Starting phenix.real_space_refine on Mon Feb 19 13:20:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7krz_23013/02_2024/7krz_23013_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7krz_23013/02_2024/7krz_23013.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7krz_23013/02_2024/7krz_23013.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7krz_23013/02_2024/7krz_23013.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7krz_23013/02_2024/7krz_23013_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7krz_23013/02_2024/7krz_23013_updated.pdb" } resolution = 3.2 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.003 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: 7 Type Number sf(0) Gaussians P 16 5.49 5 Mg 4 5.21 5 S 119 5.16 5 B 6 2.79 5 C 15667 2.51 5 N 4236 2.21 5 O 4697 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 418": "OE1" <-> "OE2" Residue "A ARG 422": "NH1" <-> "NH2" Residue "A ARG 424": "NH1" <-> "NH2" Residue "A GLU 427": "OE1" <-> "OE2" Residue "A ARG 482": "NH1" <-> "NH2" Residue "A GLU 489": "OE1" <-> "OE2" Residue "A GLU 495": "OE1" <-> "OE2" Residue "A GLU 503": "OE1" <-> "OE2" Residue "A ARG 534": "NH1" <-> "NH2" Residue "A ARG 538": "NH1" <-> "NH2" Residue "A ARG 563": "NH1" <-> "NH2" Residue "A GLU 583": "OE1" <-> "OE2" Residue "A ARG 597": "NH1" <-> "NH2" Residue "A GLU 647": "OE1" <-> "OE2" Residue "A ARG 650": "NH1" <-> "NH2" Residue "A GLU 671": "OE1" <-> "OE2" Residue "A ARG 672": "NH1" <-> "NH2" Residue "A TYR 673": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 679": "NH1" <-> "NH2" Residue "A GLU 706": "OE1" <-> "OE2" Residue "A GLU 736": "OE1" <-> "OE2" Residue "A ARG 785": "NH1" <-> "NH2" Residue "A GLU 801": "OE1" <-> "OE2" Residue "A GLU 812": "OE1" <-> "OE2" Residue "A ARG 815": "NH1" <-> "NH2" Residue "A GLU 846": "OE1" <-> "OE2" Residue "A ARG 940": "NH1" <-> "NH2" Residue "B ARG 424": "NH1" <-> "NH2" Residue "B GLU 427": "OE1" <-> "OE2" Residue "B GLU 454": "OE1" <-> "OE2" Residue "B ARG 482": "NH1" <-> "NH2" Residue "B GLU 488": "OE1" <-> "OE2" Residue "B ARG 511": "NH1" <-> "NH2" Residue "B ARG 534": "NH1" <-> "NH2" Residue "B ARG 538": "NH1" <-> "NH2" Residue "B GLU 543": "OE1" <-> "OE2" Residue "B GLU 557": "OE1" <-> "OE2" Residue "B ARG 563": "NH1" <-> "NH2" Residue "B ARG 597": "NH1" <-> "NH2" Residue "B GLU 614": "OE1" <-> "OE2" Residue "B ARG 650": "NH1" <-> "NH2" Residue "B ARG 672": "NH1" <-> "NH2" Residue "B ARG 679": "NH1" <-> "NH2" Residue "B GLU 731": "OE1" <-> "OE2" Residue "B GLU 754": "OE1" <-> "OE2" Residue "B ARG 785": "NH1" <-> "NH2" Residue "B GLU 801": "OE1" <-> "OE2" Residue "B GLU 812": "OE1" <-> "OE2" Residue "B ARG 815": "NH1" <-> "NH2" Residue "B GLU 915": "OE1" <-> "OE2" Residue "B GLU 929": "OE1" <-> "OE2" Residue "B ARG 940": "NH1" <-> "NH2" Residue "B GLU 941": "OE1" <-> "OE2" Residue "C GLU 419": "OE1" <-> "OE2" Residue "C ARG 422": "NH1" <-> "NH2" Residue "C ARG 424": "NH1" <-> "NH2" Residue "C ARG 482": "NH1" <-> "NH2" Residue "C ARG 511": "NH1" <-> "NH2" Residue "C ARG 534": "NH1" <-> "NH2" Residue "C ARG 538": "NH1" <-> "NH2" Residue "C ARG 563": "NH1" <-> "NH2" Residue "C GLU 591": "OE1" <-> "OE2" Residue "C ARG 597": "NH1" <-> "NH2" Residue "C GLU 647": "OE1" <-> "OE2" Residue "C ARG 650": "NH1" <-> "NH2" Residue "C ARG 672": "NH1" <-> "NH2" Residue "C ARG 679": "NH1" <-> "NH2" Residue "C GLU 733": "OE1" <-> "OE2" Residue "C GLU 736": "OE1" <-> "OE2" Residue "C ARG 785": "NH1" <-> "NH2" Residue "C GLU 801": "OE1" <-> "OE2" Residue "C GLU 808": "OE1" <-> "OE2" Residue "C GLU 812": "OE1" <-> "OE2" Residue "C ARG 815": "NH1" <-> "NH2" Residue "C GLU 846": "OE1" <-> "OE2" Residue "C ARG 940": "NH1" <-> "NH2" Residue "C GLU 941": "OE1" <-> "OE2" Residue "D ARG 422": "NH1" <-> "NH2" Residue "D GLU 503": "OE1" <-> "OE2" Residue "D ARG 511": "NH1" <-> "NH2" Residue "D ARG 538": "NH1" <-> "NH2" Residue "D GLU 557": "OE1" <-> "OE2" Residue "D ARG 563": "NH1" <-> "NH2" Residue "D GLU 591": "OE1" <-> "OE2" Residue "D GLU 609": "OE1" <-> "OE2" Residue "D ARG 650": "NH1" <-> "NH2" Residue "D GLU 665": "OE1" <-> "OE2" Residue "D ARG 672": "NH1" <-> "NH2" Residue "D ARG 679": "NH1" <-> "NH2" Residue "D GLU 754": "OE1" <-> "OE2" Residue "D ARG 785": "NH1" <-> "NH2" Residue "D GLU 808": "OE1" <-> "OE2" Residue "D GLU 812": "OE1" <-> "OE2" Residue "D ARG 815": "NH1" <-> "NH2" Residue "D GLU 846": "OE1" <-> "OE2" Residue "D GLU 929": "OE1" <-> "OE2" Residue "D GLU 937": "OE1" <-> "OE2" Residue "D ARG 940": "NH1" <-> "NH2" Residue "E GLU 441": "OE1" <-> "OE2" Residue "E ARG 459": "NH1" <-> "NH2" Residue "E ARG 482": "NH1" <-> "NH2" Residue "E GLU 488": "OE1" <-> "OE2" Residue "E ARG 511": "NH1" <-> "NH2" Residue "E ARG 534": "NH1" <-> "NH2" Residue "E ARG 538": "NH1" <-> "NH2" Residue "E GLU 583": "OE1" <-> "OE2" Residue "E ARG 597": "NH1" <-> "NH2" Residue "E GLU 654": "OE1" <-> "OE2" Residue "E ARG 672": "NH1" <-> "NH2" Residue "E ARG 679": "NH1" <-> "NH2" Residue "E GLU 717": "OE1" <-> "OE2" Residue "E ARG 721": "NH1" <-> "NH2" Residue "E ARG 785": "NH1" <-> "NH2" Residue "E GLU 808": "OE1" <-> "OE2" Residue "E ARG 815": "NH1" <-> "NH2" Residue "E ARG 940": "NH1" <-> "NH2" Residue "E GLU 941": "OE1" <-> "OE2" Residue "F ARG 422": "NH1" <-> "NH2" Residue "F GLU 423": "OE1" <-> "OE2" Residue "F GLU 441": "OE1" <-> "OE2" Residue "F ARG 482": "NH1" <-> "NH2" Residue "F GLU 488": "OE1" <-> "OE2" Residue "F GLU 489": "OE1" <-> "OE2" Residue "F ARG 534": "NH1" <-> "NH2" Residue "F ARG 538": "NH1" <-> "NH2" Residue "F GLU 543": "OE1" <-> "OE2" Residue "F ARG 563": "NH1" <-> "NH2" Residue "F GLU 583": "OE1" <-> "OE2" Residue "F GLU 591": "OE1" <-> "OE2" Residue "F GLU 665": "OE1" <-> "OE2" Residue "F ARG 672": "NH1" <-> "NH2" Residue "F ARG 679": "NH1" <-> "NH2" Residue "F GLU 731": "OE1" <-> "OE2" Residue "F GLU 754": "OE1" <-> "OE2" Residue "F ARG 785": "NH1" <-> "NH2" Residue "F GLU 801": "OE1" <-> "OE2" Residue "F ARG 815": "NH1" <-> "NH2" Residue "F GLU 915": "OE1" <-> "OE2" Residue "F GLU 937": "OE1" <-> "OE2" Residue "F ARG 940": "NH1" <-> "NH2" Residue "F GLU 941": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 24745 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 4098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4098 Classifications: {'peptide': 525} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 500} Chain breaks: 1 Chain: "B" Number of atoms: 4096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4096 Classifications: {'peptide': 526} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 24, 'TRANS': 501} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 4100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4100 Classifications: {'peptide': 527} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 24, 'TRANS': 502} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 4051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 4051 Classifications: {'peptide': 520} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 24, 'TRANS': 495} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 4014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 4014 Classifications: {'peptide': 517} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 24, 'TRANS': 492} Chain breaks: 2 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "F" Number of atoms: 3976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 3976 Classifications: {'peptide': 512} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 24, 'TRANS': 487} Chain breaks: 3 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "G" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 60 Classifications: {'peptide': 12} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'TRANS': 11} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'UNK:plan-1': 12} Unresolved non-hydrogen planarities: 12 Chain: "A" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 60 Unusual residues: {' MG': 1, 'ATP': 1, 'BO2': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 60 Unusual residues: {' MG': 1, 'ATP': 1, 'BO2': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 60 Unusual residues: {' MG': 1, 'ATP': 1, 'BO2': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 60 Unusual residues: {' MG': 1, 'ATP': 1, 'BO2': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 55 Unusual residues: {'ADP': 1, 'BO2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 55 Unusual residues: {'ADP': 1, 'BO2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 13.46, per 1000 atoms: 0.54 Number of scatterers: 24745 At special positions: 0 Unit cell: (135.7, 141.45, 131.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 119 16.00 P 16 15.00 Mg 4 11.99 O 4697 8.00 N 4236 7.00 C 15667 6.00 B 6 5.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 10.01 Conformation dependent library (CDL) restraints added in 4.7 seconds 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5836 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 123 helices and 25 sheets defined 41.1% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.93 Creating SS restraints... Processing helix chain 'A' and resid 418 through 424 Processing helix chain 'A' and resid 432 through 445 removed outlier: 4.689A pdb=" N VAL A 437 " --> pdb=" O HIS A 433 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS A 444 " --> pdb=" O GLU A 440 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU A 445 " --> pdb=" O GLU A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 467 Processing helix chain 'A' and resid 480 through 490 removed outlier: 3.887A pdb=" N ASP A 490 " --> pdb=" O VAL A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 510 removed outlier: 3.878A pdb=" N ARG A 500 " --> pdb=" O ASP A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 539 removed outlier: 4.202A pdb=" N ARG A 534 " --> pdb=" O SER A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 557 No H-bonds generated for 'chain 'A' and resid 555 through 557' Processing helix chain 'A' and resid 572 through 580 Processing helix chain 'A' and resid 603 through 610 Processing helix chain 'A' and resid 642 through 644 No H-bonds generated for 'chain 'A' and resid 642 through 644' Processing helix chain 'A' and resid 647 through 652 removed outlier: 3.779A pdb=" N ARG A 652 " --> pdb=" O PRO A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 682 removed outlier: 5.153A pdb=" N VAL A 675 " --> pdb=" O GLU A 671 " (cutoff:3.500A) Proline residue: A 676 - end of helix Processing helix chain 'A' and resid 693 through 702 Processing helix chain 'A' and resid 710 through 728 Processing helix chain 'A' and resid 743 through 746 No H-bonds generated for 'chain 'A' and resid 743 through 746' Processing helix chain 'A' and resid 808 through 828 Processing helix chain 'A' and resid 857 through 869 Processing helix chain 'A' and resid 895 through 904 Processing helix chain 'A' and resid 914 through 921 removed outlier: 3.568A pdb=" N LYS A 917 " --> pdb=" O ALA A 914 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N LYS A 918 " --> pdb=" O GLU A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 946 Processing helix chain 'B' and resid 417 through 420 No H-bonds generated for 'chain 'B' and resid 417 through 420' Processing helix chain 'B' and resid 424 through 426 No H-bonds generated for 'chain 'B' and resid 424 through 426' Processing helix chain 'B' and resid 432 through 445 removed outlier: 4.171A pdb=" N VAL B 437 " --> pdb=" O HIS B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 467 Processing helix chain 'B' and resid 480 through 488 Processing helix chain 'B' and resid 495 through 510 Processing helix chain 'B' and resid 532 through 539 Processing helix chain 'B' and resid 555 through 559 removed outlier: 3.671A pdb=" N LYS B 559 " --> pdb=" O ALA B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 580 Processing helix chain 'B' and resid 592 through 594 No H-bonds generated for 'chain 'B' and resid 592 through 594' Processing helix chain 'B' and resid 603 through 605 No H-bonds generated for 'chain 'B' and resid 603 through 605' Processing helix chain 'B' and resid 607 through 610 No H-bonds generated for 'chain 'B' and resid 607 through 610' Processing helix chain 'B' and resid 615 through 617 No H-bonds generated for 'chain 'B' and resid 615 through 617' Processing helix chain 'B' and resid 647 through 652 Processing helix chain 'B' and resid 663 through 682 removed outlier: 5.836A pdb=" N VAL B 675 " --> pdb=" O GLU B 671 " (cutoff:3.500A) Proline residue: B 676 - end of helix Processing helix chain 'B' and resid 693 through 702 Processing helix chain 'B' and resid 710 through 728 Processing helix chain 'B' and resid 743 through 746 No H-bonds generated for 'chain 'B' and resid 743 through 746' Processing helix chain 'B' and resid 808 through 828 Processing helix chain 'B' and resid 857 through 868 Processing helix chain 'B' and resid 895 through 904 Processing helix chain 'B' and resid 914 through 921 removed outlier: 3.696A pdb=" N LYS B 917 " --> pdb=" O ALA B 914 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LYS B 918 " --> pdb=" O GLU B 915 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR B 921 " --> pdb=" O LYS B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 939 through 946 Processing helix chain 'C' and resid 416 through 427 removed outlier: 4.234A pdb=" N GLU C 427 " --> pdb=" O GLU C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 447 removed outlier: 3.896A pdb=" N VAL C 437 " --> pdb=" O HIS C 433 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LEU C 447 " --> pdb=" O SER C 443 " (cutoff:3.500A) Processing helix chain 'C' and resid 453 through 465 Processing helix chain 'C' and resid 480 through 488 Processing helix chain 'C' and resid 495 through 510 Processing helix chain 'C' and resid 531 through 539 removed outlier: 3.846A pdb=" N SER C 535 " --> pdb=" O SER C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 555 through 559 removed outlier: 3.532A pdb=" N LYS C 559 " --> pdb=" O ALA C 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 580 Processing helix chain 'C' and resid 592 through 594 No H-bonds generated for 'chain 'C' and resid 592 through 594' Processing helix chain 'C' and resid 603 through 610 removed outlier: 4.153A pdb=" N LEU C 608 " --> pdb=" O SER C 604 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N GLU C 609 " --> pdb=" O SER C 605 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU C 610 " --> pdb=" O ALA C 606 " (cutoff:3.500A) Processing helix chain 'C' and resid 647 through 652 removed outlier: 3.755A pdb=" N ARG C 652 " --> pdb=" O PRO C 648 " (cutoff:3.500A) Processing helix chain 'C' and resid 663 through 682 removed outlier: 5.625A pdb=" N VAL C 675 " --> pdb=" O GLU C 671 " (cutoff:3.500A) Proline residue: C 676 - end of helix Processing helix chain 'C' and resid 693 through 702 Processing helix chain 'C' and resid 710 through 728 removed outlier: 3.625A pdb=" N LYS C 714 " --> pdb=" O ARG C 710 " (cutoff:3.500A) Processing helix chain 'C' and resid 743 through 746 No H-bonds generated for 'chain 'C' and resid 743 through 746' Processing helix chain 'C' and resid 808 through 828 Processing helix chain 'C' and resid 857 through 869 Processing helix chain 'C' and resid 895 through 904 Processing helix chain 'C' and resid 914 through 921 removed outlier: 3.590A pdb=" N LYS C 917 " --> pdb=" O ALA C 914 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N LYS C 918 " --> pdb=" O GLU C 915 " (cutoff:3.500A) Processing helix chain 'C' and resid 939 through 946 Processing helix chain 'D' and resid 416 through 424 Processing helix chain 'D' and resid 432 through 447 removed outlier: 4.004A pdb=" N LEU D 447 " --> pdb=" O SER D 443 " (cutoff:3.500A) Processing helix chain 'D' and resid 453 through 466 Processing helix chain 'D' and resid 480 through 488 Processing helix chain 'D' and resid 495 through 511 Processing helix chain 'D' and resid 529 through 540 removed outlier: 3.672A pdb=" N ALA D 533 " --> pdb=" O LYS D 529 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ARG D 534 " --> pdb=" O THR D 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 555 through 559 removed outlier: 4.067A pdb=" N LYS D 559 " --> pdb=" O ALA D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 571 through 580 Processing helix chain 'D' and resid 607 through 610 No H-bonds generated for 'chain 'D' and resid 607 through 610' Processing helix chain 'D' and resid 613 through 617 removed outlier: 4.373A pdb=" N ALA D 617 " --> pdb=" O PRO D 613 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 613 through 617' Processing helix chain 'D' and resid 647 through 652 Processing helix chain 'D' and resid 663 through 672 Processing helix chain 'D' and resid 674 through 682 Processing helix chain 'D' and resid 693 through 702 Processing helix chain 'D' and resid 711 through 728 Processing helix chain 'D' and resid 741 through 746 removed outlier: 3.686A pdb=" N VAL D 746 " --> pdb=" O GLN D 743 " (cutoff:3.500A) Processing helix chain 'D' and resid 808 through 828 Processing helix chain 'D' and resid 857 through 869 Processing helix chain 'D' and resid 895 through 904 Processing helix chain 'D' and resid 914 through 921 removed outlier: 5.026A pdb=" N LYS D 918 " --> pdb=" O GLU D 915 " (cutoff:3.500A) Processing helix chain 'D' and resid 939 through 946 Processing helix chain 'E' and resid 422 through 425 removed outlier: 3.563A pdb=" N LEU E 425 " --> pdb=" O ARG E 422 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 422 through 425' Processing helix chain 'E' and resid 432 through 447 Processing helix chain 'E' and resid 453 through 467 Processing helix chain 'E' and resid 480 through 490 removed outlier: 3.623A pdb=" N GLU E 489 " --> pdb=" O ALA E 485 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASP E 490 " --> pdb=" O VAL E 486 " (cutoff:3.500A) Processing helix chain 'E' and resid 495 through 511 Processing helix chain 'E' and resid 531 through 539 Processing helix chain 'E' and resid 555 through 559 removed outlier: 4.080A pdb=" N LYS E 559 " --> pdb=" O ALA E 556 " (cutoff:3.500A) Processing helix chain 'E' and resid 574 through 580 Processing helix chain 'E' and resid 604 through 611 Processing helix chain 'E' and resid 649 through 651 No H-bonds generated for 'chain 'E' and resid 649 through 651' Processing helix chain 'E' and resid 663 through 682 removed outlier: 4.689A pdb=" N VAL E 675 " --> pdb=" O GLU E 671 " (cutoff:3.500A) Proline residue: E 676 - end of helix Processing helix chain 'E' and resid 693 through 701 Processing helix chain 'E' and resid 710 through 728 Processing helix chain 'E' and resid 742 through 746 Processing helix chain 'E' and resid 808 through 828 Processing helix chain 'E' and resid 857 through 868 Processing helix chain 'E' and resid 895 through 904 Processing helix chain 'E' and resid 914 through 922 removed outlier: 4.646A pdb=" N LYS E 918 " --> pdb=" O GLU E 915 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N TYR E 921 " --> pdb=" O LYS E 918 " (cutoff:3.500A) Processing helix chain 'E' and resid 939 through 946 Processing helix chain 'F' and resid 423 through 425 No H-bonds generated for 'chain 'F' and resid 423 through 425' Processing helix chain 'F' and resid 432 through 447 removed outlier: 3.890A pdb=" N VAL F 437 " --> pdb=" O HIS F 433 " (cutoff:3.500A) Processing helix chain 'F' and resid 455 through 465 Processing helix chain 'F' and resid 480 through 489 Processing helix chain 'F' and resid 495 through 511 Processing helix chain 'F' and resid 531 through 539 Processing helix chain 'F' and resid 572 through 580 Processing helix chain 'F' and resid 592 through 594 No H-bonds generated for 'chain 'F' and resid 592 through 594' Processing helix chain 'F' and resid 603 through 610 Processing helix chain 'F' and resid 647 through 652 Processing helix chain 'F' and resid 663 through 672 Processing helix chain 'F' and resid 674 through 682 Processing helix chain 'F' and resid 693 through 703 Processing helix chain 'F' and resid 710 through 729 removed outlier: 3.720A pdb=" N LYS F 714 " --> pdb=" O ARG F 710 " (cutoff:3.500A) Processing helix chain 'F' and resid 742 through 746 removed outlier: 3.664A pdb=" N VAL F 746 " --> pdb=" O GLN F 743 " (cutoff:3.500A) Processing helix chain 'F' and resid 808 through 828 Processing helix chain 'F' and resid 857 through 868 Processing helix chain 'F' and resid 895 through 905 Processing helix chain 'F' and resid 914 through 921 removed outlier: 4.896A pdb=" N LYS F 918 " --> pdb=" O GLU F 915 " (cutoff:3.500A) Processing helix chain 'F' and resid 939 through 946 Processing sheet with id= A, first strand: chain 'A' and resid 654 through 657 removed outlier: 6.365A pdb=" N PHE A 635 " --> pdb=" O LEU A 519 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N PHE A 521 " --> pdb=" O PHE A 635 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N CYS A 637 " --> pdb=" O PHE A 521 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 765 through 769 Processing sheet with id= C, first strand: chain 'A' and resid 781 through 784 removed outlier: 6.058A pdb=" N SER A 799 " --> pdb=" O ILE A 840 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N LEU A 842 " --> pdb=" O SER A 799 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N GLU A 801 " --> pdb=" O LEU A 842 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 877 through 879 removed outlier: 6.593A pdb=" N CYS A 909 " --> pdb=" O ALA A 878 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N GLU A 932 " --> pdb=" O ILE A 910 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N LEU A 912 " --> pdb=" O GLU A 932 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N HIS A 934 " --> pdb=" O LEU A 912 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 654 through 657 removed outlier: 6.389A pdb=" N PHE B 635 " --> pdb=" O LEU B 519 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N PHE B 521 " --> pdb=" O PHE B 635 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N CYS B 637 " --> pdb=" O PHE B 521 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU B 634 " --> pdb=" O PRO B 585 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N GLU B 543 " --> pdb=" O LEU B 586 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N LEU B 588 " --> pdb=" O GLU B 543 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N PHE B 545 " --> pdb=" O LEU B 588 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N ASP B 590 " --> pdb=" O PHE B 545 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N PHE B 547 " --> pdb=" O ASP B 590 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 689 through 691 removed outlier: 7.357A pdb=" N VAL B 735 " --> pdb=" O LYS B 690 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'B' and resid 780 through 784 removed outlier: 5.929A pdb=" N SER B 799 " --> pdb=" O ILE B 840 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N LEU B 842 " --> pdb=" O SER B 799 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N GLU B 801 " --> pdb=" O LEU B 842 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N VAL B 844 " --> pdb=" O GLU B 801 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N THR B 803 " --> pdb=" O VAL B 844 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 909 through 913 removed outlier: 6.146A pdb=" N GLU B 932 " --> pdb=" O ILE B 910 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N LEU B 912 " --> pdb=" O GLU B 932 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N HIS B 934 " --> pdb=" O LEU B 912 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'C' and resid 654 through 657 removed outlier: 6.318A pdb=" N PHE C 635 " --> pdb=" O LEU C 519 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N PHE C 521 " --> pdb=" O PHE C 635 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N CYS C 637 " --> pdb=" O PHE C 521 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR C 638 " --> pdb=" O ILE C 589 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 689 through 691 removed outlier: 8.105A pdb=" N VAL C 735 " --> pdb=" O LYS C 690 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'C' and resid 765 through 770 removed outlier: 3.501A pdb=" N VAL C 765 " --> pdb=" O VAL C 780 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 781 through 784 removed outlier: 6.094A pdb=" N SER C 799 " --> pdb=" O ILE C 840 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N LEU C 842 " --> pdb=" O SER C 799 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N GLU C 801 " --> pdb=" O LEU C 842 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 877 through 879 removed outlier: 6.435A pdb=" N CYS C 909 " --> pdb=" O ALA C 878 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N GLU C 932 " --> pdb=" O ILE C 910 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N LEU C 912 " --> pdb=" O GLU C 932 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N HIS C 934 " --> pdb=" O LEU C 912 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'D' and resid 654 through 657 removed outlier: 6.325A pdb=" N PHE D 635 " --> pdb=" O LEU D 519 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N PHE D 521 " --> pdb=" O PHE D 635 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N CYS D 637 " --> pdb=" O PHE D 521 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 689 through 691 removed outlier: 6.833A pdb=" N VAL D 735 " --> pdb=" O LYS D 690 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'D' and resid 764 through 771 removed outlier: 6.094A pdb=" N SER D 799 " --> pdb=" O ILE D 840 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N LEU D 842 " --> pdb=" O SER D 799 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N GLU D 801 " --> pdb=" O LEU D 842 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N VAL D 844 " --> pdb=" O GLU D 801 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N THR D 803 " --> pdb=" O VAL D 844 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 877 through 879 removed outlier: 6.522A pdb=" N CYS D 909 " --> pdb=" O ALA D 878 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N GLU D 932 " --> pdb=" O ILE D 910 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N LEU D 912 " --> pdb=" O GLU D 932 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N HIS D 934 " --> pdb=" O LEU D 912 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'E' and resid 654 through 657 removed outlier: 6.430A pdb=" N PHE E 635 " --> pdb=" O LEU E 519 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N PHE E 521 " --> pdb=" O PHE E 635 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N CYS E 637 " --> pdb=" O PHE E 521 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N PHE E 545 " --> pdb=" O LEU E 588 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ASP E 590 " --> pdb=" O PHE E 545 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N PHE E 547 " --> pdb=" O ASP E 590 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 689 through 691 removed outlier: 6.802A pdb=" N VAL E 735 " --> pdb=" O LYS E 690 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'E' and resid 765 through 770 removed outlier: 6.110A pdb=" N SER E 799 " --> pdb=" O ILE E 840 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N LEU E 842 " --> pdb=" O SER E 799 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N GLU E 801 " --> pdb=" O LEU E 842 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N VAL E 844 " --> pdb=" O GLU E 801 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N THR E 803 " --> pdb=" O VAL E 844 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 877 through 879 removed outlier: 6.565A pdb=" N CYS E 909 " --> pdb=" O ALA E 878 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLU E 932 " --> pdb=" O ILE E 910 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N LEU E 912 " --> pdb=" O GLU E 932 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N HIS E 934 " --> pdb=" O LEU E 912 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'F' and resid 653 through 657 removed outlier: 6.179A pdb=" N ILE F 518 " --> pdb=" O GLU F 654 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N ILE F 656 " --> pdb=" O ILE F 518 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N CYS F 520 " --> pdb=" O ILE F 656 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LEU F 519 " --> pdb=" O PHE F 635 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASP F 590 " --> pdb=" O PHE F 547 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'F' and resid 765 through 770 Processing sheet with id= X, first strand: chain 'F' and resid 781 through 784 removed outlier: 6.061A pdb=" N SER F 799 " --> pdb=" O ILE F 840 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N LEU F 842 " --> pdb=" O SER F 799 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N GLU F 801 " --> pdb=" O LEU F 842 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'F' and resid 877 through 879 removed outlier: 6.528A pdb=" N CYS F 909 " --> pdb=" O ALA F 878 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N GLU F 932 " --> pdb=" O ILE F 910 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N LEU F 912 " --> pdb=" O GLU F 932 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N HIS F 934 " --> pdb=" O LEU F 912 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y 873 hydrogen bonds defined for protein. 2475 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: 8.20 Time building geometry restraints manager: 10.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 4170 1.30 - 1.43: 6008 1.43 - 1.56: 14787 1.56 - 1.68: 32 1.68 - 1.81: 196 Bond restraints: 25193 Sorted by residual: bond pdb=" C4 ATP D1000 " pdb=" C5 ATP D1000 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.71e+01 bond pdb=" C4 ATP C1000 " pdb=" C5 ATP C1000 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.52e+01 bond pdb=" C4 ATP A1000 " pdb=" C5 ATP A1000 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.45e+01 bond pdb=" C4 ATP B1000 " pdb=" C5 ATP B1000 " ideal model delta sigma weight residual 1.388 1.460 -0.072 1.00e-02 1.00e+04 5.15e+01 bond pdb=" C5 ATP A1000 " pdb=" C6 ATP A1000 " ideal model delta sigma weight residual 1.409 1.476 -0.067 1.00e-02 1.00e+04 4.42e+01 ... (remaining 25188 not shown) Histogram of bond angle deviations from ideal: 98.58 - 106.13: 657 106.13 - 113.67: 14501 113.67 - 121.21: 12790 121.21 - 128.76: 6044 128.76 - 136.30: 131 Bond angle restraints: 34123 Sorted by residual: angle pdb=" PB ATP D1000 " pdb=" O3B ATP D1000 " pdb=" PG ATP D1000 " ideal model delta sigma weight residual 139.87 121.86 18.01 1.00e+00 1.00e+00 3.24e+02 angle pdb=" PA ATP C1000 " pdb=" O3A ATP C1000 " pdb=" PB ATP C1000 " ideal model delta sigma weight residual 136.83 121.22 15.61 1.00e+00 1.00e+00 2.44e+02 angle pdb=" PA ATP D1000 " pdb=" O3A ATP D1000 " pdb=" PB ATP D1000 " ideal model delta sigma weight residual 136.83 121.39 15.44 1.00e+00 1.00e+00 2.38e+02 angle pdb=" PB ATP A1000 " pdb=" O3B ATP A1000 " pdb=" PG ATP A1000 " ideal model delta sigma weight residual 139.87 124.54 15.33 1.00e+00 1.00e+00 2.35e+02 angle pdb=" PA ATP A1000 " pdb=" O3A ATP A1000 " pdb=" PB ATP A1000 " ideal model delta sigma weight residual 136.83 121.82 15.01 1.00e+00 1.00e+00 2.25e+02 ... (remaining 34118 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 13913 17.90 - 35.79: 1186 35.79 - 53.69: 235 53.69 - 71.59: 54 71.59 - 89.49: 40 Dihedral angle restraints: 15428 sinusoidal: 6373 harmonic: 9055 Sorted by residual: dihedral pdb=" CA PRO D 845 " pdb=" C PRO D 845 " pdb=" N GLU D 846 " pdb=" CA GLU D 846 " ideal model delta harmonic sigma weight residual 180.00 -154.70 -25.30 0 5.00e+00 4.00e-02 2.56e+01 dihedral pdb=" CA PRO A 845 " pdb=" C PRO A 845 " pdb=" N GLU A 846 " pdb=" CA GLU A 846 " ideal model delta harmonic sigma weight residual -180.00 -156.41 -23.59 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA THR A 752 " pdb=" C THR A 752 " pdb=" N VAL A 753 " pdb=" CA VAL A 753 " ideal model delta harmonic sigma weight residual 180.00 -156.78 -23.22 0 5.00e+00 4.00e-02 2.16e+01 ... (remaining 15425 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2255 0.035 - 0.070: 1159 0.070 - 0.105: 353 0.105 - 0.139: 123 0.139 - 0.174: 19 Chirality restraints: 3909 Sorted by residual: chirality pdb=" C21 BO2 B1002 " pdb=" B26 BO2 B1002 " pdb=" C22 BO2 B1002 " pdb=" N20 BO2 B1002 " both_signs ideal model delta sigma weight residual False 2.49 2.66 -0.17 2.00e-01 2.50e+01 7.59e-01 chirality pdb=" C1' ATP B1000 " pdb=" C2' ATP B1000 " pdb=" N9 ATP B1000 " pdb=" O4' ATP B1000 " both_signs ideal model delta sigma weight residual False 2.41 2.58 -0.17 2.00e-01 2.50e+01 7.51e-01 chirality pdb=" C3' ADP E1001 " pdb=" C2' ADP E1001 " pdb=" C4' ADP E1001 " pdb=" O3' ADP E1001 " both_signs ideal model delta sigma weight residual False -2.51 -2.67 0.16 2.00e-01 2.50e+01 6.30e-01 ... (remaining 3906 not shown) Planarity restraints: 4358 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO E 761 " 0.040 5.00e-02 4.00e+02 6.03e-02 5.82e+00 pdb=" N PRO E 762 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO E 762 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO E 762 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET B 569 " 0.038 5.00e-02 4.00e+02 5.64e-02 5.09e+00 pdb=" N PRO B 570 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO B 570 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 570 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 761 " -0.032 5.00e-02 4.00e+02 4.83e-02 3.73e+00 pdb=" N PRO B 762 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 762 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 762 " -0.027 5.00e-02 4.00e+02 ... (remaining 4355 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.50: 139 2.50 - 3.10: 18254 3.10 - 3.70: 37451 3.70 - 4.30: 56560 4.30 - 4.90: 93663 Nonbonded interactions: 206067 Sorted by model distance: nonbonded pdb=" O1G ATP C1000 " pdb="MG MG C1001 " model vdw 1.906 2.170 nonbonded pdb=" O2B ATP A1000 " pdb="MG MG A1001 " model vdw 1.935 2.170 nonbonded pdb=" O3G ATP D1000 " pdb="MG MG D1001 " model vdw 1.984 2.170 nonbonded pdb=" OG1 THR C 530 " pdb="MG MG C1001 " model vdw 2.025 2.170 nonbonded pdb=" OG1 THR B 530 " pdb="MG MG B1001 " model vdw 2.038 2.170 ... (remaining 206062 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' and (resid 421 through 426 or (resid 427 and (name N or name CA or na \ me C or name O or name CB )) or resid 428 through 461 or (resid 462 and (name N \ or name CA or name C or name O or name CB )) or resid 463 through 550 or resid 5 \ 56 through 562 or (resid 563 and (name N or name CA or name C or name O or name \ CB )) or resid 564 through 596 or resid 603 through 631 or (resid 632 and (name \ N or name CA or name C or name O or name CB )) or resid 633 through 649 or (resi \ d 650 and (name N or name CA or name C or name O or name CB )) or resid 651 or ( \ resid 652 and (name N or name CA or name C or name O or name CB )) or resid 653 \ through 685 or (resid 686 and (name N or name CA or name C or name O or name CB \ )) or resid 687 through 689 or (resid 690 and (name N or name CA or name C or na \ me O or name CB )) or resid 691 through 788 or resid 796 through 947)) selection = (chain 'B' and (resid 421 through 426 or (resid 427 and (name N or name CA or na \ me C or name O or name CB )) or resid 428 through 461 or (resid 462 and (name N \ or name CA or name C or name O or name CB )) or resid 463 through 550 or resid 5 \ 56 through 562 or (resid 563 and (name N or name CA or name C or name O or name \ CB )) or resid 564 through 596 or resid 603 through 631 or (resid 632 and (name \ N or name CA or name C or name O or name CB )) or resid 633 through 649 or (resi \ d 650 and (name N or name CA or name C or name O or name CB )) or resid 651 or ( \ resid 652 and (name N or name CA or name C or name O or name CB )) or resid 653 \ through 685 or (resid 686 and (name N or name CA or name C or name O or name CB \ )) or resid 687 through 689 or (resid 690 and (name N or name CA or name C or na \ me O or name CB )) or resid 691 through 788 or resid 796 through 947)) selection = (chain 'C' and (resid 421 through 426 or (resid 427 and (name N or name CA or na \ me C or name O or name CB )) or resid 428 through 461 or (resid 462 and (name N \ or name CA or name C or name O or name CB )) or resid 463 through 550 or resid 5 \ 56 through 562 or (resid 563 and (name N or name CA or name C or name O or name \ CB )) or resid 564 through 596 or resid 603 through 631 or (resid 632 and (name \ N or name CA or name C or name O or name CB )) or resid 633 through 649 or (resi \ d 650 and (name N or name CA or name C or name O or name CB )) or resid 651 or ( \ resid 652 and (name N or name CA or name C or name O or name CB )) or resid 653 \ through 685 or (resid 686 and (name N or name CA or name C or name O or name CB \ )) or resid 687 through 689 or (resid 690 and (name N or name CA or name C or na \ me O or name CB )) or resid 691 through 788 or resid 796 through 947)) selection = (chain 'D' and (resid 421 through 426 or (resid 427 and (name N or name CA or na \ me C or name O or name CB )) or resid 428 through 461 or (resid 462 and (name N \ or name CA or name C or name O or name CB )) or resid 463 through 550 or resid 5 \ 56 through 562 or (resid 563 and (name N or name CA or name C or name O or name \ CB )) or resid 564 through 631 or (resid 632 and (name N or name CA or name C or \ name O or name CB )) or resid 633 through 649 or (resid 650 and (name N or name \ CA or name C or name O or name CB )) or resid 651 or (resid 652 and (name N or \ name CA or name C or name O or name CB )) or resid 653 through 685 or (resid 686 \ and (name N or name CA or name C or name O or name CB )) or resid 687 through 9 \ 47)) selection = (chain 'E' and (resid 421 through 461 or (resid 462 and (name N or name CA or na \ me C or name O or name CB )) or resid 463 through 550 or resid 556 through 596 o \ r resid 603 through 631 or (resid 632 and (name N or name CA or name C or name O \ or name CB )) or resid 633 through 651 or (resid 652 and (name N or name CA or \ name C or name O or name CB )) or resid 653 through 689 or (resid 690 and (name \ N or name CA or name C or name O or name CB )) or resid 691 through 788 or resid \ 796 through 947)) selection = (chain 'F' and (resid 421 through 426 or (resid 427 and (name N or name CA or na \ me C or name O or name CB )) or resid 428 through 562 or (resid 563 and (name N \ or name CA or name C or name O or name CB )) or resid 564 through 596 or resid 6 \ 03 through 685 or (resid 686 and (name N or name CA or name C or name O or name \ CB )) or resid 687 through 689 or (resid 690 and (name N or name CA or name C or \ name O or name CB )) or resid 691 through 788 or resid 796 through 947)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.010 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: 6.400 Check model and map are aligned: 0.380 Set scattering table: 0.240 Process input model: 66.240 Find NCS groups from input model: 2.040 Set up NCS constraints: 0.100 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 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 : 0.007 0.108 25193 Z= 0.490 Angle : 0.799 18.008 34123 Z= 0.470 Chirality : 0.047 0.174 3909 Planarity : 0.005 0.060 4358 Dihedral : 14.695 89.486 9592 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 0.19 % Allowed : 6.68 % Favored : 93.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.84 (0.13), residues: 3095 helix: -1.08 (0.12), residues: 1338 sheet: -1.65 (0.25), residues: 405 loop : -2.78 (0.14), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 770 HIS 0.005 0.001 HIS F 491 PHE 0.019 0.002 PHE C 820 TYR 0.016 0.002 TYR A 939 ARG 0.008 0.001 ARG C 710 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 2663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 382 time to evaluate : 2.761 Fit side-chains REVERT: A 562 ARG cc_start: 0.7431 (mpt180) cc_final: 0.7203 (mtt90) REVERT: A 569 MET cc_start: 0.8397 (mtm) cc_final: 0.8140 (mtp) REVERT: A 651 ASP cc_start: 0.7557 (m-30) cc_final: 0.7321 (m-30) REVERT: A 810 MET cc_start: 0.8064 (ttt) cc_final: 0.7820 (ttt) REVERT: A 915 GLU cc_start: 0.7606 (mt-10) cc_final: 0.7199 (mp0) REVERT: A 922 ASP cc_start: 0.6613 (t0) cc_final: 0.6148 (t0) REVERT: B 579 LYS cc_start: 0.8037 (mttm) cc_final: 0.7832 (mtmm) REVERT: B 597 ARG cc_start: 0.7101 (ptp-110) cc_final: 0.6760 (ptp90) REVERT: B 776 SER cc_start: 0.8583 (t) cc_final: 0.8319 (m) REVERT: B 808 GLU cc_start: 0.6810 (mm-30) cc_final: 0.6551 (tp30) REVERT: B 918 LYS cc_start: 0.7646 (mmtm) cc_final: 0.7318 (tptt) REVERT: C 423 GLU cc_start: 0.7362 (tm-30) cc_final: 0.7129 (tm-30) REVERT: C 424 ARG cc_start: 0.8451 (mtt180) cc_final: 0.8098 (mtt180) REVERT: C 459 ARG cc_start: 0.8049 (ttp80) cc_final: 0.7842 (ttp80) REVERT: C 655 MET cc_start: 0.8118 (mmm) cc_final: 0.7598 (mmm) REVERT: C 713 GLN cc_start: 0.7934 (tt0) cc_final: 0.7670 (mt0) REVERT: D 552 MET cc_start: 0.8592 (ttp) cc_final: 0.8286 (ttm) REVERT: D 569 MET cc_start: 0.8311 (mmm) cc_final: 0.8099 (mmm) REVERT: D 686 GLU cc_start: 0.8142 (tm-30) cc_final: 0.7884 (tp30) REVERT: D 785 ARG cc_start: 0.7829 (mtp-110) cc_final: 0.7322 (mtp180) REVERT: D 915 GLU cc_start: 0.7661 (mt-10) cc_final: 0.7179 (mp0) REVERT: E 432 LYS cc_start: 0.7920 (tmmt) cc_final: 0.7592 (ttpt) REVERT: E 475 ASN cc_start: 0.7522 (t0) cc_final: 0.7241 (t0) REVERT: E 552 MET cc_start: 0.5452 (ppp) cc_final: 0.5160 (ptm) REVERT: E 811 LYS cc_start: 0.7885 (mttt) cc_final: 0.7624 (mttp) REVERT: E 918 LYS cc_start: 0.7914 (pttp) cc_final: 0.7657 (ptpt) REVERT: F 459 ARG cc_start: 0.7163 (ttt180) cc_final: 0.6825 (ttt-90) REVERT: F 482 ARG cc_start: 0.8128 (tmt170) cc_final: 0.7861 (ttp80) REVERT: F 786 ARG cc_start: 0.7473 (mtp180) cc_final: 0.7249 (mtp180) outliers start: 5 outliers final: 4 residues processed: 387 average time/residue: 0.4482 time to fit residues: 251.5764 Evaluate side-chains 290 residues out of total 2663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 286 time to evaluate : 3.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain D residue 611 LEU Chi-restraints excluded: chain D residue 764 VAL Chi-restraints excluded: chain F residue 764 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 262 optimal weight: 10.0000 chunk 235 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 80 optimal weight: 0.8980 chunk 159 optimal weight: 9.9990 chunk 125 optimal weight: 2.9990 chunk 243 optimal weight: 5.9990 chunk 94 optimal weight: 0.5980 chunk 148 optimal weight: 0.6980 chunk 181 optimal weight: 0.7980 chunk 282 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 456 ASN A 475 ASN A 515 GLN A 832 ASN ** B 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 477 ASN C 615 GLN D 713 GLN E 711 ASN E 839 HIS F 456 ASN F 575 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25193 Z= 0.170 Angle : 0.533 8.777 34123 Z= 0.268 Chirality : 0.041 0.157 3909 Planarity : 0.004 0.053 4358 Dihedral : 10.419 87.808 3670 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.13 % Allowed : 9.43 % Favored : 89.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.14), residues: 3095 helix: 0.27 (0.14), residues: 1332 sheet: -1.02 (0.26), residues: 393 loop : -2.18 (0.15), residues: 1370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 470 HIS 0.004 0.001 HIS B 843 PHE 0.015 0.001 PHE B 504 TYR 0.015 0.001 TYR A 939 ARG 0.005 0.000 ARG E 562 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 305 time to evaluate : 2.731 Fit side-chains REVERT: A 456 ASN cc_start: 0.8111 (m-40) cc_final: 0.7780 (m-40) REVERT: A 562 ARG cc_start: 0.7351 (mpt180) cc_final: 0.7132 (mtt90) REVERT: A 609 GLU cc_start: 0.7467 (mt-10) cc_final: 0.7035 (mt-10) REVERT: A 651 ASP cc_start: 0.7518 (m-30) cc_final: 0.7280 (m-30) REVERT: A 810 MET cc_start: 0.8280 (ttt) cc_final: 0.7991 (ttt) REVERT: A 922 ASP cc_start: 0.6989 (t0) cc_final: 0.6510 (t0) REVERT: B 482 ARG cc_start: 0.7554 (tmm160) cc_final: 0.7221 (tmm160) REVERT: B 597 ARG cc_start: 0.7049 (ptp-110) cc_final: 0.6711 (ptp90) REVERT: B 625 ASP cc_start: 0.8097 (OUTLIER) cc_final: 0.7773 (t0) REVERT: B 808 GLU cc_start: 0.7110 (mm-30) cc_final: 0.6789 (tp30) REVERT: B 918 LYS cc_start: 0.7515 (mmtm) cc_final: 0.7299 (tptt) REVERT: C 423 GLU cc_start: 0.7329 (tm-30) cc_final: 0.7030 (tm-30) REVERT: C 459 ARG cc_start: 0.7999 (ttp80) cc_final: 0.7780 (ttp80) REVERT: C 651 ASP cc_start: 0.8000 (t0) cc_final: 0.7734 (t70) REVERT: C 918 LYS cc_start: 0.7841 (mmtt) cc_final: 0.7371 (mmtt) REVERT: D 686 GLU cc_start: 0.8010 (tm-30) cc_final: 0.7733 (tp30) REVERT: D 785 ARG cc_start: 0.7955 (mtp-110) cc_final: 0.7316 (mtp180) REVERT: D 915 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7251 (mp0) REVERT: D 937 GLU cc_start: 0.7572 (mt-10) cc_final: 0.7322 (mt-10) REVERT: E 460 ASN cc_start: 0.7651 (m-40) cc_final: 0.7406 (m-40) REVERT: E 475 ASN cc_start: 0.7450 (t0) cc_final: 0.7154 (t0) REVERT: E 811 LYS cc_start: 0.7936 (mttt) cc_final: 0.7681 (mttp) REVERT: F 459 ARG cc_start: 0.7056 (ttt180) cc_final: 0.6786 (ttt-90) REVERT: F 547 PHE cc_start: 0.7824 (p90) cc_final: 0.7391 (p90) REVERT: F 569 MET cc_start: 0.6066 (mmm) cc_final: 0.5832 (mmm) REVERT: F 918 LYS cc_start: 0.7983 (tttt) cc_final: 0.7641 (tttp) outliers start: 30 outliers final: 21 residues processed: 327 average time/residue: 0.4391 time to fit residues: 213.0842 Evaluate side-chains 305 residues out of total 2663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 283 time to evaluate : 3.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain B residue 625 ASP Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 764 VAL Chi-restraints excluded: chain C residue 846 GLU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 611 LEU Chi-restraints excluded: chain D residue 764 VAL Chi-restraints excluded: chain E residue 514 THR Chi-restraints excluded: chain E residue 618 ASN Chi-restraints excluded: chain E residue 624 LEU Chi-restraints excluded: chain E residue 764 VAL Chi-restraints excluded: chain F residue 428 LEU Chi-restraints excluded: chain F residue 465 LEU Chi-restraints excluded: chain F residue 566 VAL Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 764 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 156 optimal weight: 2.9990 chunk 87 optimal weight: 7.9990 chunk 235 optimal weight: 4.9990 chunk 192 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 282 optimal weight: 7.9990 chunk 305 optimal weight: 0.9980 chunk 251 optimal weight: 0.7980 chunk 280 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 226 optimal weight: 4.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 832 ASN B 484 GLN ** B 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 743 GLN F 433 HIS F 456 ASN ** F 839 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25193 Z= 0.193 Angle : 0.515 6.466 34123 Z= 0.260 Chirality : 0.041 0.164 3909 Planarity : 0.004 0.053 4358 Dihedral : 9.974 89.400 3670 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 1.55 % Allowed : 11.02 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.15), residues: 3095 helix: 0.75 (0.14), residues: 1335 sheet: -0.60 (0.26), residues: 406 loop : -1.86 (0.16), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 470 HIS 0.003 0.001 HIS E 843 PHE 0.015 0.001 PHE F 545 TYR 0.015 0.001 TYR A 939 ARG 0.007 0.000 ARG E 562 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 307 time to evaluate : 2.847 Fit side-chains REVERT: A 609 GLU cc_start: 0.7467 (mt-10) cc_final: 0.7044 (mt-10) REVERT: A 918 LYS cc_start: 0.7729 (mptt) cc_final: 0.7242 (ptpt) REVERT: A 922 ASP cc_start: 0.7225 (t0) cc_final: 0.6764 (t0) REVERT: B 423 GLU cc_start: 0.7689 (tp30) cc_final: 0.7447 (tp30) REVERT: B 482 ARG cc_start: 0.7558 (tmm160) cc_final: 0.7118 (tmm160) REVERT: B 597 ARG cc_start: 0.6999 (ptp-110) cc_final: 0.6648 (ptp90) REVERT: B 625 ASP cc_start: 0.8144 (OUTLIER) cc_final: 0.7844 (t0) REVERT: B 808 GLU cc_start: 0.7162 (mm-30) cc_final: 0.6827 (tp30) REVERT: B 811 LYS cc_start: 0.8196 (mttm) cc_final: 0.7906 (mttp) REVERT: C 423 GLU cc_start: 0.7316 (tm-30) cc_final: 0.7000 (tm-30) REVERT: C 459 ARG cc_start: 0.7995 (ttp80) cc_final: 0.7763 (ttp80) REVERT: C 651 ASP cc_start: 0.7866 (t0) cc_final: 0.7630 (t70) REVERT: C 918 LYS cc_start: 0.7764 (mmtt) cc_final: 0.7388 (mmtp) REVERT: D 419 GLU cc_start: 0.7269 (mp0) cc_final: 0.7013 (mp0) REVERT: D 440 GLU cc_start: 0.7592 (mt-10) cc_final: 0.7382 (mt-10) REVERT: D 785 ARG cc_start: 0.8120 (mtp-110) cc_final: 0.7402 (mtp180) REVERT: D 915 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7274 (mp0) REVERT: D 937 GLU cc_start: 0.7600 (mt-10) cc_final: 0.7305 (mt-10) REVERT: E 460 ASN cc_start: 0.7699 (m-40) cc_final: 0.7438 (m-40) REVERT: E 475 ASN cc_start: 0.7418 (t0) cc_final: 0.7178 (t0) REVERT: E 653 MET cc_start: 0.6723 (OUTLIER) cc_final: 0.6417 (ptt) REVERT: E 778 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8071 (pp) REVERT: E 811 LYS cc_start: 0.7998 (mttt) cc_final: 0.7725 (mttp) REVERT: F 459 ARG cc_start: 0.7074 (ttt180) cc_final: 0.6821 (ttt-90) REVERT: F 547 PHE cc_start: 0.7694 (p90) cc_final: 0.7313 (p90) REVERT: F 655 MET cc_start: 0.6962 (mmm) cc_final: 0.5094 (ptm) REVERT: F 918 LYS cc_start: 0.7861 (tttt) cc_final: 0.7567 (tttp) outliers start: 41 outliers final: 24 residues processed: 337 average time/residue: 0.4487 time to fit residues: 225.3051 Evaluate side-chains 309 residues out of total 2663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 282 time to evaluate : 2.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 771 THR Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 625 ASP Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 785 ARG Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 764 VAL Chi-restraints excluded: chain C residue 846 GLU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 611 LEU Chi-restraints excluded: chain D residue 764 VAL Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 582 THR Chi-restraints excluded: chain E residue 618 ASN Chi-restraints excluded: chain E residue 624 LEU Chi-restraints excluded: chain E residue 653 MET Chi-restraints excluded: chain E residue 744 ASP Chi-restraints excluded: chain E residue 764 VAL Chi-restraints excluded: chain E residue 778 LEU Chi-restraints excluded: chain F residue 465 LEU Chi-restraints excluded: chain F residue 566 VAL Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 752 THR Chi-restraints excluded: chain F residue 764 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 279 optimal weight: 7.9990 chunk 212 optimal weight: 0.0980 chunk 146 optimal weight: 4.9990 chunk 31 optimal weight: 0.0980 chunk 135 optimal weight: 5.9990 chunk 189 optimal weight: 7.9990 chunk 283 optimal weight: 6.9990 chunk 300 optimal weight: 0.2980 chunk 148 optimal weight: 0.0060 chunk 269 optimal weight: 6.9990 chunk 81 optimal weight: 0.0470 overall best weight: 0.1094 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 832 ASN ** B 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 615 GLN E 575 GLN F 456 ASN ** F 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 839 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 25193 Z= 0.115 Angle : 0.473 10.065 34123 Z= 0.236 Chirality : 0.039 0.148 3909 Planarity : 0.004 0.048 4358 Dihedral : 9.169 88.797 3670 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.47 % Allowed : 11.89 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.15), residues: 3095 helix: 1.22 (0.14), residues: 1332 sheet: -0.28 (0.26), residues: 425 loop : -1.60 (0.16), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 464 HIS 0.002 0.000 HIS C 433 PHE 0.014 0.001 PHE B 504 TYR 0.009 0.001 TYR C 565 ARG 0.007 0.000 ARG E 562 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 312 time to evaluate : 2.827 Fit side-chains REVERT: A 456 ASN cc_start: 0.7534 (m-40) cc_final: 0.7314 (m-40) REVERT: A 609 GLU cc_start: 0.7313 (mt-10) cc_final: 0.6943 (mt-10) REVERT: A 922 ASP cc_start: 0.7165 (t0) cc_final: 0.6686 (t0) REVERT: B 482 ARG cc_start: 0.7531 (tmm160) cc_final: 0.7128 (tmm160) REVERT: B 547 PHE cc_start: 0.8136 (t80) cc_final: 0.7619 (t80) REVERT: B 579 LYS cc_start: 0.8059 (mtmm) cc_final: 0.7850 (mtmm) REVERT: B 597 ARG cc_start: 0.6797 (ptp-110) cc_final: 0.6425 (ptp90) REVERT: B 625 ASP cc_start: 0.8115 (OUTLIER) cc_final: 0.7857 (t0) REVERT: B 808 GLU cc_start: 0.7172 (mm-30) cc_final: 0.6873 (tp30) REVERT: B 811 LYS cc_start: 0.8204 (mttm) cc_final: 0.7933 (mttp) REVERT: C 423 GLU cc_start: 0.7308 (tm-30) cc_final: 0.6982 (tm-30) REVERT: C 459 ARG cc_start: 0.7977 (ttp80) cc_final: 0.7745 (ttp80) REVERT: C 651 ASP cc_start: 0.7889 (t0) cc_final: 0.7591 (t0) REVERT: C 750 VAL cc_start: 0.8286 (t) cc_final: 0.8084 (t) REVERT: C 918 LYS cc_start: 0.7779 (mmtt) cc_final: 0.7423 (mmtp) REVERT: D 440 GLU cc_start: 0.7568 (mt-10) cc_final: 0.7343 (mt-10) REVERT: D 482 ARG cc_start: 0.7488 (tmt170) cc_final: 0.7275 (tmt170) REVERT: D 649 LEU cc_start: 0.8567 (tp) cc_final: 0.8289 (tp) REVERT: D 785 ARG cc_start: 0.8032 (mtp-110) cc_final: 0.7322 (mtp180) REVERT: D 915 GLU cc_start: 0.7598 (mt-10) cc_final: 0.7216 (mp0) REVERT: D 937 GLU cc_start: 0.7595 (mt-10) cc_final: 0.7306 (mt-10) REVERT: E 460 ASN cc_start: 0.7628 (m-40) cc_final: 0.7338 (m-40) REVERT: E 653 MET cc_start: 0.6652 (OUTLIER) cc_final: 0.6329 (ptt) REVERT: E 778 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8088 (pp) REVERT: E 811 LYS cc_start: 0.7920 (mttt) cc_final: 0.7653 (mttp) REVERT: F 459 ARG cc_start: 0.7131 (ttt180) cc_final: 0.6853 (ttp-170) REVERT: F 547 PHE cc_start: 0.7732 (p90) cc_final: 0.7382 (p90) REVERT: F 655 MET cc_start: 0.7075 (mmm) cc_final: 0.5226 (ptm) outliers start: 39 outliers final: 22 residues processed: 341 average time/residue: 0.4430 time to fit residues: 223.4044 Evaluate side-chains 309 residues out of total 2663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 284 time to evaluate : 2.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 832 ASN Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain B residue 625 ASP Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 618 ASN Chi-restraints excluded: chain C residue 764 VAL Chi-restraints excluded: chain C residue 846 GLU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 611 LEU Chi-restraints excluded: chain D residue 764 VAL Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 514 THR Chi-restraints excluded: chain E residue 569 MET Chi-restraints excluded: chain E residue 624 LEU Chi-restraints excluded: chain E residue 653 MET Chi-restraints excluded: chain E residue 764 VAL Chi-restraints excluded: chain E residue 778 LEU Chi-restraints excluded: chain E residue 849 THR Chi-restraints excluded: chain F residue 465 LEU Chi-restraints excluded: chain F residue 566 VAL Chi-restraints excluded: chain F residue 764 VAL Chi-restraints excluded: chain F residue 771 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 250 optimal weight: 0.6980 chunk 170 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 223 optimal weight: 5.9990 chunk 124 optimal weight: 0.8980 chunk 256 optimal weight: 3.9990 chunk 207 optimal weight: 0.0370 chunk 0 optimal weight: 8.9990 chunk 153 optimal weight: 0.9980 chunk 269 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 overall best weight: 1.3260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 484 GLN C 477 ASN D 615 GLN F 456 ASN ** F 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25193 Z= 0.210 Angle : 0.513 7.043 34123 Z= 0.258 Chirality : 0.041 0.160 3909 Planarity : 0.004 0.048 4358 Dihedral : 9.518 88.548 3669 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.85 % Allowed : 12.08 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.15), residues: 3095 helix: 1.24 (0.14), residues: 1332 sheet: -0.13 (0.27), residues: 405 loop : -1.55 (0.16), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 470 HIS 0.004 0.001 HIS E 843 PHE 0.019 0.002 PHE C 820 TYR 0.016 0.002 TYR F 939 ARG 0.007 0.000 ARG E 562 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 294 time to evaluate : 3.066 Fit side-chains REVERT: A 569 MET cc_start: 0.8133 (mtp) cc_final: 0.7897 (mtp) REVERT: A 609 GLU cc_start: 0.7400 (mt-10) cc_final: 0.6985 (mt-10) REVERT: A 785 ARG cc_start: 0.7783 (OUTLIER) cc_final: 0.7518 (mtp-110) REVERT: A 849 THR cc_start: 0.8547 (OUTLIER) cc_final: 0.8325 (t) REVERT: A 918 LYS cc_start: 0.7583 (mptt) cc_final: 0.7098 (ptpt) REVERT: A 922 ASP cc_start: 0.7383 (t0) cc_final: 0.6939 (t0) REVERT: B 482 ARG cc_start: 0.7573 (tmm160) cc_final: 0.7155 (tmm160) REVERT: B 547 PHE cc_start: 0.8169 (t80) cc_final: 0.7674 (t80) REVERT: B 597 ARG cc_start: 0.6990 (ptp-110) cc_final: 0.6614 (ptp90) REVERT: B 625 ASP cc_start: 0.8135 (OUTLIER) cc_final: 0.7879 (t0) REVERT: B 778 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8198 (pp) REVERT: B 808 GLU cc_start: 0.7247 (mm-30) cc_final: 0.6893 (tp30) REVERT: B 811 LYS cc_start: 0.8264 (mttm) cc_final: 0.7992 (mttp) REVERT: C 423 GLU cc_start: 0.7336 (tm-30) cc_final: 0.7011 (tm-30) REVERT: C 459 ARG cc_start: 0.7914 (ttp80) cc_final: 0.7694 (ttp80) REVERT: C 651 ASP cc_start: 0.8052 (t0) cc_final: 0.7694 (t0) REVERT: C 827 GLN cc_start: 0.7865 (pp30) cc_final: 0.7616 (pp30) REVERT: C 918 LYS cc_start: 0.7800 (mmtt) cc_final: 0.7077 (mmmt) REVERT: D 440 GLU cc_start: 0.7574 (mt-10) cc_final: 0.7357 (mt-10) REVERT: D 649 LEU cc_start: 0.8545 (tp) cc_final: 0.8291 (tp) REVERT: D 785 ARG cc_start: 0.8166 (mtp-110) cc_final: 0.7519 (mtp180) REVERT: D 808 GLU cc_start: 0.7150 (mm-30) cc_final: 0.6933 (mm-30) REVERT: D 915 GLU cc_start: 0.7702 (mt-10) cc_final: 0.7250 (mp0) REVERT: E 460 ASN cc_start: 0.7694 (m-40) cc_final: 0.7413 (m-40) REVERT: E 552 MET cc_start: 0.5362 (ppp) cc_final: 0.4988 (ptm) REVERT: E 653 MET cc_start: 0.6546 (OUTLIER) cc_final: 0.6321 (ptt) REVERT: E 684 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8534 (mp) REVERT: E 778 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.8025 (pp) REVERT: E 811 LYS cc_start: 0.7974 (mttt) cc_final: 0.7700 (mttp) REVERT: F 482 ARG cc_start: 0.8019 (tmt170) cc_final: 0.7772 (ttp80) REVERT: F 547 PHE cc_start: 0.7754 (p90) cc_final: 0.7379 (p90) REVERT: F 655 MET cc_start: 0.7059 (mmm) cc_final: 0.5237 (ptm) outliers start: 49 outliers final: 34 residues processed: 328 average time/residue: 0.4759 time to fit residues: 234.0116 Evaluate side-chains 324 residues out of total 2663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 283 time to evaluate : 2.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 754 GLU Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 771 THR Chi-restraints excluded: chain A residue 785 ARG Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain B residue 625 ASP Chi-restraints excluded: chain B residue 641 VAL Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 785 ARG Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 618 ASN Chi-restraints excluded: chain C residue 764 VAL Chi-restraints excluded: chain C residue 846 GLU Chi-restraints excluded: chain C residue 862 THR Chi-restraints excluded: chain D residue 417 ILE Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 489 GLU Chi-restraints excluded: chain D residue 611 LEU Chi-restraints excluded: chain D residue 764 VAL Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 514 THR Chi-restraints excluded: chain E residue 582 THR Chi-restraints excluded: chain E residue 618 ASN Chi-restraints excluded: chain E residue 624 LEU Chi-restraints excluded: chain E residue 653 MET Chi-restraints excluded: chain E residue 684 LEU Chi-restraints excluded: chain E residue 744 ASP Chi-restraints excluded: chain E residue 764 VAL Chi-restraints excluded: chain E residue 778 LEU Chi-restraints excluded: chain E residue 849 THR Chi-restraints excluded: chain F residue 465 LEU Chi-restraints excluded: chain F residue 566 VAL Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 752 THR Chi-restraints excluded: chain F residue 764 VAL Chi-restraints excluded: chain F residue 813 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 101 optimal weight: 2.9990 chunk 270 optimal weight: 0.9990 chunk 59 optimal weight: 9.9990 chunk 176 optimal weight: 0.7980 chunk 74 optimal weight: 0.3980 chunk 300 optimal weight: 4.9990 chunk 249 optimal weight: 0.6980 chunk 139 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 99 optimal weight: 0.7980 chunk 157 optimal weight: 5.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 805 GLN D 615 GLN ** F 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 25193 Z= 0.148 Angle : 0.483 7.777 34123 Z= 0.242 Chirality : 0.040 0.154 3909 Planarity : 0.004 0.046 4358 Dihedral : 9.214 87.924 3669 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.89 % Allowed : 12.79 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.15), residues: 3095 helix: 1.40 (0.14), residues: 1329 sheet: -0.02 (0.26), residues: 418 loop : -1.44 (0.16), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 470 HIS 0.003 0.001 HIS B 451 PHE 0.014 0.001 PHE B 504 TYR 0.012 0.001 TYR E 492 ARG 0.007 0.000 ARG E 562 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 282 time to evaluate : 2.891 Fit side-chains REVERT: A 609 GLU cc_start: 0.7410 (mt-10) cc_final: 0.6997 (mt-10) REVERT: A 918 LYS cc_start: 0.7662 (mptt) cc_final: 0.7118 (ptpt) REVERT: A 922 ASP cc_start: 0.7406 (t0) cc_final: 0.6974 (t0) REVERT: B 482 ARG cc_start: 0.7549 (tmm160) cc_final: 0.7135 (tmm160) REVERT: B 597 ARG cc_start: 0.6953 (ptp-110) cc_final: 0.6583 (ptp90) REVERT: B 625 ASP cc_start: 0.8114 (OUTLIER) cc_final: 0.7883 (t0) REVERT: B 778 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8214 (pp) REVERT: B 808 GLU cc_start: 0.7266 (mm-30) cc_final: 0.6867 (tp30) REVERT: B 811 LYS cc_start: 0.8245 (mttm) cc_final: 0.7972 (mttp) REVERT: C 423 GLU cc_start: 0.7331 (tm-30) cc_final: 0.7006 (tm-30) REVERT: C 459 ARG cc_start: 0.7909 (ttp80) cc_final: 0.7692 (ttp80) REVERT: C 651 ASP cc_start: 0.8059 (t0) cc_final: 0.7707 (t0) REVERT: C 827 GLN cc_start: 0.7803 (pp30) cc_final: 0.7547 (pp30) REVERT: C 918 LYS cc_start: 0.7783 (mmtt) cc_final: 0.7125 (mmmt) REVERT: D 482 ARG cc_start: 0.7538 (tmt170) cc_final: 0.7336 (ttt-90) REVERT: D 626 VAL cc_start: 0.8759 (OUTLIER) cc_final: 0.8547 (m) REVERT: D 649 LEU cc_start: 0.8576 (tp) cc_final: 0.8337 (tp) REVERT: D 785 ARG cc_start: 0.8144 (mtp-110) cc_final: 0.7380 (mtp180) REVERT: D 915 GLU cc_start: 0.7710 (mt-10) cc_final: 0.7241 (mp0) REVERT: E 460 ASN cc_start: 0.7622 (m-40) cc_final: 0.7322 (m-40) REVERT: E 552 MET cc_start: 0.5280 (ppp) cc_final: 0.4996 (ptm) REVERT: E 653 MET cc_start: 0.6498 (OUTLIER) cc_final: 0.6265 (ptt) REVERT: E 684 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8508 (mp) REVERT: E 778 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8051 (pp) REVERT: E 811 LYS cc_start: 0.7958 (mttt) cc_final: 0.7686 (mttp) REVERT: F 482 ARG cc_start: 0.7996 (tmt170) cc_final: 0.7726 (ttp80) REVERT: F 547 PHE cc_start: 0.7674 (p90) cc_final: 0.7335 (p90) REVERT: F 655 MET cc_start: 0.7094 (mmm) cc_final: 0.5301 (ptm) outliers start: 50 outliers final: 35 residues processed: 318 average time/residue: 0.4510 time to fit residues: 211.5465 Evaluate side-chains 318 residues out of total 2663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 277 time to evaluate : 2.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 754 GLU Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 771 THR Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain B residue 576 CYS Chi-restraints excluded: chain B residue 625 ASP Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 785 ARG Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 618 ASN Chi-restraints excluded: chain C residue 764 VAL Chi-restraints excluded: chain C residue 846 GLU Chi-restraints excluded: chain C residue 862 THR Chi-restraints excluded: chain D residue 417 ILE Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 566 VAL Chi-restraints excluded: chain D residue 611 LEU Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 764 VAL Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 582 THR Chi-restraints excluded: chain E residue 618 ASN Chi-restraints excluded: chain E residue 624 LEU Chi-restraints excluded: chain E residue 653 MET Chi-restraints excluded: chain E residue 684 LEU Chi-restraints excluded: chain E residue 735 VAL Chi-restraints excluded: chain E residue 744 ASP Chi-restraints excluded: chain E residue 764 VAL Chi-restraints excluded: chain E residue 778 LEU Chi-restraints excluded: chain E residue 849 THR Chi-restraints excluded: chain F residue 465 LEU Chi-restraints excluded: chain F residue 473 TYR Chi-restraints excluded: chain F residue 752 THR Chi-restraints excluded: chain F residue 764 VAL Chi-restraints excluded: chain F residue 771 THR Chi-restraints excluded: chain F residue 778 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 290 optimal weight: 0.0670 chunk 33 optimal weight: 9.9990 chunk 171 optimal weight: 0.7980 chunk 219 optimal weight: 5.9990 chunk 170 optimal weight: 1.9990 chunk 253 optimal weight: 1.9990 chunk 168 optimal weight: 6.9990 chunk 299 optimal weight: 5.9990 chunk 187 optimal weight: 5.9990 chunk 182 optimal weight: 6.9990 chunk 138 optimal weight: 5.9990 overall best weight: 2.1724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 615 GLN ** F 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 25193 Z= 0.304 Angle : 0.568 8.566 34123 Z= 0.285 Chirality : 0.043 0.156 3909 Planarity : 0.004 0.048 4358 Dihedral : 9.905 89.695 3669 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.15 % Allowed : 13.09 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.15), residues: 3095 helix: 1.15 (0.14), residues: 1330 sheet: -0.17 (0.27), residues: 409 loop : -1.52 (0.16), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 770 HIS 0.006 0.001 HIS E 843 PHE 0.023 0.002 PHE B 820 TYR 0.023 0.002 TYR F 939 ARG 0.007 0.001 ARG E 562 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 290 time to evaluate : 3.046 Fit side-chains REVERT: A 918 LYS cc_start: 0.7777 (mptt) cc_final: 0.7260 (ptpt) REVERT: A 922 ASP cc_start: 0.7567 (t0) cc_final: 0.7196 (t0) REVERT: B 423 GLU cc_start: 0.7780 (tp30) cc_final: 0.7578 (tp30) REVERT: B 597 ARG cc_start: 0.7014 (ptp-110) cc_final: 0.6642 (ptp90) REVERT: B 625 ASP cc_start: 0.8168 (OUTLIER) cc_final: 0.7909 (t0) REVERT: B 778 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8199 (pp) REVERT: B 808 GLU cc_start: 0.7411 (mm-30) cc_final: 0.6952 (tp30) REVERT: B 811 LYS cc_start: 0.8207 (mttm) cc_final: 0.7940 (mttp) REVERT: C 423 GLU cc_start: 0.7282 (tm-30) cc_final: 0.6969 (tm-30) REVERT: C 918 LYS cc_start: 0.7828 (mmtt) cc_final: 0.7160 (mmmt) REVERT: D 655 MET cc_start: 0.8473 (mmt) cc_final: 0.8181 (mmt) REVERT: D 770 TRP cc_start: 0.7388 (OUTLIER) cc_final: 0.6382 (p90) REVERT: D 915 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7385 (mp0) REVERT: E 460 ASN cc_start: 0.7739 (m-40) cc_final: 0.7455 (m-40) REVERT: E 552 MET cc_start: 0.5107 (ppp) cc_final: 0.4864 (ptm) REVERT: E 653 MET cc_start: 0.6460 (OUTLIER) cc_final: 0.6215 (ptt) REVERT: E 811 LYS cc_start: 0.7960 (mttt) cc_final: 0.7752 (mttp) REVERT: E 918 LYS cc_start: 0.8088 (ptpt) cc_final: 0.7558 (tmtt) REVERT: F 482 ARG cc_start: 0.8059 (tmt170) cc_final: 0.7807 (ttp80) REVERT: F 547 PHE cc_start: 0.7693 (p90) cc_final: 0.7301 (p90) REVERT: F 655 MET cc_start: 0.7001 (mmm) cc_final: 0.5095 (ptm) outliers start: 57 outliers final: 44 residues processed: 330 average time/residue: 0.4354 time to fit residues: 212.9438 Evaluate side-chains 327 residues out of total 2663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 279 time to evaluate : 2.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 754 GLU Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 771 THR Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain B residue 576 CYS Chi-restraints excluded: chain B residue 625 ASP Chi-restraints excluded: chain B residue 641 VAL Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 785 ARG Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 618 ASN Chi-restraints excluded: chain C residue 764 VAL Chi-restraints excluded: chain C residue 846 GLU Chi-restraints excluded: chain C residue 862 THR Chi-restraints excluded: chain D residue 417 ILE Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 489 GLU Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 566 VAL Chi-restraints excluded: chain D residue 611 LEU Chi-restraints excluded: chain D residue 744 ASP Chi-restraints excluded: chain D residue 764 VAL Chi-restraints excluded: chain D residue 770 TRP Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 582 THR Chi-restraints excluded: chain E residue 618 ASN Chi-restraints excluded: chain E residue 624 LEU Chi-restraints excluded: chain E residue 641 VAL Chi-restraints excluded: chain E residue 653 MET Chi-restraints excluded: chain E residue 735 VAL Chi-restraints excluded: chain E residue 744 ASP Chi-restraints excluded: chain E residue 764 VAL Chi-restraints excluded: chain E residue 778 LEU Chi-restraints excluded: chain E residue 849 THR Chi-restraints excluded: chain F residue 430 VAL Chi-restraints excluded: chain F residue 465 LEU Chi-restraints excluded: chain F residue 473 TYR Chi-restraints excluded: chain F residue 566 VAL Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 752 THR Chi-restraints excluded: chain F residue 764 VAL Chi-restraints excluded: chain F residue 778 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 185 optimal weight: 4.9990 chunk 119 optimal weight: 1.9990 chunk 179 optimal weight: 0.9990 chunk 90 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 190 optimal weight: 0.9990 chunk 204 optimal weight: 0.7980 chunk 148 optimal weight: 0.6980 chunk 27 optimal weight: 7.9990 chunk 235 optimal weight: 4.9990 chunk 272 optimal weight: 3.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 805 GLN F 433 HIS ** F 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25193 Z= 0.187 Angle : 0.516 8.673 34123 Z= 0.259 Chirality : 0.041 0.148 3909 Planarity : 0.004 0.048 4358 Dihedral : 9.535 89.662 3669 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.96 % Allowed : 13.40 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.15), residues: 3095 helix: 1.31 (0.14), residues: 1328 sheet: -0.14 (0.27), residues: 410 loop : -1.40 (0.16), residues: 1357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 470 HIS 0.003 0.001 HIS E 843 PHE 0.019 0.001 PHE F 545 TYR 0.014 0.001 TYR F 939 ARG 0.006 0.000 ARG E 562 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 280 time to evaluate : 2.962 Fit side-chains REVERT: A 456 ASN cc_start: 0.7985 (m-40) cc_final: 0.7763 (m-40) REVERT: A 609 GLU cc_start: 0.7461 (mt-10) cc_final: 0.7052 (mt-10) REVERT: A 918 LYS cc_start: 0.7765 (mptt) cc_final: 0.7257 (ptpt) REVERT: A 922 ASP cc_start: 0.7591 (t0) cc_final: 0.7229 (t0) REVERT: B 597 ARG cc_start: 0.6985 (ptp-110) cc_final: 0.6607 (ptp90) REVERT: B 625 ASP cc_start: 0.8164 (OUTLIER) cc_final: 0.7910 (t0) REVERT: B 778 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8181 (pp) REVERT: C 423 GLU cc_start: 0.7369 (tm-30) cc_final: 0.7044 (tm-30) REVERT: C 918 LYS cc_start: 0.7764 (mmtt) cc_final: 0.7141 (mmmt) REVERT: D 655 MET cc_start: 0.8502 (mmt) cc_final: 0.8178 (mmt) REVERT: D 770 TRP cc_start: 0.7356 (OUTLIER) cc_final: 0.6322 (p90) REVERT: D 785 ARG cc_start: 0.8106 (mtp-110) cc_final: 0.7397 (mtp180) REVERT: D 915 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7395 (mp0) REVERT: E 652 ARG cc_start: 0.5147 (mpt90) cc_final: 0.4750 (mmp-170) REVERT: E 653 MET cc_start: 0.6430 (OUTLIER) cc_final: 0.6184 (ptt) REVERT: E 684 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8494 (mp) REVERT: E 778 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.8067 (pp) REVERT: E 811 LYS cc_start: 0.7939 (mttt) cc_final: 0.7668 (mttp) REVERT: E 918 LYS cc_start: 0.8062 (ptpt) cc_final: 0.7504 (tmtt) REVERT: F 482 ARG cc_start: 0.8016 (tmt170) cc_final: 0.7787 (ttp80) REVERT: F 655 MET cc_start: 0.6977 (mmm) cc_final: 0.5160 (ptm) REVERT: F 662 VAL cc_start: 0.8215 (m) cc_final: 0.7827 (p) outliers start: 52 outliers final: 43 residues processed: 319 average time/residue: 0.4353 time to fit residues: 206.1988 Evaluate side-chains 321 residues out of total 2663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 272 time to evaluate : 2.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 754 GLU Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 771 THR Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain B residue 576 CYS Chi-restraints excluded: chain B residue 625 ASP Chi-restraints excluded: chain B residue 641 VAL Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 785 ARG Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 618 ASN Chi-restraints excluded: chain C residue 764 VAL Chi-restraints excluded: chain C residue 846 GLU Chi-restraints excluded: chain C residue 849 THR Chi-restraints excluded: chain C residue 862 THR Chi-restraints excluded: chain D residue 417 ILE Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 566 VAL Chi-restraints excluded: chain D residue 611 LEU Chi-restraints excluded: chain D residue 744 ASP Chi-restraints excluded: chain D residue 764 VAL Chi-restraints excluded: chain D residue 770 TRP Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 582 THR Chi-restraints excluded: chain E residue 618 ASN Chi-restraints excluded: chain E residue 624 LEU Chi-restraints excluded: chain E residue 641 VAL Chi-restraints excluded: chain E residue 653 MET Chi-restraints excluded: chain E residue 684 LEU Chi-restraints excluded: chain E residue 735 VAL Chi-restraints excluded: chain E residue 744 ASP Chi-restraints excluded: chain E residue 764 VAL Chi-restraints excluded: chain E residue 778 LEU Chi-restraints excluded: chain E residue 849 THR Chi-restraints excluded: chain F residue 465 LEU Chi-restraints excluded: chain F residue 473 TYR Chi-restraints excluded: chain F residue 566 VAL Chi-restraints excluded: chain F residue 752 THR Chi-restraints excluded: chain F residue 764 VAL Chi-restraints excluded: chain F residue 771 THR Chi-restraints excluded: chain F residue 778 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 287 optimal weight: 1.9990 chunk 262 optimal weight: 0.3980 chunk 279 optimal weight: 0.6980 chunk 168 optimal weight: 5.9990 chunk 121 optimal weight: 0.8980 chunk 219 optimal weight: 6.9990 chunk 85 optimal weight: 9.9990 chunk 252 optimal weight: 0.9980 chunk 264 optimal weight: 9.9990 chunk 278 optimal weight: 0.5980 chunk 183 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 615 GLN F 433 HIS ** F 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 25193 Z= 0.149 Angle : 0.493 9.377 34123 Z= 0.246 Chirality : 0.040 0.149 3909 Planarity : 0.004 0.047 4358 Dihedral : 9.142 88.773 3669 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 1.96 % Allowed : 13.51 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.15), residues: 3095 helix: 1.50 (0.14), residues: 1329 sheet: -0.01 (0.26), residues: 418 loop : -1.28 (0.16), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 770 HIS 0.003 0.001 HIS E 843 PHE 0.019 0.001 PHE F 545 TYR 0.011 0.001 TYR F 939 ARG 0.007 0.000 ARG E 562 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 279 time to evaluate : 3.114 Fit side-chains REVERT: A 609 GLU cc_start: 0.7461 (mt-10) cc_final: 0.7044 (mt-10) REVERT: A 918 LYS cc_start: 0.7749 (mptt) cc_final: 0.7288 (ptpt) REVERT: B 597 ARG cc_start: 0.6841 (ptp-110) cc_final: 0.6462 (ptp90) REVERT: B 625 ASP cc_start: 0.8157 (OUTLIER) cc_final: 0.7878 (t0) REVERT: B 778 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8180 (pp) REVERT: C 423 GLU cc_start: 0.7332 (tm-30) cc_final: 0.7002 (tm-30) REVERT: C 918 LYS cc_start: 0.7728 (mmtt) cc_final: 0.7154 (mmmt) REVERT: D 626 VAL cc_start: 0.8833 (OUTLIER) cc_final: 0.8627 (m) REVERT: D 649 LEU cc_start: 0.8595 (tp) cc_final: 0.8381 (tp) REVERT: D 655 MET cc_start: 0.8515 (mmt) cc_final: 0.8149 (mmt) REVERT: D 770 TRP cc_start: 0.7347 (OUTLIER) cc_final: 0.6364 (p90) REVERT: D 785 ARG cc_start: 0.8093 (mtp-110) cc_final: 0.7381 (mtp180) REVERT: D 915 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7246 (mp0) REVERT: E 653 MET cc_start: 0.6552 (OUTLIER) cc_final: 0.6268 (ptt) REVERT: E 684 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8485 (mp) REVERT: E 778 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8068 (pp) REVERT: E 811 LYS cc_start: 0.7924 (mttt) cc_final: 0.7651 (mttp) REVERT: E 918 LYS cc_start: 0.8020 (ptpt) cc_final: 0.7453 (tmtt) REVERT: F 482 ARG cc_start: 0.7971 (tmt170) cc_final: 0.7720 (ttp80) REVERT: F 547 PHE cc_start: 0.7609 (p90) cc_final: 0.7339 (p90) REVERT: F 655 MET cc_start: 0.6970 (mmm) cc_final: 0.5138 (ptm) REVERT: F 662 VAL cc_start: 0.8112 (m) cc_final: 0.7726 (p) outliers start: 52 outliers final: 42 residues processed: 316 average time/residue: 0.4232 time to fit residues: 198.7236 Evaluate side-chains 320 residues out of total 2663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 271 time to evaluate : 2.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 754 GLU Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 771 THR Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain B residue 576 CYS Chi-restraints excluded: chain B residue 625 ASP Chi-restraints excluded: chain B residue 641 VAL Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 785 ARG Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 618 ASN Chi-restraints excluded: chain C residue 764 VAL Chi-restraints excluded: chain C residue 778 LEU Chi-restraints excluded: chain C residue 846 GLU Chi-restraints excluded: chain C residue 849 THR Chi-restraints excluded: chain C residue 862 THR Chi-restraints excluded: chain D residue 417 ILE Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 489 GLU Chi-restraints excluded: chain D residue 566 VAL Chi-restraints excluded: chain D residue 611 LEU Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 764 VAL Chi-restraints excluded: chain D residue 770 TRP Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 582 THR Chi-restraints excluded: chain E residue 624 LEU Chi-restraints excluded: chain E residue 641 VAL Chi-restraints excluded: chain E residue 653 MET Chi-restraints excluded: chain E residue 684 LEU Chi-restraints excluded: chain E residue 735 VAL Chi-restraints excluded: chain E residue 744 ASP Chi-restraints excluded: chain E residue 764 VAL Chi-restraints excluded: chain E residue 778 LEU Chi-restraints excluded: chain E residue 849 THR Chi-restraints excluded: chain F residue 430 VAL Chi-restraints excluded: chain F residue 465 LEU Chi-restraints excluded: chain F residue 473 TYR Chi-restraints excluded: chain F residue 566 VAL Chi-restraints excluded: chain F residue 752 THR Chi-restraints excluded: chain F residue 764 VAL Chi-restraints excluded: chain F residue 771 THR Chi-restraints excluded: chain F residue 778 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 295 optimal weight: 5.9990 chunk 180 optimal weight: 0.9980 chunk 140 optimal weight: 2.9990 chunk 205 optimal weight: 1.9990 chunk 309 optimal weight: 1.9990 chunk 285 optimal weight: 4.9990 chunk 246 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 190 optimal weight: 0.9990 chunk 151 optimal weight: 0.9990 chunk 195 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 615 GLN F 433 HIS ** F 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 743 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 25193 Z= 0.221 Angle : 0.528 9.647 34123 Z= 0.265 Chirality : 0.041 0.146 3909 Planarity : 0.004 0.047 4358 Dihedral : 9.411 89.021 3669 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.00 % Allowed : 13.70 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.15), residues: 3095 helix: 1.40 (0.14), residues: 1328 sheet: -0.00 (0.26), residues: 418 loop : -1.31 (0.16), residues: 1349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 770 HIS 0.004 0.001 HIS E 843 PHE 0.020 0.002 PHE F 545 TYR 0.017 0.002 TYR A 939 ARG 0.007 0.000 ARG E 562 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 276 time to evaluate : 2.885 Fit side-chains REVERT: A 609 GLU cc_start: 0.7461 (mt-10) cc_final: 0.7059 (mt-10) REVERT: A 849 THR cc_start: 0.8559 (OUTLIER) cc_final: 0.8345 (t) REVERT: A 918 LYS cc_start: 0.7843 (mptt) cc_final: 0.7249 (ptpt) REVERT: A 922 ASP cc_start: 0.7946 (m-30) cc_final: 0.7656 (m-30) REVERT: B 597 ARG cc_start: 0.6874 (ptp-110) cc_final: 0.6482 (ptp90) REVERT: B 625 ASP cc_start: 0.8167 (OUTLIER) cc_final: 0.7904 (t0) REVERT: B 778 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8178 (pp) REVERT: C 423 GLU cc_start: 0.7343 (tm-30) cc_final: 0.7011 (tm-30) REVERT: C 651 ASP cc_start: 0.7996 (t0) cc_final: 0.7733 (t70) REVERT: C 918 LYS cc_start: 0.7729 (mmtt) cc_final: 0.7308 (mmtp) REVERT: D 626 VAL cc_start: 0.8917 (OUTLIER) cc_final: 0.8712 (m) REVERT: D 649 LEU cc_start: 0.8618 (tp) cc_final: 0.8397 (tp) REVERT: D 655 MET cc_start: 0.8509 (mmt) cc_final: 0.8187 (mmt) REVERT: D 770 TRP cc_start: 0.7366 (OUTLIER) cc_final: 0.6392 (p90) REVERT: D 785 ARG cc_start: 0.8125 (mtp-110) cc_final: 0.7390 (mtp180) REVERT: D 915 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7444 (mp0) REVERT: E 653 MET cc_start: 0.6603 (OUTLIER) cc_final: 0.6309 (ptt) REVERT: E 684 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8493 (mp) REVERT: E 778 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8004 (pp) REVERT: E 811 LYS cc_start: 0.7939 (mttt) cc_final: 0.7727 (mttp) REVERT: E 918 LYS cc_start: 0.8055 (ptpt) cc_final: 0.7506 (tmtt) REVERT: F 482 ARG cc_start: 0.7980 (tmt170) cc_final: 0.7720 (ttp80) REVERT: F 547 PHE cc_start: 0.7546 (p90) cc_final: 0.7289 (p90) REVERT: F 655 MET cc_start: 0.7047 (mmm) cc_final: 0.5157 (ptm) REVERT: F 662 VAL cc_start: 0.8182 (m) cc_final: 0.7792 (p) outliers start: 53 outliers final: 43 residues processed: 316 average time/residue: 0.4393 time to fit residues: 208.8582 Evaluate side-chains 327 residues out of total 2663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 276 time to evaluate : 3.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 754 GLU Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 771 THR Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain B residue 576 CYS Chi-restraints excluded: chain B residue 625 ASP Chi-restraints excluded: chain B residue 641 VAL Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 785 ARG Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 618 ASN Chi-restraints excluded: chain C residue 764 VAL Chi-restraints excluded: chain C residue 778 LEU Chi-restraints excluded: chain C residue 846 GLU Chi-restraints excluded: chain C residue 849 THR Chi-restraints excluded: chain C residue 862 THR Chi-restraints excluded: chain D residue 417 ILE Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 489 GLU Chi-restraints excluded: chain D residue 566 VAL Chi-restraints excluded: chain D residue 611 LEU Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 744 ASP Chi-restraints excluded: chain D residue 764 VAL Chi-restraints excluded: chain D residue 770 TRP Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 582 THR Chi-restraints excluded: chain E residue 624 LEU Chi-restraints excluded: chain E residue 641 VAL Chi-restraints excluded: chain E residue 653 MET Chi-restraints excluded: chain E residue 684 LEU Chi-restraints excluded: chain E residue 735 VAL Chi-restraints excluded: chain E residue 744 ASP Chi-restraints excluded: chain E residue 764 VAL Chi-restraints excluded: chain E residue 778 LEU Chi-restraints excluded: chain E residue 849 THR Chi-restraints excluded: chain F residue 430 VAL Chi-restraints excluded: chain F residue 465 LEU Chi-restraints excluded: chain F residue 566 VAL Chi-restraints excluded: chain F residue 752 THR Chi-restraints excluded: chain F residue 764 VAL Chi-restraints excluded: chain F residue 771 THR Chi-restraints excluded: chain F residue 778 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 262 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 chunk 227 optimal weight: 10.0000 chunk 36 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 247 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 253 optimal weight: 0.4980 chunk 31 optimal weight: 0.6980 chunk 45 optimal weight: 0.0670 chunk 216 optimal weight: 3.9990 overall best weight: 1.0320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 615 GLN F 433 HIS ** F 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.137063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.116873 restraints weight = 33543.965| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.01 r_work: 0.3147 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 25193 Z= 0.180 Angle : 0.508 9.600 34123 Z= 0.254 Chirality : 0.041 0.147 3909 Planarity : 0.004 0.047 4358 Dihedral : 9.259 89.525 3669 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.92 % Allowed : 13.77 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.15), residues: 3095 helix: 1.48 (0.14), residues: 1329 sheet: -0.04 (0.26), residues: 422 loop : -1.26 (0.16), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 770 HIS 0.003 0.001 HIS E 843 PHE 0.025 0.001 PHE C 545 TYR 0.014 0.001 TYR F 939 ARG 0.007 0.000 ARG E 562 =============================================================================== Job complete usr+sys time: 5268.25 seconds wall clock time: 97 minutes 1.33 seconds (5821.33 seconds total)