdb=" O ALA B 571 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N GLU B 578 " --> pdb=" O VAL B 574 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR B 579 " --> pdb=" O PHE B 575 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N PHE B 580 " --> pdb=" O VAL B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 613 removed outlier: 3.703A pdb=" N TRP B 607 " --> pdb=" O GLY B 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 653 Processing helix chain 'B' and resid 669 through 672 No H-bonds generated for 'chain 'B' and resid 669 through 672' Processing helix chain 'B' and resid 674 through 676 No H-bonds generated for 'chain 'B' and resid 674 through 676' Processing helix chain 'B' and resid 691 through 695 Processing helix chain 'B' and resid 701 through 709 removed outlier: 3.519A pdb=" N TYR B 705 " --> pdb=" O GLU B 701 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY B 707 " --> pdb=" O HIS B 703 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N LYS B 708 " --> pdb=" O ALA B 704 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N PHE B 709 " --> pdb=" O TYR B 705 " (cutoff:3.500A) Processing helix chain 'B' and resid 715 through 722 Processing helix chain 'B' and resid 734 through 741 removed outlier: 4.377A pdb=" N GLY B 741 " --> pdb=" O ASN B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 774 through 786 Processing helix chain 'B' and resid 789 through 796 Processing helix chain 'B' and resid 816 through 843 removed outlier: 3.784A pdb=" N GLY B 820 " --> pdb=" O ASN B 817 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N PHE B 842 " --> pdb=" O GLU B 839 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 50 Processing helix chain 'C' and resid 73 through 79 Processing helix chain 'C' and resid 107 through 114 removed outlier: 4.629A pdb=" N TYR C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 157 removed outlier: 4.000A pdb=" N SER C 148 " --> pdb=" O TYR C 144 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N SER C 149 " --> pdb=" O SER C 145 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N VAL C 150 " --> pdb=" O HIS C 146 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N TRP C 151 " --> pdb=" O GLN C 147 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG C 156 " --> pdb=" O PHE C 152 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL C 157 " --> pdb=" O GLU C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 182 Processing helix chain 'C' and resid 226 through 234 Processing helix chain 'C' and resid 246 through 261 removed outlier: 4.652A pdb=" N MET C 258 " --> pdb=" O ARG C 254 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU C 259 " --> pdb=" O ALA C 255 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N MET C 261 " --> pdb=" O ALA C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 265 No H-bonds generated for 'chain 'C' and resid 263 through 265' Processing helix chain 'C' and resid 273 through 275 No H-bonds generated for 'chain 'C' and resid 273 through 275' Processing helix chain 'C' and resid 277 through 282 removed outlier: 5.223A pdb=" N TYR C 282 " --> pdb=" O ASN C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 316 Processing helix chain 'C' and resid 339 through 346 Processing helix chain 'C' and resid 366 through 368 No H-bonds generated for 'chain 'C' and resid 366 through 368' Processing helix chain 'C' and resid 479 through 490 Processing helix chain 'C' and resid 521 through 527 Processing helix chain 'C' and resid 544 through 547 No H-bonds generated for 'chain 'C' and resid 544 through 547' Processing helix chain 'C' and resid 575 through 578 Proline residue: C 578 - end of helix No H-bonds generated for 'chain 'C' and resid 575 through 578' Processing helix chain 'C' and resid 583 through 602 removed outlier: 3.823A pdb=" N GLY C 588 " --> pdb=" O TRP C 584 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU C 589 " --> pdb=" O LEU C 585 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 636 Processing helix chain 'C' and resid 648 through 679 removed outlier: 4.118A pdb=" N ILE C 652 " --> pdb=" O PHE C 648 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU C 653 " --> pdb=" O SER C 649 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU C 678 " --> pdb=" O ALA C 674 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASP C 679 " --> pdb=" O PHE C 675 " (cutoff:3.500A) Processing helix chain 'C' and resid 691 through 694 No H-bonds generated for 'chain 'C' and resid 691 through 694' Processing helix chain 'C' and resid 709 through 715 Processing helix chain 'C' and resid 722 through 728 Processing helix chain 'C' and resid 736 through 743 Processing helix chain 'C' and resid 754 through 764 removed outlier: 3.660A pdb=" N LYS C 764 " --> pdb=" O GLU C 760 " (cutoff:3.500A) Processing helix chain 'C' and resid 790 through 802 Processing helix chain 'C' and resid 805 through 813 Processing helix chain 'C' and resid 836 through 861 removed outlier: 3.840A pdb=" N PHE C 853 " --> pdb=" O ILE C 849 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE C 854 " --> pdb=" O PHE C 850 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA C 857 " --> pdb=" O PHE C 853 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 91 removed outlier: 3.645A pdb=" N SER D 90 " --> pdb=" O CYS D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 116 removed outlier: 3.555A pdb=" N ALA D 109 " --> pdb=" O GLU D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 163 Processing helix chain 'D' and resid 180 through 190 Processing helix chain 'D' and resid 214 through 222 removed outlier: 3.517A pdb=" N LYS D 221 " --> pdb=" O GLN D 217 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS D 222 " --> pdb=" O ASN D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 246 removed outlier: 3.545A pdb=" N SER D 246 " --> pdb=" O GLU D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 262 No H-bonds generated for 'chain 'D' and resid 260 through 262' Processing helix chain 'D' and resid 289 through 309 Processing helix chain 'D' and resid 329 through 338 removed outlier: 3.618A pdb=" N TYR D 338 " --> pdb=" O MET D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 471 removed outlier: 3.788A pdb=" N SER D 471 " --> pdb=" O LYS D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 497 through 502 Processing helix chain 'D' and resid 517 through 522 Processing helix chain 'D' and resid 558 through 580 removed outlier: 5.006A pdb=" N PHE D 563 " --> pdb=" O TRP D 559 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL D 569 " --> pdb=" O MET D 565 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL D 572 " --> pdb=" O ILE D 568 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE D 575 " --> pdb=" O ALA D 571 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLU D 578 " --> pdb=" O VAL D 574 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR D 579 " --> pdb=" O PHE D 575 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N PHE D 580 " --> pdb=" O VAL D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 602 through 613 removed outlier: 3.703A pdb=" N TRP D 607 " --> pdb=" O GLY D 603 " (cutoff:3.500A) Processing helix chain 'D' and resid 628 through 653 Processing helix chain 'D' and resid 669 through 672 No H-bonds generated for 'chain 'D' and resid 669 through 672' Processing helix chain 'D' and resid 674 through 676 No H-bonds generated for 'chain 'D' and resid 674 through 676' Processing helix chain 'D' and resid 691 through 695 Processing helix chain 'D' and resid 701 through 709 removed outlier: 3.519A pdb=" N TYR D 705 " --> pdb=" O GLU D 701 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY D 707 " --> pdb=" O HIS D 703 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N LYS D 708 " --> pdb=" O ALA D 704 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N PHE D 709 " --> pdb=" O TYR D 705 " (cutoff:3.500A) Processing helix chain 'D' and resid 715 through 722 Processing helix chain 'D' and resid 734 through 741 removed outlier: 4.376A pdb=" N GLY D 741 " --> pdb=" O ASN D 737 " (cutoff:3.500A) Processing helix chain 'D' and resid 774 through 786 Processing helix chain 'D' and resid 789 through 796 Processing helix chain 'D' and resid 816 through 843 removed outlier: 3.784A pdb=" N GLY D 820 " --> pdb=" O ASN D 817 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N PHE D 842 " --> pdb=" O GLU D 839 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 30 through 32 Processing sheet with id= B, first strand: chain 'A' and resid 239 through 243 removed outlier: 4.061A pdb=" N VAL A 239 " --> pdb=" O HIS A 162 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER A 243 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N LYS A 211 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N LEU A 165 " --> pdb=" O LYS A 211 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N GLU A 213 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 12.670A pdb=" N VAL A 167 " --> pdb=" O GLU A 213 " (cutoff:3.500A) removed outlier: 9.472A pdb=" N VAL A 215 " --> pdb=" O VAL A 167 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 289 through 292 Processing sheet with id= D, first strand: chain 'A' and resid 375 through 377 Processing sheet with id= E, first strand: chain 'A' and resid 420 through 422 removed outlier: 6.709A pdb=" N GLU A 496 " --> pdb=" O ILE A 421 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'A' and resid 455 through 458 Processing sheet with id= G, first strand: chain 'A' and resid 749 through 753 Processing sheet with id= H, first strand: chain 'B' and resid 38 through 42 removed outlier: 3.763A pdb=" N ILE B 40 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA B 100 " --> pdb=" O ILE B 40 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL B 42 " --> pdb=" O ALA B 100 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 256 through 258 removed outlier: 6.958A pdb=" N ILE B 228 " --> pdb=" O ILE B 257 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N ILE B 171 " --> pdb=" O GLU B 200 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N VAL B 202 " --> pdb=" O ILE B 171 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N THR B 173 " --> pdb=" O VAL B 202 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 279 through 281 removed outlier: 4.072A pdb=" N LEU B 366 " --> pdb=" O GLU B 374 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 405 through 409 removed outlier: 6.834A pdb=" N THR B 475 " --> pdb=" O LEU B 406 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N ILE B 408 " --> pdb=" O THR B 475 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ASP B 477 " --> pdb=" O ILE B 408 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'B' and resid 488 through 490 Processing sheet with id= M, first strand: chain 'B' and resid 530 through 532 Processing sheet with id= N, first strand: chain 'B' and resid 534 through 537 Processing sheet with id= O, first strand: chain 'C' and resid 30 through 32 Processing sheet with id= P, first strand: chain 'C' and resid 239 through 243 removed outlier: 4.022A pdb=" N VAL C 239 " --> pdb=" O HIS C 162 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER C 243 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N LYS C 211 " --> pdb=" O ILE C 163 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N LEU C 165 " --> pdb=" O LYS C 211 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N GLU C 213 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 12.660A pdb=" N VAL C 167 " --> pdb=" O GLU C 213 " (cutoff:3.500A) removed outlier: 9.401A pdb=" N VAL C 215 " --> pdb=" O VAL C 167 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 289 through 292 Processing sheet with id= R, first strand: chain 'C' and resid 375 through 377 Processing sheet with id= S, first strand: chain 'C' and resid 420 through 422 removed outlier: 6.696A pdb=" N GLU C 496 " --> pdb=" O ILE C 421 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'C' and resid 455 through 458 Processing sheet with id= U, first strand: chain 'C' and resid 750 through 753 Processing sheet with id= V, first strand: chain 'D' and resid 38 through 42 removed outlier: 3.762A pdb=" N ILE D 40 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA D 100 " --> pdb=" O ILE D 40 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL D 42 " --> pdb=" O ALA D 100 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 256 through 258 removed outlier: 6.957A pdb=" N ILE D 228 " --> pdb=" O ILE D 257 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N ILE D 171 " --> pdb=" O GLU D 200 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N VAL D 202 " --> pdb=" O ILE D 171 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N THR D 173 " --> pdb=" O VAL D 202 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 279 through 281 removed outlier: 4.072A pdb=" N LEU D 366 " --> pdb=" O GLU D 374 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'D' and resid 405 through 409 removed outlier: 6.834A pdb=" N THR D 475 " --> pdb=" O LEU D 406 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N ILE D 408 " --> pdb=" O THR D 475 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ASP D 477 " --> pdb=" O ILE D 408 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain 'D' and resid 488 through 490 Processing sheet with id= AA, first strand: chain 'D' and resid 530 through 532 Processing sheet with id= AB, first strand: chain 'D' and resid 534 through 537 766 hydrogen bonds defined for protein. 2049 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: 8.05 Time building geometry restraints manager: 10.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3918 1.31 - 1.44: 6372 1.44 - 1.57: 13338 1.57 - 1.70: 4 1.70 - 1.83: 240 Bond restraints: 23872 Sorted by residual: bond pdb=" C1 QGP D 901 " pdb=" P QGP D 901 " ideal model delta sigma weight residual 1.862 1.591 0.271 2.00e-02 2.50e+03 1.84e+02 bond pdb=" C1 QGP B 901 " pdb=" P QGP B 901 " ideal model delta sigma weight residual 1.862 1.591 0.271 2.00e-02 2.50e+03 1.83e+02 bond pdb=" C4 QGP B 901 " pdb=" O6 QGP B 901 " ideal model delta sigma weight residual 1.401 1.224 0.177 2.00e-02 2.50e+03 7.81e+01 bond pdb=" C4 QGP D 901 " pdb=" O6 QGP D 901 " ideal model delta sigma weight residual 1.401 1.225 0.176 2.00e-02 2.50e+03 7.78e+01 bond pdb=" C16 QGP B 901 " pdb=" C9 QGP B 901 " ideal model delta sigma weight residual 1.527 1.373 0.154 2.00e-02 2.50e+03 5.90e+01 ... (remaining 23867 not shown) Histogram of bond angle deviations from ideal: 98.37 - 105.53: 483 105.53 - 112.68: 13109 112.68 - 119.84: 7989 119.84 - 126.99: 10717 126.99 - 134.15: 292 Bond angle restraints: 32590 Sorted by residual: angle pdb=" N VAL C 225 " pdb=" CA VAL C 225 " pdb=" C VAL C 225 " ideal model delta sigma weight residual 113.20 108.26 4.94 9.60e-01 1.09e+00 2.65e+01 angle pdb=" N VAL A 225 " pdb=" CA VAL A 225 " pdb=" C VAL A 225 " ideal model delta sigma weight residual 113.20 108.28 4.92 9.60e-01 1.09e+00 2.62e+01 angle pdb=" N HIS B 802 " pdb=" CA HIS B 802 " pdb=" C HIS B 802 " ideal model delta sigma weight residual 113.88 108.32 5.56 1.23e+00 6.61e-01 2.04e+01 angle pdb=" N HIS D 802 " pdb=" CA HIS D 802 " pdb=" C HIS D 802 " ideal model delta sigma weight residual 113.88 108.41 5.47 1.23e+00 6.61e-01 1.98e+01 angle pdb=" C GLN C 378 " pdb=" N ASN C 379 " pdb=" CA ASN C 379 " ideal model delta sigma weight residual 121.54 129.69 -8.15 1.91e+00 2.74e-01 1.82e+01 ... (remaining 32585 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.29: 13149 23.29 - 46.58: 840 46.58 - 69.86: 135 69.86 - 93.15: 32 93.15 - 116.44: 14 Dihedral angle restraints: 14170 sinusoidal: 5152 harmonic: 9018 Sorted by residual: dihedral pdb=" CB CYS D 746 " pdb=" SG CYS D 746 " pdb=" SG CYS D 801 " pdb=" CB CYS D 801 " ideal model delta sinusoidal sigma weight residual -86.00 -155.88 69.88 1 1.00e+01 1.00e-02 6.30e+01 dihedral pdb=" CB CYS B 746 " pdb=" SG CYS B 746 " pdb=" SG CYS B 801 " pdb=" CB CYS B 801 " ideal model delta sinusoidal sigma weight residual -86.00 -155.88 69.88 1 1.00e+01 1.00e-02 6.30e+01 dihedral pdb=" CB CYS A 441 " pdb=" SG CYS A 441 " pdb=" SG CYS A 475 " pdb=" CB CYS A 475 " ideal model delta sinusoidal sigma weight residual 93.00 33.79 59.21 1 1.00e+01 1.00e-02 4.69e+01 ... (remaining 14167 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.119: 3758 0.119 - 0.238: 98 0.238 - 0.357: 2 0.357 - 0.476: 2 0.476 - 0.595: 2 Chirality restraints: 3862 Sorted by residual: chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.35e+02 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.32e+02 chirality pdb=" CG LEU A 119 " pdb=" CB LEU A 119 " pdb=" CD1 LEU A 119 " pdb=" CD2 LEU A 119 " both_signs ideal model delta sigma weight residual False -2.59 -1.99 -0.59 2.00e-01 2.50e+01 8.85e+00 ... (remaining 3859 not shown) Planarity restraints: 4144 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 128 " 0.012 2.00e-02 2.50e+03 2.35e-02 5.51e+00 pdb=" C GLY B 128 " -0.041 2.00e-02 2.50e+03 pdb=" O GLY B 128 " 0.015 2.00e-02 2.50e+03 pdb=" N GLY B 129 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY D 128 " -0.012 2.00e-02 2.50e+03 2.35e-02 5.51e+00 pdb=" C GLY D 128 " 0.041 2.00e-02 2.50e+03 pdb=" O GLY D 128 " -0.015 2.00e-02 2.50e+03 pdb=" N GLY D 129 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 700 " -0.011 2.00e-02 2.50e+03 2.18e-02 4.77e+00 pdb=" C ALA B 700 " 0.038 2.00e-02 2.50e+03 pdb=" O ALA B 700 " -0.014 2.00e-02 2.50e+03 pdb=" N GLU B 701 " -0.013 2.00e-02 2.50e+03 ... (remaining 4141 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.66: 712 2.66 - 3.22: 25485 3.22 - 3.78: 34903 3.78 - 4.34: 44111 4.34 - 4.90: 68330 Nonbonded interactions: 173541 Sorted by model distance: nonbonded pdb=" NH2 ARG A 233 " pdb=" O MET A 258 " model vdw 2.095 2.520 nonbonded pdb=" NH2 ARG C 233 " pdb=" O MET C 258 " model vdw 2.105 2.520 nonbonded pdb=" O MET B 829 " pdb=" OG SER B 832 " model vdw 2.137 2.440 nonbonded pdb=" O MET D 829 " pdb=" OG SER D 832 " model vdw 2.138 2.440 nonbonded pdb=" O LYS B 380 " pdb=" OG SER B 383 " model vdw 2.166 2.440 ... (remaining 173536 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 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.870 Check model and map are aligned: 0.360 Set scattering table: 0.210 Process input model: 65.390 Find NCS groups from input model: 1.850 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.271 23872 Z= 0.638 Angle : 0.944 12.115 32590 Z= 0.520 Chirality : 0.054 0.595 3862 Planarity : 0.005 0.049 4134 Dihedral : 16.312 116.438 8292 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 18.95 Ramachandran Plot: Outliers : 0.20 % Allowed : 18.01 % Favored : 81.79 % Rotamer: Outliers : 0.72 % Allowed : 11.62 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -4.87 (0.12), residues: 3076 helix: -2.02 (0.12), residues: 1176 sheet: -3.78 (0.20), residues: 366 loop : -4.20 (0.12), residues: 1534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 268 HIS 0.009 0.002 HIS A 801 PHE 0.020 0.002 PHE B 99 TYR 0.023 0.002 TYR C 816 ARG 0.005 0.001 ARG D 375 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 317 time to evaluate : 2.878 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 640 ILE cc_start: 0.8369 (tp) cc_final: 0.8163 (tt) REVERT: A 655 MET cc_start: 0.7126 (tmm) cc_final: 0.6885 (tmm) REVERT: A 662 MET cc_start: 0.9031 (tmm) cc_final: 0.8803 (tmm) REVERT: B 632 VAL cc_start: 0.8531 (OUTLIER) cc_final: 0.8322 (t) REVERT: B 818 MET cc_start: 0.7685 (mpp) cc_final: 0.7255 (mtm) REVERT: C 258 MET cc_start: 0.6779 (tmm) cc_final: 0.6401 (tmm) REVERT: D 73 MET cc_start: 0.7493 (mtt) cc_final: 0.7122 (mtt) REVERT: D 139 GLU cc_start: 0.6173 (mm-30) cc_final: 0.5910 (mm-30) REVERT: D 142 MET cc_start: 0.6951 (tpp) cc_final: 0.6748 (mmt) REVERT: D 562 MET cc_start: 0.7615 (ppp) cc_final: 0.7333 (ppp) REVERT: D 632 VAL cc_start: 0.8759 (OUTLIER) cc_final: 0.8478 (t) REVERT: D 818 MET cc_start: 0.7123 (mpp) cc_final: 0.6515 (mtm) outliers start: 17 outliers final: 5 residues processed: 333 average time/residue: 0.3012 time to fit residues: 165.2899 Evaluate side-chains 225 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 218 time to evaluate : 2.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain D residue 546 SER Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain D residue 632 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 261 optimal weight: 20.0000 chunk 234 optimal weight: 6.9990 chunk 130 optimal weight: 0.7980 chunk 80 optimal weight: 10.0000 chunk 158 optimal weight: 40.0000 chunk 125 optimal weight: 0.9980 chunk 242 optimal weight: 0.0470 chunk 94 optimal weight: 8.9990 chunk 147 optimal weight: 7.9990 chunk 180 optimal weight: 0.9990 chunk 281 optimal weight: 2.9990 overall best weight: 1.1682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN A 47 ASN A 146 HIS A 161 ASN A 291 GLN A 671 ASN A 707 GLN ** A 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 731 ASN A 745 ASN A 763 GLN B 184 ASN B 656 GLN B 767 GLN C 47 ASN C 146 HIS C 161 ASN C 291 GLN C 671 ASN C 707 GLN ** C 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 731 ASN C 745 ASN C 763 GLN D 184 ASN D 656 GLN D 767 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23872 Z= 0.201 Angle : 0.690 14.244 32590 Z= 0.356 Chirality : 0.048 0.546 3862 Planarity : 0.004 0.051 4134 Dihedral : 10.381 105.566 3564 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.86 % Favored : 89.08 % Rotamer: Outliers : 2.38 % Allowed : 15.74 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -3.26 (0.14), residues: 3076 helix: -0.44 (0.14), residues: 1192 sheet: -2.74 (0.26), residues: 300 loop : -3.58 (0.14), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 197 HIS 0.004 0.001 HIS A 392 PHE 0.015 0.001 PHE A 137 TYR 0.013 0.001 TYR C 668 ARG 0.003 0.000 ARG C 233 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 288 time to evaluate : 2.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 MET cc_start: 0.7169 (ppp) cc_final: 0.5757 (mmt) REVERT: A 640 ILE cc_start: 0.8331 (tp) cc_final: 0.8106 (tt) REVERT: B 818 MET cc_start: 0.7163 (mpp) cc_final: 0.6756 (mtm) REVERT: D 42 VAL cc_start: 0.7270 (p) cc_final: 0.6961 (p) REVERT: D 137 LYS cc_start: 0.6920 (tppp) cc_final: 0.6718 (mmmm) REVERT: D 139 GLU cc_start: 0.5843 (mm-30) cc_final: 0.5545 (mm-30) REVERT: D 551 LEU cc_start: 0.7446 (tp) cc_final: 0.7180 (tt) REVERT: D 632 VAL cc_start: 0.8544 (OUTLIER) cc_final: 0.8216 (t) REVERT: D 818 MET cc_start: 0.7019 (mpp) cc_final: 0.6171 (mtm) outliers start: 56 outliers final: 30 residues processed: 336 average time/residue: 0.2744 time to fit residues: 157.7059 Evaluate side-chains 273 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 242 time to evaluate : 2.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 261 MET Chi-restraints excluded: chain A residue 268 TRP Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 819 CYS Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 430 MET Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 815 ILE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 177 GLN Chi-restraints excluded: chain C residue 261 MET Chi-restraints excluded: chain C residue 590 SER Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 841 VAL Chi-restraints excluded: chain C residue 845 ILE Chi-restraints excluded: chain D residue 161 MET Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 546 SER Chi-restraints excluded: chain D residue 563 PHE Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain D residue 632 VAL Chi-restraints excluded: chain D residue 815 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 156 optimal weight: 4.9990 chunk 87 optimal weight: 10.0000 chunk 234 optimal weight: 30.0000 chunk 191 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 282 optimal weight: 0.0470 chunk 304 optimal weight: 0.0870 chunk 251 optimal weight: 0.9990 chunk 279 optimal weight: 2.9990 chunk 96 optimal weight: 0.5980 chunk 226 optimal weight: 2.9990 overall best weight: 0.7460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 GLN C 414 GLN C 726 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23872 Z= 0.168 Angle : 0.646 11.928 32590 Z= 0.330 Chirality : 0.046 0.542 3862 Planarity : 0.004 0.054 4134 Dihedral : 9.349 92.736 3563 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.44 % Favored : 88.56 % Rotamer: Outliers : 2.98 % Allowed : 17.79 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.65 (0.15), residues: 3076 helix: 0.16 (0.15), residues: 1210 sheet: -2.49 (0.27), residues: 298 loop : -3.33 (0.14), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP B 197 HIS 0.002 0.001 HIS B 703 PHE 0.018 0.001 PHE C 137 TYR 0.011 0.001 TYR C 668 ARG 0.004 0.000 ARG D 337 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 274 time to evaluate : 2.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 818 MET cc_start: 0.7060 (mpp) cc_final: 0.6704 (mtm) REVERT: D 551 LEU cc_start: 0.7279 (tp) cc_final: 0.7049 (tp) REVERT: D 632 VAL cc_start: 0.8551 (OUTLIER) cc_final: 0.8237 (t) REVERT: D 818 MET cc_start: 0.6979 (mpp) cc_final: 0.6262 (mtm) outliers start: 70 outliers final: 43 residues processed: 325 average time/residue: 0.2812 time to fit residues: 156.7273 Evaluate side-chains 285 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 241 time to evaluate : 2.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 268 TRP Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 765 CYS Chi-restraints excluded: chain A residue 819 CYS Chi-restraints excluded: chain A residue 838 PHE Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 430 MET Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 177 GLN Chi-restraints excluded: chain C residue 261 MET Chi-restraints excluded: chain C residue 477 TYR Chi-restraints excluded: chain C residue 663 ILE Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 765 CYS Chi-restraints excluded: chain C residue 838 PHE Chi-restraints excluded: chain C residue 845 ILE Chi-restraints excluded: chain C residue 846 VAL Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 161 MET Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 388 TYR Chi-restraints excluded: chain D residue 546 SER Chi-restraints excluded: chain D residue 557 CYS Chi-restraints excluded: chain D residue 558 VAL Chi-restraints excluded: chain D residue 563 PHE Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain D residue 632 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 278 optimal weight: 8.9990 chunk 212 optimal weight: 0.9980 chunk 146 optimal weight: 9.9990 chunk 31 optimal weight: 4.9990 chunk 134 optimal weight: 0.0980 chunk 189 optimal weight: 0.5980 chunk 283 optimal weight: 0.7980 chunk 299 optimal weight: 5.9990 chunk 147 optimal weight: 0.0670 chunk 268 optimal weight: 2.9990 chunk 80 optimal weight: 0.0050 overall best weight: 0.3132 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.105 23872 Z= 0.158 Angle : 0.630 11.602 32590 Z= 0.317 Chirality : 0.046 0.705 3862 Planarity : 0.004 0.055 4134 Dihedral : 8.239 77.287 3562 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.79 % Favored : 90.21 % Rotamer: Outliers : 2.94 % Allowed : 18.60 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.22 (0.15), residues: 3076 helix: 0.47 (0.15), residues: 1206 sheet: -2.20 (0.28), residues: 300 loop : -3.04 (0.15), residues: 1570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP D 197 HIS 0.004 0.001 HIS C 171 PHE 0.024 0.001 PHE D 575 TYR 0.011 0.001 TYR C 282 ARG 0.002 0.000 ARG D 337 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 286 time to evaluate : 2.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 MET cc_start: 0.6678 (ppp) cc_final: 0.5379 (mmt) REVERT: A 579 PHE cc_start: 0.7947 (OUTLIER) cc_final: 0.7074 (m-10) REVERT: B 307 MET cc_start: 0.6589 (tpp) cc_final: 0.5251 (tmm) REVERT: B 551 LEU cc_start: 0.7590 (OUTLIER) cc_final: 0.7321 (tp) REVERT: B 818 MET cc_start: 0.6910 (mpp) cc_final: 0.6480 (mtm) REVERT: C 579 PHE cc_start: 0.8076 (OUTLIER) cc_final: 0.7292 (m-10) REVERT: C 677 VAL cc_start: 0.8803 (t) cc_final: 0.8586 (t) REVERT: C 783 MET cc_start: 0.6175 (mtm) cc_final: 0.5966 (mtm) REVERT: D 632 VAL cc_start: 0.8676 (OUTLIER) cc_final: 0.8467 (t) REVERT: D 818 MET cc_start: 0.6922 (mpp) cc_final: 0.6071 (mtm) outliers start: 69 outliers final: 40 residues processed: 341 average time/residue: 0.2678 time to fit residues: 156.9316 Evaluate side-chains 298 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 254 time to evaluate : 2.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 268 TRP Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain A residue 579 PHE Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 819 CYS Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 430 MET Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 177 GLN Chi-restraints excluded: chain C residue 268 TRP Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 477 TYR Chi-restraints excluded: chain C residue 579 PHE Chi-restraints excluded: chain C residue 663 ILE Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain C residue 831 CYS Chi-restraints excluded: chain C residue 838 PHE Chi-restraints excluded: chain C residue 841 VAL Chi-restraints excluded: chain C residue 845 ILE Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 74 ASN Chi-restraints excluded: chain D residue 161 MET Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 388 TYR Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 557 CYS Chi-restraints excluded: chain D residue 563 PHE Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 626 THR Chi-restraints excluded: chain D residue 632 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 249 optimal weight: 8.9990 chunk 170 optimal weight: 20.0000 chunk 4 optimal weight: 10.0000 chunk 223 optimal weight: 8.9990 chunk 123 optimal weight: 0.5980 chunk 255 optimal weight: 9.9990 chunk 207 optimal weight: 0.0010 chunk 0 optimal weight: 20.0000 chunk 153 optimal weight: 6.9990 chunk 268 optimal weight: 10.0000 chunk 75 optimal weight: 4.9990 overall best weight: 4.3192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 ASN ** A 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 127 HIS B 385 GLN C 171 HIS C 671 ASN D 127 HIS D 385 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 23872 Z= 0.403 Angle : 0.763 10.980 32590 Z= 0.388 Chirality : 0.049 0.729 3862 Planarity : 0.004 0.056 4134 Dihedral : 7.764 88.700 3559 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.84 % Favored : 87.16 % Rotamer: Outliers : 4.89 % Allowed : 20.98 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.37 (0.15), residues: 3076 helix: 0.33 (0.15), residues: 1210 sheet: -2.20 (0.28), residues: 296 loop : -3.14 (0.15), residues: 1570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 268 HIS 0.007 0.001 HIS C 801 PHE 0.024 0.002 PHE B 99 TYR 0.018 0.002 TYR B 282 ARG 0.005 0.001 ARG D 375 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 228 time to evaluate : 2.823 Fit side-chains revert: symmetry clash REVERT: A 347 MET cc_start: 0.6801 (ppp) cc_final: 0.5537 (mmt) REVERT: A 579 PHE cc_start: 0.8518 (OUTLIER) cc_final: 0.7721 (m-10) REVERT: B 307 MET cc_start: 0.6658 (tpp) cc_final: 0.5809 (tmm) REVERT: B 551 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7719 (tt) REVERT: B 818 MET cc_start: 0.7549 (mpp) cc_final: 0.6572 (mtm) REVERT: C 375 MET cc_start: 0.7047 (tpp) cc_final: 0.6050 (tpp) REVERT: C 579 PHE cc_start: 0.8528 (OUTLIER) cc_final: 0.7883 (m-10) REVERT: D 273 PHE cc_start: 0.8213 (OUTLIER) cc_final: 0.7576 (t80) REVERT: D 632 VAL cc_start: 0.8780 (OUTLIER) cc_final: 0.8514 (t) REVERT: D 818 MET cc_start: 0.7005 (mpp) cc_final: 0.6216 (mtm) outliers start: 115 outliers final: 78 residues processed: 325 average time/residue: 0.2710 time to fit residues: 151.3116 Evaluate side-chains 300 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 217 time to evaluate : 2.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 268 TRP Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain A residue 479 PHE Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 518 GLU Chi-restraints excluded: chain A residue 579 PHE Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 816 TYR Chi-restraints excluded: chain A residue 819 CYS Chi-restraints excluded: chain A residue 838 PHE Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 846 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 166 TRP Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 430 MET Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 557 CYS Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 610 TRP Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 177 GLN Chi-restraints excluded: chain C residue 268 TRP Chi-restraints excluded: chain C residue 477 TYR Chi-restraints excluded: chain C residue 479 PHE Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 579 PHE Chi-restraints excluded: chain C residue 590 SER Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 663 ILE Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain C residue 797 ILE Chi-restraints excluded: chain C residue 816 TYR Chi-restraints excluded: chain C residue 819 CYS Chi-restraints excluded: chain C residue 838 PHE Chi-restraints excluded: chain C residue 841 VAL Chi-restraints excluded: chain C residue 845 ILE Chi-restraints excluded: chain D residue 74 ASN Chi-restraints excluded: chain D residue 161 MET Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 273 PHE Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 557 CYS Chi-restraints excluded: chain D residue 558 VAL Chi-restraints excluded: chain D residue 563 PHE Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 626 THR Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain D residue 632 VAL Chi-restraints excluded: chain D residue 645 SER Chi-restraints excluded: chain D residue 647 THR Chi-restraints excluded: chain D residue 660 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 100 optimal weight: 9.9990 chunk 269 optimal weight: 5.9990 chunk 59 optimal weight: 0.8980 chunk 175 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 chunk 299 optimal weight: 3.9990 chunk 248 optimal weight: 0.0370 chunk 138 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 99 optimal weight: 0.4980 chunk 157 optimal weight: 9.9990 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 171 HIS C 177 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 23872 Z= 0.167 Angle : 0.639 15.517 32590 Z= 0.322 Chirality : 0.048 1.083 3862 Planarity : 0.004 0.057 4134 Dihedral : 7.137 86.983 3559 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.01 % Favored : 89.99 % Rotamer: Outliers : 3.32 % Allowed : 22.04 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.95 (0.15), residues: 3076 helix: 0.63 (0.15), residues: 1194 sheet: -1.89 (0.32), residues: 244 loop : -2.83 (0.14), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 197 HIS 0.005 0.001 HIS A 171 PHE 0.009 0.001 PHE B 146 TYR 0.015 0.001 TYR B 179 ARG 0.002 0.000 ARG B 540 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 259 time to evaluate : 2.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 MET cc_start: 0.6527 (ppp) cc_final: 0.5404 (mmt) REVERT: A 579 PHE cc_start: 0.8097 (OUTLIER) cc_final: 0.7252 (m-10) REVERT: B 307 MET cc_start: 0.6784 (tpp) cc_final: 0.5645 (tmm) REVERT: B 818 MET cc_start: 0.7019 (mpp) cc_final: 0.6338 (mtm) REVERT: C 491 MET cc_start: 0.7088 (mtp) cc_final: 0.6883 (mtt) REVERT: C 579 PHE cc_start: 0.8219 (OUTLIER) cc_final: 0.7468 (m-10) REVERT: D 139 GLU cc_start: 0.5700 (mm-30) cc_final: 0.5429 (mm-30) REVERT: D 200 GLU cc_start: 0.7503 (mm-30) cc_final: 0.7300 (mm-30) REVERT: D 613 VAL cc_start: 0.8453 (p) cc_final: 0.8208 (p) REVERT: D 632 VAL cc_start: 0.8801 (OUTLIER) cc_final: 0.8533 (t) REVERT: D 818 MET cc_start: 0.6926 (mpp) cc_final: 0.6128 (mtm) outliers start: 78 outliers final: 53 residues processed: 322 average time/residue: 0.2661 time to fit residues: 147.4437 Evaluate side-chains 299 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 243 time to evaluate : 2.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 261 MET Chi-restraints excluded: chain A residue 268 TRP Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 579 PHE Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 816 TYR Chi-restraints excluded: chain A residue 819 CYS Chi-restraints excluded: chain A residue 831 CYS Chi-restraints excluded: chain A residue 838 PHE Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 430 MET Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 557 CYS Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 653 PHE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 268 TRP Chi-restraints excluded: chain C residue 387 ILE Chi-restraints excluded: chain C residue 477 TYR Chi-restraints excluded: chain C residue 579 PHE Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain C residue 816 TYR Chi-restraints excluded: chain C residue 831 CYS Chi-restraints excluded: chain C residue 838 PHE Chi-restraints excluded: chain C residue 841 VAL Chi-restraints excluded: chain C residue 845 ILE Chi-restraints excluded: chain C residue 846 VAL Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 74 ASN Chi-restraints excluded: chain D residue 161 MET Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 557 CYS Chi-restraints excluded: chain D residue 558 VAL Chi-restraints excluded: chain D residue 563 PHE Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 626 THR Chi-restraints excluded: chain D residue 632 VAL Chi-restraints excluded: chain D residue 653 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 289 optimal weight: 0.9990 chunk 33 optimal weight: 6.9990 chunk 170 optimal weight: 10.0000 chunk 219 optimal weight: 0.0770 chunk 169 optimal weight: 0.9990 chunk 252 optimal weight: 3.9990 chunk 167 optimal weight: 1.9990 chunk 298 optimal weight: 4.9990 chunk 186 optimal weight: 0.1980 chunk 182 optimal weight: 0.6980 chunk 137 optimal weight: 7.9990 overall best weight: 0.5942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 171 HIS ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 171 HIS C 817 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 23872 Z= 0.158 Angle : 0.633 16.673 32590 Z= 0.315 Chirality : 0.045 0.751 3862 Planarity : 0.004 0.057 4134 Dihedral : 6.714 81.992 3559 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.37 % Favored : 89.63 % Rotamer: Outliers : 3.06 % Allowed : 22.64 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.82 (0.15), residues: 3076 helix: 0.74 (0.15), residues: 1188 sheet: -1.97 (0.28), residues: 312 loop : -2.73 (0.15), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP D 285 HIS 0.005 0.001 HIS A 134 PHE 0.011 0.001 PHE B 114 TYR 0.021 0.001 TYR B 179 ARG 0.003 0.000 ARG A 692 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 267 time to evaluate : 2.789 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 347 MET cc_start: 0.6829 (ppp) cc_final: 0.5591 (mmt) REVERT: A 579 PHE cc_start: 0.8198 (OUTLIER) cc_final: 0.7491 (m-10) REVERT: B 818 MET cc_start: 0.6900 (mpp) cc_final: 0.6210 (mtm) REVERT: C 491 MET cc_start: 0.7092 (mtp) cc_final: 0.6816 (mtt) REVERT: C 579 PHE cc_start: 0.8187 (OUTLIER) cc_final: 0.7430 (m-10) REVERT: D 632 VAL cc_start: 0.8767 (OUTLIER) cc_final: 0.8567 (t) REVERT: D 818 MET cc_start: 0.6918 (mpp) cc_final: 0.6071 (mtm) outliers start: 72 outliers final: 49 residues processed: 322 average time/residue: 0.2744 time to fit residues: 152.4396 Evaluate side-chains 302 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 250 time to evaluate : 2.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 268 TRP Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain A residue 479 PHE Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 579 PHE Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 816 TYR Chi-restraints excluded: chain A residue 819 CYS Chi-restraints excluded: chain A residue 838 PHE Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 430 MET Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 557 CYS Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 653 PHE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 268 TRP Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 387 ILE Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 477 TYR Chi-restraints excluded: chain C residue 479 PHE Chi-restraints excluded: chain C residue 579 PHE Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain C residue 817 GLN Chi-restraints excluded: chain C residue 819 CYS Chi-restraints excluded: chain C residue 838 PHE Chi-restraints excluded: chain C residue 841 VAL Chi-restraints excluded: chain C residue 845 ILE Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 74 ASN Chi-restraints excluded: chain D residue 134 MET Chi-restraints excluded: chain D residue 161 MET Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 388 TYR Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 557 CYS Chi-restraints excluded: chain D residue 558 VAL Chi-restraints excluded: chain D residue 626 THR Chi-restraints excluded: chain D residue 632 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 184 optimal weight: 0.0030 chunk 119 optimal weight: 0.8980 chunk 178 optimal weight: 0.9990 chunk 90 optimal weight: 6.9990 chunk 58 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 189 optimal weight: 3.9990 chunk 203 optimal weight: 0.7980 chunk 147 optimal weight: 0.0370 chunk 27 optimal weight: 0.7980 chunk 234 optimal weight: 6.9990 overall best weight: 0.5068 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 171 HIS ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 171 HIS ** C 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.3374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 23872 Z= 0.159 Angle : 0.644 17.056 32590 Z= 0.317 Chirality : 0.047 1.050 3862 Planarity : 0.004 0.056 4134 Dihedral : 6.457 71.239 3559 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % Rotamer: Outliers : 2.68 % Allowed : 23.83 % Favored : 73.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.67 (0.15), residues: 3076 helix: 0.83 (0.15), residues: 1178 sheet: -1.82 (0.27), residues: 332 loop : -2.60 (0.15), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP C 336 HIS 0.004 0.001 HIS A 134 PHE 0.059 0.001 PHE B 143 TYR 0.027 0.001 TYR C 816 ARG 0.005 0.000 ARG C 815 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 276 time to evaluate : 2.684 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 347 MET cc_start: 0.6740 (ppp) cc_final: 0.5598 (mmt) REVERT: A 579 PHE cc_start: 0.8218 (OUTLIER) cc_final: 0.7598 (m-10) REVERT: B 307 MET cc_start: 0.6650 (tpp) cc_final: 0.6006 (tpp) REVERT: B 818 MET cc_start: 0.6838 (mpp) cc_final: 0.6176 (mtm) REVERT: C 491 MET cc_start: 0.7031 (mtp) cc_final: 0.6820 (mtt) REVERT: C 579 PHE cc_start: 0.7989 (OUTLIER) cc_final: 0.7293 (m-10) REVERT: D 818 MET cc_start: 0.6762 (mpp) cc_final: 0.5987 (mtm) outliers start: 63 outliers final: 51 residues processed: 324 average time/residue: 0.2770 time to fit residues: 153.9259 Evaluate side-chains 315 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 262 time to evaluate : 2.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 268 TRP Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain A residue 479 PHE Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 579 PHE Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 816 TYR Chi-restraints excluded: chain A residue 819 CYS Chi-restraints excluded: chain A residue 838 PHE Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 430 MET Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 557 CYS Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 268 TRP Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 387 ILE Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 477 TYR Chi-restraints excluded: chain C residue 479 PHE Chi-restraints excluded: chain C residue 579 PHE Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain C residue 816 TYR Chi-restraints excluded: chain C residue 838 PHE Chi-restraints excluded: chain C residue 841 VAL Chi-restraints excluded: chain C residue 845 ILE Chi-restraints excluded: chain D residue 74 ASN Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 134 MET Chi-restraints excluded: chain D residue 161 MET Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 557 CYS Chi-restraints excluded: chain D residue 558 VAL Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 626 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 271 optimal weight: 10.0000 chunk 286 optimal weight: 2.9990 chunk 261 optimal weight: 0.9980 chunk 278 optimal weight: 0.6980 chunk 167 optimal weight: 0.4980 chunk 121 optimal weight: 0.6980 chunk 218 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 251 optimal weight: 5.9990 chunk 263 optimal weight: 8.9990 chunk 277 optimal weight: 5.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 171 HIS A 726 HIS ** C 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 171 HIS C 817 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 23872 Z= 0.159 Angle : 0.630 17.211 32590 Z= 0.312 Chirality : 0.046 0.938 3862 Planarity : 0.004 0.056 4134 Dihedral : 6.290 64.488 3558 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.01 % Favored : 89.99 % Rotamer: Outliers : 2.47 % Allowed : 24.38 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.62 (0.15), residues: 3076 helix: 0.85 (0.15), residues: 1180 sheet: -1.77 (0.27), residues: 332 loop : -2.57 (0.15), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 336 HIS 0.004 0.000 HIS A 134 PHE 0.039 0.001 PHE B 143 TYR 0.021 0.001 TYR B 179 ARG 0.001 0.000 ARG C 815 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 264 time to evaluate : 2.642 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 347 MET cc_start: 0.6714 (ppp) cc_final: 0.5583 (mmt) REVERT: A 579 PHE cc_start: 0.8307 (OUTLIER) cc_final: 0.7663 (m-10) REVERT: B 307 MET cc_start: 0.6605 (tpp) cc_final: 0.6034 (tpp) REVERT: B 788 GLU cc_start: 0.7616 (mp0) cc_final: 0.7277 (mp0) REVERT: B 818 MET cc_start: 0.6844 (mpp) cc_final: 0.6040 (mtm) REVERT: C 518 GLU cc_start: 0.7125 (OUTLIER) cc_final: 0.6745 (pm20) REVERT: C 579 PHE cc_start: 0.8122 (OUTLIER) cc_final: 0.7473 (m-10) REVERT: D 818 MET cc_start: 0.6756 (mpp) cc_final: 0.5986 (mtm) outliers start: 58 outliers final: 50 residues processed: 310 average time/residue: 0.2812 time to fit residues: 149.2926 Evaluate side-chains 309 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 256 time to evaluate : 2.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 268 TRP Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain A residue 479 PHE Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain A residue 579 PHE Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 816 TYR Chi-restraints excluded: chain A residue 819 CYS Chi-restraints excluded: chain A residue 838 PHE Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 430 MET Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 557 CYS Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 268 TRP Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 387 ILE Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 477 TYR Chi-restraints excluded: chain C residue 479 PHE Chi-restraints excluded: chain C residue 518 GLU Chi-restraints excluded: chain C residue 576 MET Chi-restraints excluded: chain C residue 579 PHE Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain C residue 817 GLN Chi-restraints excluded: chain C residue 838 PHE Chi-restraints excluded: chain C residue 841 VAL Chi-restraints excluded: chain C residue 845 ILE Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 74 ASN Chi-restraints excluded: chain D residue 134 MET Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 557 CYS Chi-restraints excluded: chain D residue 558 VAL Chi-restraints excluded: chain D residue 626 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 182 optimal weight: 8.9990 chunk 294 optimal weight: 10.0000 chunk 179 optimal weight: 5.9990 chunk 139 optimal weight: 7.9990 chunk 204 optimal weight: 3.9990 chunk 308 optimal weight: 7.9990 chunk 284 optimal weight: 4.9990 chunk 245 optimal weight: 5.9990 chunk 25 optimal weight: 0.0060 chunk 189 optimal weight: 4.9990 chunk 150 optimal weight: 5.9990 overall best weight: 4.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 HIS C 171 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 23872 Z= 0.376 Angle : 0.749 17.187 32590 Z= 0.376 Chirality : 0.049 0.909 3862 Planarity : 0.004 0.054 4134 Dihedral : 6.630 66.915 3558 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.13 % Favored : 87.87 % Rotamer: Outliers : 2.85 % Allowed : 24.64 % Favored : 72.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.80 (0.15), residues: 3076 helix: 0.73 (0.15), residues: 1184 sheet: -2.00 (0.27), residues: 326 loop : -2.68 (0.15), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP D 285 HIS 0.005 0.001 HIS D 802 PHE 0.033 0.002 PHE B 143 TYR 0.017 0.002 TYR C 816 ARG 0.014 0.001 ARG C 815 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 233 time to evaluate : 2.591 Fit side-chains revert: symmetry clash REVERT: A 576 MET cc_start: 0.5642 (OUTLIER) cc_final: 0.5388 (tpt) REVERT: A 579 PHE cc_start: 0.8424 (OUTLIER) cc_final: 0.7626 (m-10) REVERT: B 818 MET cc_start: 0.7104 (mpp) cc_final: 0.6290 (mtm) REVERT: C 576 MET cc_start: 0.5617 (OUTLIER) cc_final: 0.5383 (tpt) REVERT: C 579 PHE cc_start: 0.8442 (OUTLIER) cc_final: 0.7719 (m-10) REVERT: D 818 MET cc_start: 0.6989 (mpp) cc_final: 0.6178 (mtm) outliers start: 67 outliers final: 54 residues processed: 287 average time/residue: 0.2748 time to fit residues: 135.4815 Evaluate side-chains 283 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 225 time to evaluate : 2.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 268 TRP Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain A residue 479 PHE Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain A residue 579 PHE Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 816 TYR Chi-restraints excluded: chain A residue 819 CYS Chi-restraints excluded: chain A residue 838 PHE Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 430 MET Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 557 CYS Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 261 MET Chi-restraints excluded: chain C residue 268 TRP Chi-restraints excluded: chain C residue 387 ILE Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 477 TYR Chi-restraints excluded: chain C residue 479 PHE Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 576 MET Chi-restraints excluded: chain C residue 579 PHE Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain C residue 838 PHE Chi-restraints excluded: chain C residue 841 VAL Chi-restraints excluded: chain C residue 845 ILE Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 74 ASN Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 134 MET Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 557 CYS Chi-restraints excluded: chain D residue 558 VAL Chi-restraints excluded: chain D residue 626 THR Chi-restraints excluded: chain D residue 653 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 195 optimal weight: 1.9990 chunk 261 optimal weight: 8.9990 chunk 75 optimal weight: 9.9990 chunk 226 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 chunk 246 optimal weight: 1.9990 chunk 103 optimal weight: 7.9990 chunk 252 optimal weight: 7.9990 chunk 31 optimal weight: 8.9990 chunk 45 optimal weight: 0.6980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 171 HIS C 817 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.106669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.088765 restraints weight = 70971.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.092051 restraints weight = 40546.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.092370 restraints weight = 26544.190| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23872 Z= 0.218 Angle : 0.674 17.247 32590 Z= 0.335 Chirality : 0.047 0.857 3862 Planarity : 0.004 0.056 4134 Dihedral : 6.519 63.385 3558 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.34 % Favored : 89.66 % Rotamer: Outliers : 2.68 % Allowed : 24.81 % Favored : 72.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.67 (0.15), residues: 3076 helix: 0.87 (0.16), residues: 1184 sheet: -1.94 (0.27), residues: 324 loop : -2.62 (0.15), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP D 285 HIS 0.003 0.001 HIS A 134 PHE 0.034 0.001 PHE B 143 TYR 0.020 0.001 TYR B 179 ARG 0.004 0.000 ARG B 337 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4084.89 seconds wall clock time: 75 minutes 56.33 seconds (4556.33 seconds total)