Starting phenix.real_space_refine on Sat Feb 17 19:29:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oem_20030/02_2024/6oem_20030.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oem_20030/02_2024/6oem_20030.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oem_20030/02_2024/6oem_20030.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oem_20030/02_2024/6oem_20030.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oem_20030/02_2024/6oem_20030.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oem_20030/02_2024/6oem_20030.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.004 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 Zn 2 6.06 5 P 204 5.49 5 Mg 2 5.21 5 S 106 5.16 5 C 11819 2.51 5 N 3476 2.21 5 O 4098 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 407": "NH1" <-> "NH2" Residue "A ARG 442": "NH1" <-> "NH2" Residue "A ARG 471": "NH1" <-> "NH2" Residue "A GLU 607": "OE1" <-> "OE2" Residue "A ARG 773": "NH1" <-> "NH2" Residue "A ARG 775": "NH1" <-> "NH2" Residue "A ARG 826": "NH1" <-> "NH2" Residue "A ARG 880": "NH1" <-> "NH2" Residue "A ARG 894": "NH1" <-> "NH2" Residue "A ARG 915": "NH1" <-> "NH2" Residue "A GLU 983": "OE1" <-> "OE2" Residue "C ARG 401": "NH1" <-> "NH2" Residue "C ARG 409": "NH1" <-> "NH2" Residue "C ARG 773": "NH1" <-> "NH2" Residue "C ARG 826": "NH1" <-> "NH2" Residue "C ARG 838": "NH1" <-> "NH2" Residue "C ARG 915": "NH1" <-> "NH2" Residue "C ARG 927": "NH1" <-> "NH2" Residue "C ARG 970": "NH1" <-> "NH2" Residue "B ARG 123": "NH1" <-> "NH2" Residue "B ARG 148": "NH1" <-> "NH2" Residue "B ARG 237": "NH1" <-> "NH2" Residue "B ARG 284": "NH1" <-> "NH2" Residue "B ARG 349": "NH1" <-> "NH2" Residue "D PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 123": "NH1" <-> "NH2" Residue "D ARG 148": "NH1" <-> "NH2" Residue "D ARG 237": "NH1" <-> "NH2" Residue "D ARG 284": "NH1" <-> "NH2" Residue "D ARG 349": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 19707 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4774 Classifications: {'peptide': 606} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 580} Chain breaks: 1 Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 90 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 7, 'ARG:plan': 4, 'ASN:plan1': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 69 Chain: "C" Number of atoms: 4843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 611, 4843 Classifications: {'peptide': 611} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 585} Chain breaks: 1 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 68 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 51 Chain: "B" Number of atoms: 2668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2668 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 19, 'TRANS': 326} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "D" Number of atoms: 2671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2671 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 19, 'TRANS': 326} Chain breaks: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "G" Number of atoms: 1163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 1163 Classifications: {'DNA': 57} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 56} Chain: "I" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 936 Classifications: {'DNA': 46} Link IDs: {'rna3p': 45} Chain: "F" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 947 Classifications: {'DNA': 46} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 45} Chain: "J" Number of atoms: 1171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 1171 Classifications: {'DNA': 57} Link IDs: {'rna3p': 56} Chain: "N" Number of atoms: 242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 242 Classifications: {'peptide': 36} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 2, 'TRANS': 33} Chain breaks: 1 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "H" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 288 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 3, 'TRANS': 51} Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 203 Unresolved non-hydrogen dihedrals: 149 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 3, 'TYR:plan': 3, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 97 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2544 SG CYS A 727 88.110 24.912 57.634 1.00 91.74 S ATOM 2565 SG CYS A 730 88.645 22.480 57.782 1.00 90.71 S ATOM 7353 SG CYS C 727 61.828 106.636 58.091 1.00 82.68 S ATOM 7374 SG CYS C 730 61.375 108.925 56.753 1.00 82.68 S Time building chain proxies: 10.59, per 1000 atoms: 0.54 Number of scatterers: 19707 At special positions: 0 Unit cell: (150.87, 132.68, 157.29, 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) Zn 2 29.99 S 106 16.00 P 204 15.00 Mg 2 11.99 O 4098 8.00 N 3476 7.00 C 11819 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.72 Conformation dependent library (CDL) restraints added in 2.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1102 " pdb="ZN ZN A1102 " - pdb=" NE2 HIS A 937 " pdb="ZN ZN A1102 " - pdb=" SG CYS A 727 " pdb="ZN ZN A1102 " - pdb=" NE2 HIS A 942 " pdb="ZN ZN A1102 " - pdb=" SG CYS A 730 " pdb=" ZN C1102 " pdb="ZN ZN C1102 " - pdb=" NE2 HIS C 937 " pdb="ZN ZN C1102 " - pdb=" SG CYS C 727 " pdb="ZN ZN C1102 " - pdb=" NE2 HIS C 942 " pdb="ZN ZN C1102 " - pdb=" SG CYS C 730 " Number of angles added : 4 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3738 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 22 sheets defined 39.2% alpha, 19.2% beta 102 base pairs and 164 stacking pairs defined. Time for finding SS restraints: 7.49 Creating SS restraints... Processing helix chain 'A' and resid 400 through 423 removed outlier: 5.608A pdb=" N GLU A 410 " --> pdb=" O HIS A 406 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N LEU A 411 " --> pdb=" O ARG A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 442 Processing helix chain 'A' and resid 444 through 457 removed outlier: 3.501A pdb=" N ALA A 448 " --> pdb=" O GLU A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 474 Processing helix chain 'A' and resid 478 through 493 Processing helix chain 'A' and resid 499 through 511 Processing helix chain 'A' and resid 558 through 570 Processing helix chain 'A' and resid 570 through 581 Processing helix chain 'A' and resid 664 through 683 Proline residue: A 674 - end of helix Processing helix chain 'A' and resid 708 through 716 Processing helix chain 'A' and resid 733 through 740 Processing helix chain 'A' and resid 749 through 763 removed outlier: 3.712A pdb=" N ASN A 753 " --> pdb=" O SER A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 777 Processing helix chain 'A' and resid 792 through 812 removed outlier: 3.804A pdb=" N ASN A 800 " --> pdb=" O CYS A 796 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU A 803 " --> pdb=" O GLY A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 841 Processing helix chain 'A' and resid 850 through 858 removed outlier: 3.647A pdb=" N ALA A 854 " --> pdb=" O ASN A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 859 through 868 removed outlier: 3.586A pdb=" N VAL A 863 " --> pdb=" O THR A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 874 through 894 removed outlier: 4.075A pdb=" N ALA A 878 " --> pdb=" O GLU A 874 " (cutoff:3.500A) Proline residue: A 891 - end of helix Processing helix chain 'A' and resid 902 through 907 removed outlier: 3.556A pdb=" N LEU A 906 " --> pdb=" O CYS A 902 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 923 removed outlier: 3.547A pdb=" N LEU A 920 " --> pdb=" O PHE A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 941 Processing helix chain 'A' and resid 942 through 950 removed outlier: 3.569A pdb=" N ILE A 946 " --> pdb=" O HIS A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 975 Processing helix chain 'A' and resid 981 through 995 removed outlier: 4.274A pdb=" N GLU A 985 " --> pdb=" O CYS A 981 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR A 995 " --> pdb=" O HIS A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 996 through 1004 Processing helix chain 'A' and resid 1005 through 1007 No H-bonds generated for 'chain 'A' and resid 1005 through 1007' Processing helix chain 'C' and resid 395 through 399 Processing helix chain 'C' and resid 400 through 423 removed outlier: 5.733A pdb=" N GLU C 410 " --> pdb=" O HIS C 406 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N LEU C 411 " --> pdb=" O ARG C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 441 Processing helix chain 'C' and resid 444 through 457 Processing helix chain 'C' and resid 463 through 474 Processing helix chain 'C' and resid 477 through 493 Processing helix chain 'C' and resid 499 through 509 Processing helix chain 'C' and resid 558 through 570 Processing helix chain 'C' and resid 570 through 581 Processing helix chain 'C' and resid 664 through 683 removed outlier: 3.503A pdb=" N LEU C 668 " --> pdb=" O ASP C 664 " (cutoff:3.500A) Proline residue: C 674 - end of helix Processing helix chain 'C' and resid 708 through 713 Processing helix chain 'C' and resid 733 through 740 removed outlier: 3.772A pdb=" N GLN C 739 " --> pdb=" O LEU C 735 " (cutoff:3.500A) Processing helix chain 'C' and resid 749 through 763 Processing helix chain 'C' and resid 768 through 776 Processing helix chain 'C' and resid 792 through 813 removed outlier: 3.744A pdb=" N CYS C 796 " --> pdb=" O ASP C 792 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS C 806 " --> pdb=" O ALA C 802 " (cutoff:3.500A) Processing helix chain 'C' and resid 822 through 841 Processing helix chain 'C' and resid 850 through 858 Processing helix chain 'C' and resid 859 through 868 Processing helix chain 'C' and resid 872 through 894 removed outlier: 3.965A pdb=" N HIS C 876 " --> pdb=" O SER C 872 " (cutoff:3.500A) Proline residue: C 891 - end of helix Processing helix chain 'C' and resid 902 through 907 Processing helix chain 'C' and resid 908 through 923 Processing helix chain 'C' and resid 933 through 941 Processing helix chain 'C' and resid 942 through 950 Processing helix chain 'C' and resid 963 through 974 removed outlier: 3.894A pdb=" N LEU C 967 " --> pdb=" O SER C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 981 through 995 removed outlier: 4.158A pdb=" N GLU C 985 " --> pdb=" O CYS C 981 " (cutoff:3.500A) Processing helix chain 'C' and resid 996 through 1004 Processing helix chain 'C' and resid 1005 through 1008 removed outlier: 3.583A pdb=" N ALA C1008 " --> pdb=" O ALA C1005 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1005 through 1008' Processing helix chain 'B' and resid 308 through 314 Processing helix chain 'D' and resid 308 through 314 Processing helix chain 'N' and resid 100 through 117 Proline residue: N 111 - end of helix Processing helix chain 'N' and resid 123 through 136 Processing helix chain 'H' and resid 102 through 117 Proline residue: H 111 - end of helix Processing helix chain 'H' and resid 121 through 136 Processing helix chain 'H' and resid 137 through 140 Processing helix chain 'H' and resid 141 through 155 Processing sheet with id=AA1, first strand: chain 'A' and resid 518 through 519 removed outlier: 6.124A pdb=" N PHE A 591 " --> pdb=" O LYS A 699 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ILE A 701 " --> pdb=" O PHE A 591 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N VAL A 593 " --> pdb=" O ILE A 701 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N ARG A 703 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL A 595 " --> pdb=" O ARG A 703 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N THR A 705 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N GLU A 597 " --> pdb=" O THR A 705 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N THR A 592 " --> pdb=" O ILE A 629 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ILE A 629 " --> pdb=" O THR A 592 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL A 594 " --> pdb=" O MET A 627 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG A 621 " --> pdb=" O ASP A 600 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ALA A 619 " --> pdb=" O MET A 602 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL A 620 " --> pdb=" O LEU A 657 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N LEU A 657 " --> pdb=" O VAL A 620 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N PHE A 622 " --> pdb=" O LEU A 655 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 518 through 519 removed outlier: 6.124A pdb=" N PHE A 591 " --> pdb=" O LYS A 699 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ILE A 701 " --> pdb=" O PHE A 591 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N VAL A 593 " --> pdb=" O ILE A 701 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N ARG A 703 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL A 595 " --> pdb=" O ARG A 703 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N THR A 705 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N GLU A 597 " --> pdb=" O THR A 705 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N THR A 592 " --> pdb=" O ILE A 629 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ILE A 629 " --> pdb=" O THR A 592 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL A 594 " --> pdb=" O MET A 627 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG A 621 " --> pdb=" O ASP A 600 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ALA A 619 " --> pdb=" O MET A 602 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ILE A 631 " --> pdb=" O LYS A 639 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N LYS A 639 " --> pdb=" O ILE A 631 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 518 through 519 removed outlier: 9.880A pdb=" N PHE C 591 " --> pdb=" O PHE C 700 " (cutoff:3.500A) removed outlier: 10.573A pdb=" N PHE C 702 " --> pdb=" O PHE C 591 " (cutoff:3.500A) removed outlier: 10.517A pdb=" N VAL C 593 " --> pdb=" O PHE C 702 " (cutoff:3.500A) removed outlier: 10.916A pdb=" N GLY C 704 " --> pdb=" O VAL C 593 " (cutoff:3.500A) removed outlier: 11.092A pdb=" N VAL C 595 " --> pdb=" O GLY C 704 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N GLY C 706 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLU C 597 " --> pdb=" O GLY C 706 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N THR C 592 " --> pdb=" O ILE C 629 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ILE C 629 " --> pdb=" O THR C 592 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL C 594 " --> pdb=" O MET C 627 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N ALA C 619 " --> pdb=" O MET C 602 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 535 through 536 removed outlier: 6.666A pdb=" N PHE C 622 " --> pdb=" O LEU C 655 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N LEU C 657 " --> pdb=" O VAL C 620 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N VAL C 620 " --> pdb=" O LEU C 657 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ILE C 631 " --> pdb=" O LYS C 639 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N LYS C 639 " --> pdb=" O ILE C 631 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N HIS C 633 " --> pdb=" O ASN C 637 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ASN C 637 " --> pdb=" O HIS C 633 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 3 through 5 removed outlier: 3.505A pdb=" N PHE B 318 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 20 through 24 removed outlier: 3.819A pdb=" N LYS B 58 " --> pdb=" O HIS B 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 50 through 51 Processing sheet with id=AA8, first strand: chain 'B' and resid 75 through 80 removed outlier: 3.595A pdb=" N CYS B 78 " --> pdb=" O ILE B 92 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE B 92 " --> pdb=" O CYS B 78 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE B 107 " --> pdb=" O LYS B 127 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 112 through 116 removed outlier: 7.031A pdb=" N THR B 121 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N LYS B 115 " --> pdb=" O LYS B 119 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N LYS B 119 " --> pdb=" O LYS B 115 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 130 through 131 removed outlier: 6.630A pdb=" N VAL B 130 " --> pdb=" O ALA B 192 " (cutoff:3.500A) removed outlier: 8.489A pdb=" N SER B 194 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER B 141 " --> pdb=" O PHE B 156 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 159 through 161 Processing sheet with id=AB3, first strand: chain 'B' and resid 208 through 211 removed outlier: 3.617A pdb=" N LEU B 233 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU B 252 " --> pdb=" O LEU B 233 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 263 through 267 removed outlier: 3.713A pdb=" N THR B 264 " --> pdb=" O VAL B 272 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N GLU B 270 " --> pdb=" O THR B 266 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 3 through 5 Processing sheet with id=AB6, first strand: chain 'D' and resid 20 through 24 removed outlier: 3.789A pdb=" N LYS D 58 " --> pdb=" O HIS D 47 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 50 through 51 Processing sheet with id=AB8, first strand: chain 'D' and resid 75 through 80 Processing sheet with id=AB9, first strand: chain 'D' and resid 112 through 116 removed outlier: 6.784A pdb=" N THR D 121 " --> pdb=" O ALA D 113 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LYS D 115 " --> pdb=" O LYS D 119 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N LYS D 119 " --> pdb=" O LYS D 115 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 130 through 131 removed outlier: 6.048A pdb=" N VAL D 130 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N SER D 194 " --> pdb=" O VAL D 130 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER D 141 " --> pdb=" O PHE D 156 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 159 through 161 Processing sheet with id=AC3, first strand: chain 'D' and resid 208 through 211 removed outlier: 3.813A pdb=" N LEU D 233 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU D 252 " --> pdb=" O LEU D 233 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 263 through 267 removed outlier: 3.780A pdb=" N THR D 264 " --> pdb=" O VAL D 272 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N GLU D 270 " --> pdb=" O THR D 266 " (cutoff:3.500A) 715 hydrogen bonds defined for protein. 2028 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 253 hydrogen bonds 506 hydrogen bond angles 0 basepair planarities 102 basepair parallelities 164 stacking parallelities Total time for adding SS restraints: 10.31 Time building geometry restraints manager: 9.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5238 1.34 - 1.45: 4567 1.45 - 1.57: 10187 1.57 - 1.69: 406 1.69 - 1.81: 160 Bond restraints: 20558 Sorted by residual: bond pdb=" N GLU A 983 " pdb=" CA GLU A 983 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.19e-02 7.06e+03 6.15e+00 bond pdb=" N HIS C 609 " pdb=" CA HIS C 609 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.18e-02 7.18e+03 6.11e+00 bond pdb=" N ARG C 972 " pdb=" CA ARG C 972 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.33e-02 5.65e+03 5.97e+00 bond pdb=" N GLU C 983 " pdb=" CA GLU C 983 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.19e-02 7.06e+03 5.84e+00 bond pdb=" N GLU A 607 " pdb=" CA GLU A 607 " ideal model delta sigma weight residual 1.463 1.488 -0.025 1.24e-02 6.50e+03 4.08e+00 ... (remaining 20553 not shown) Histogram of bond angle deviations from ideal: 99.60 - 106.47: 1811 106.47 - 113.35: 10855 113.35 - 120.22: 7673 120.22 - 127.09: 7738 127.09 - 133.96: 631 Bond angle restraints: 28708 Sorted by residual: angle pdb=" N VAL A 742 " pdb=" CA VAL A 742 " pdb=" C VAL A 742 " ideal model delta sigma weight residual 106.21 110.09 -3.88 1.07e+00 8.73e-01 1.32e+01 angle pdb=" CA GLU A 607 " pdb=" C GLU A 607 " pdb=" O GLU A 607 " ideal model delta sigma weight residual 122.38 118.44 3.94 1.49e+00 4.50e-01 6.98e+00 angle pdb=" C3' DT G 25 " pdb=" O3' DT G 25 " pdb=" P DG G 26 " ideal model delta sigma weight residual 120.20 124.09 -3.89 1.50e+00 4.44e-01 6.71e+00 angle pdb=" CA GLU A 983 " pdb=" C GLU A 983 " pdb=" O GLU A 983 " ideal model delta sigma weight residual 120.82 118.16 2.66 1.05e+00 9.07e-01 6.42e+00 angle pdb=" CA HIS C 609 " pdb=" C HIS C 609 " pdb=" O HIS C 609 " ideal model delta sigma weight residual 120.90 118.31 2.59 1.03e+00 9.43e-01 6.30e+00 ... (remaining 28703 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.92: 10890 35.92 - 71.84: 883 71.84 - 107.76: 8 107.76 - 143.68: 7 143.68 - 179.60: 5 Dihedral angle restraints: 11793 sinusoidal: 5998 harmonic: 5795 Sorted by residual: dihedral pdb=" C4' DT J 14 " pdb=" C3' DT J 14 " pdb=" O3' DT J 14 " pdb=" P DT J 15 " ideal model delta sinusoidal sigma weight residual 220.00 40.40 179.60 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DT G 29 " pdb=" C3' DT G 29 " pdb=" O3' DT G 29 " pdb=" P DT G 30 " ideal model delta sinusoidal sigma weight residual 220.00 40.97 179.03 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DA F 33 " pdb=" C3' DA F 33 " pdb=" O3' DA F 33 " pdb=" P DG F 34 " ideal model delta sinusoidal sigma weight residual 220.00 42.48 177.52 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 11790 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 2228 0.029 - 0.059: 655 0.059 - 0.088: 159 0.088 - 0.118: 131 0.118 - 0.147: 12 Chirality restraints: 3185 Sorted by residual: chirality pdb=" CA ILE C 631 " pdb=" N ILE C 631 " pdb=" C ILE C 631 " pdb=" CB ILE C 631 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.43e-01 chirality pdb=" CA ILE B 331 " pdb=" N ILE B 331 " pdb=" C ILE B 331 " pdb=" CB ILE B 331 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.54e-01 chirality pdb=" CA ILE D 331 " pdb=" N ILE D 331 " pdb=" C ILE D 331 " pdb=" CB ILE D 331 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.46e-01 ... (remaining 3182 not shown) Planarity restraints: 2980 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT G 24 " -0.018 2.00e-02 2.50e+03 9.54e-03 2.27e+00 pdb=" N1 DT G 24 " 0.023 2.00e-02 2.50e+03 pdb=" C2 DT G 24 " 0.000 2.00e-02 2.50e+03 pdb=" O2 DT G 24 " 0.002 2.00e-02 2.50e+03 pdb=" N3 DT G 24 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DT G 24 " -0.002 2.00e-02 2.50e+03 pdb=" O4 DT G 24 " -0.005 2.00e-02 2.50e+03 pdb=" C5 DT G 24 " -0.001 2.00e-02 2.50e+03 pdb=" C7 DT G 24 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DT G 24 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 870 " -0.020 5.00e-02 4.00e+02 3.10e-02 1.54e+00 pdb=" N PRO A 871 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO A 871 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 871 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 520 " -0.019 5.00e-02 4.00e+02 2.85e-02 1.30e+00 pdb=" N PRO A 521 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO A 521 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 521 " -0.016 5.00e-02 4.00e+02 ... (remaining 2977 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 69 2.50 - 3.10: 13244 3.10 - 3.70: 31187 3.70 - 4.30: 43109 4.30 - 4.90: 67157 Nonbonded interactions: 154766 Sorted by model distance: nonbonded pdb=" OD2 ASP C 708 " pdb="MG MG C1101 " model vdw 1.897 2.170 nonbonded pdb=" OD1 ASP C 600 " pdb="MG MG C1101 " model vdw 1.901 2.170 nonbonded pdb=" OD2 ASP A 708 " pdb="MG MG A1101 " model vdw 1.901 2.170 nonbonded pdb=" OD1 ASP A 600 " pdb="MG MG A1101 " model vdw 1.906 2.170 nonbonded pdb=" OD1 ASP A 546 " pdb=" OG SER B 260 " model vdw 2.210 2.440 ... (remaining 154761 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 400 through 406 or (resid 407 and (name N or name CA or na \ me C or name O or name CB )) or resid 408 through 427 or (resid 428 through 429 \ and (name N or name CA or name C or name O or name CB )) or resid 430 through 45 \ 7 or (resid 458 and (name N or name CA or name C or name O or name CB )) or resi \ d 459 through 584 or (resid 585 and (name N or name CA or name C or name O or na \ me CB )) or resid 586 through 847 or (resid 848 and (name N or name CA or name C \ or name O or name CB )) or resid 849 through 903 or (resid 904 and (name N or n \ ame CA or name C or name O or name CB )) or resid 905 through 955 or (resid 956 \ and (name N or name CA or name C or name O or name CB )) or resid 961 through 10 \ 08 or resid 1101 through 1102)) selection = (chain 'C' and (resid 400 through 408 or (resid 409 and (name N or name CA or na \ me C or name O or name CB )) or resid 410 through 631 or (resid 632 and (name N \ or name CA or name C or name O or name CB )) or resid 633 through 638 or (resid \ 639 and (name N or name CA or name C or name O or name CB )) or resid 640 throug \ h 751 or (resid 752 and (name N or name CA or name C or name O or name CB )) or \ resid 753 through 757 or (resid 758 and (name N or name CA or name C or name O o \ r name CB )) or resid 759 through 810 or (resid 811 and (name N or name CA or na \ me C or name O or name CB )) or resid 812 through 819 or (resid 820 through 821 \ and (name N or name CA or name C or name O or name CB )) or resid 822 or (resid \ 823 and (name N or name CA or name C or name O or name CB )) or resid 824 throug \ h 834 or (resid 835 and (name N or name CA or name C or name O or name CB )) or \ resid 836 through 837 or (resid 838 through 839 and (name N or name CA or name C \ or name O or name CB )) or resid 840 through 860 or (resid 861 and (name N or n \ ame CA or name C or name O or name CB )) or resid 862 through 926 or (resid 927 \ through 928 and (name N or name CA or name C or name O or name CB )) or resid 92 \ 9 through 947 or (resid 948 and (name N or name CA or name C or name O or name C \ B )) or resid 949 through 956 or resid 961 through 1008 or resid 1101 through 11 \ 02)) } ncs_group { reference = chain 'B' selection = (chain 'D' and (resid 1 through 338 or (resid 339 and (name N or name CA or name \ C or name O or name CB )) or resid 340 through 351)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.530 Check model and map are aligned: 0.320 Set scattering table: 0.200 Process input model: 64.290 Find NCS groups from input model: 1.090 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 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 : 0.002 0.050 20558 Z= 0.134 Angle : 0.493 6.051 28708 Z= 0.290 Chirality : 0.036 0.147 3185 Planarity : 0.003 0.031 2980 Dihedral : 20.020 179.604 8055 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.19 % Allowed : 7.49 % Favored : 90.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % 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: -2.82 (0.16), residues: 1978 helix: -0.65 (0.17), residues: 736 sheet: -1.80 (0.25), residues: 349 loop : -2.98 (0.17), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 893 HIS 0.002 0.000 HIS A 836 PHE 0.012 0.001 PHE A 911 TYR 0.009 0.001 TYR C 998 ARG 0.001 0.000 ARG B 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 199 time to evaluate : 1.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 402 ARG cc_start: 0.6252 (tpt90) cc_final: 0.6047 (ttp80) REVERT: A 408 LEU cc_start: 0.9084 (mt) cc_final: 0.8808 (tt) REVERT: A 726 ILE cc_start: 0.6513 (OUTLIER) cc_final: 0.6286 (pp) REVERT: A 919 LEU cc_start: 0.8506 (mt) cc_final: 0.8008 (mm) REVERT: C 858 MET cc_start: 0.7452 (mmm) cc_final: 0.7103 (mmm) REVERT: B 152 MET cc_start: 0.6971 (tpp) cc_final: 0.6276 (tpp) REVERT: B 232 ASN cc_start: 0.6573 (m-40) cc_final: 0.6283 (t0) REVERT: D 189 PHE cc_start: 0.8006 (m-80) cc_final: 0.7596 (t80) REVERT: D 285 MET cc_start: 0.8388 (mmt) cc_final: 0.8017 (mmm) outliers start: 36 outliers final: 6 residues processed: 228 average time/residue: 0.3177 time to fit residues: 111.3741 Evaluate side-chains 121 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 114 time to evaluate : 2.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 658 MET Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 726 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 181 optimal weight: 8.9990 chunk 162 optimal weight: 7.9990 chunk 90 optimal weight: 9.9990 chunk 55 optimal weight: 20.0000 chunk 109 optimal weight: 9.9990 chunk 87 optimal weight: 10.0000 chunk 168 optimal weight: 6.9990 chunk 65 optimal weight: 10.0000 chunk 102 optimal weight: 9.9990 chunk 125 optimal weight: 6.9990 chunk 195 optimal weight: 8.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 473 ASN A 480 GLN A 498 GLN A 581 GLN A 739 GLN A 744 HIS ** A 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 860 GLN A 991 HIS C 463 GLN C 473 ASN C 495 GLN C 515 HIS C 636 GLN C 739 GLN C 744 HIS C 800 ASN C 852 ASN B 47 HIS B 89 HIS ** B 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 GLN B 222 HIS ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 GLN D 89 HIS D 94 HIS D 101 ASN ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 313 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.068 20558 Z= 0.548 Angle : 0.861 12.085 28708 Z= 0.459 Chirality : 0.049 0.238 3185 Planarity : 0.007 0.050 2980 Dihedral : 25.579 175.724 4439 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 17.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.15 % Favored : 90.85 % Rotamer: Outliers : 3.90 % Allowed : 12.36 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % 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: -2.22 (0.18), residues: 1978 helix: -0.22 (0.18), residues: 754 sheet: -1.18 (0.30), residues: 305 loop : -2.71 (0.18), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP B 317 HIS 0.015 0.003 HIS A 876 PHE 0.035 0.003 PHE D 62 TYR 0.027 0.003 TYR D 234 ARG 0.008 0.001 ARG C 840 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 96 time to evaluate : 1.965 Fit side-chains revert: symmetry clash REVERT: A 402 ARG cc_start: 0.6203 (tpt90) cc_final: 0.5923 (ttp80) REVERT: D 189 PHE cc_start: 0.8029 (m-80) cc_final: 0.7611 (t80) REVERT: N 109 TYR cc_start: 0.5249 (m-10) cc_final: 0.4569 (t80) outliers start: 64 outliers final: 33 residues processed: 153 average time/residue: 0.2631 time to fit residues: 67.5782 Evaluate side-chains 116 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 83 time to evaluate : 2.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 759 VAL Chi-restraints excluded: chain A residue 837 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 975 ASN Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 633 HIS Chi-restraints excluded: chain C residue 715 VAL Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 833 LEU Chi-restraints excluded: chain C residue 906 LEU Chi-restraints excluded: chain C residue 921 SER Chi-restraints excluded: chain C residue 975 ASN Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 287 CYS Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 151 SER Chi-restraints excluded: chain D residue 191 CYS Chi-restraints excluded: chain D residue 242 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 108 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 162 optimal weight: 5.9990 chunk 132 optimal weight: 0.4980 chunk 53 optimal weight: 5.9990 chunk 195 optimal weight: 7.9990 chunk 211 optimal weight: 50.0000 chunk 174 optimal weight: 8.9990 chunk 193 optimal weight: 6.9990 chunk 66 optimal weight: 7.9990 chunk 156 optimal weight: 0.5980 overall best weight: 3.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 480 GLN A 750 HIS ** A 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 GLN C 637 ASN C 860 GLN B 94 HIS B 181 HIS ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20558 Z= 0.277 Angle : 0.628 10.113 28708 Z= 0.339 Chirality : 0.041 0.187 3185 Planarity : 0.004 0.054 2980 Dihedral : 25.496 176.121 4432 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 3.65 % Allowed : 13.89 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % 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: -1.59 (0.18), residues: 1978 helix: 0.43 (0.19), residues: 758 sheet: -0.96 (0.29), residues: 332 loop : -2.48 (0.19), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 519 HIS 0.007 0.001 HIS C 991 PHE 0.019 0.002 PHE A 808 TYR 0.013 0.002 TYR D 344 ARG 0.004 0.000 ARG C 927 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 90 time to evaluate : 2.024 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 402 ARG cc_start: 0.6196 (tpt90) cc_final: 0.5984 (ttp80) REVERT: C 858 MET cc_start: 0.7621 (mmm) cc_final: 0.7367 (mmm) REVERT: C 1001 LYS cc_start: 0.9276 (OUTLIER) cc_final: 0.9050 (ttpp) REVERT: B 294 ASP cc_start: 0.6166 (OUTLIER) cc_final: 0.5202 (m-30) REVERT: D 189 PHE cc_start: 0.8061 (m-80) cc_final: 0.7655 (t80) REVERT: N 109 TYR cc_start: 0.5375 (m-10) cc_final: 0.4760 (t80) outliers start: 60 outliers final: 37 residues processed: 139 average time/residue: 0.2805 time to fit residues: 65.1198 Evaluate side-chains 124 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 85 time to evaluate : 2.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 627 MET Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 759 VAL Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 837 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 975 ASN Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 633 HIS Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 731 ASP Chi-restraints excluded: chain C residue 807 ILE Chi-restraints excluded: chain C residue 833 LEU Chi-restraints excluded: chain C residue 921 SER Chi-restraints excluded: chain C residue 1001 LYS Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 146 TYR Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 287 CYS Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 313 HIS Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 151 SER Chi-restraints excluded: chain D residue 191 CYS Chi-restraints excluded: chain D residue 324 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 193 optimal weight: 8.9990 chunk 147 optimal weight: 1.9990 chunk 101 optimal weight: 6.9990 chunk 21 optimal weight: 8.9990 chunk 93 optimal weight: 4.9990 chunk 131 optimal weight: 0.8980 chunk 196 optimal weight: 7.9990 chunk 207 optimal weight: 6.9990 chunk 102 optimal weight: 10.0000 chunk 186 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 HIS ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.3900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 20558 Z= 0.288 Angle : 0.628 9.141 28708 Z= 0.341 Chirality : 0.041 0.166 3185 Planarity : 0.004 0.049 2980 Dihedral : 25.516 173.779 4432 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 4.81 % Allowed : 14.25 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % 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: -1.37 (0.19), residues: 1978 helix: 0.60 (0.19), residues: 759 sheet: -0.88 (0.29), residues: 338 loop : -2.33 (0.20), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 317 HIS 0.007 0.001 HIS C 991 PHE 0.022 0.002 PHE B 29 TYR 0.014 0.002 TYR D 234 ARG 0.005 0.001 ARG C 927 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 87 time to evaluate : 2.059 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 510 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8728 (tt) REVERT: A 731 ASP cc_start: 0.8845 (OUTLIER) cc_final: 0.8606 (p0) REVERT: C 559 TYR cc_start: 0.8131 (OUTLIER) cc_final: 0.7856 (m-80) REVERT: C 858 MET cc_start: 0.7629 (mmm) cc_final: 0.7186 (mmm) REVERT: C 883 MET cc_start: 0.8153 (tpt) cc_final: 0.7556 (tpt) REVERT: C 887 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8459 (mm) REVERT: C 1001 LYS cc_start: 0.9275 (OUTLIER) cc_final: 0.9018 (ttpp) REVERT: B 294 ASP cc_start: 0.6423 (OUTLIER) cc_final: 0.5526 (m-30) REVERT: D 65 ASP cc_start: 0.8334 (OUTLIER) cc_final: 0.8067 (p0) REVERT: D 189 PHE cc_start: 0.8136 (m-80) cc_final: 0.7724 (t80) REVERT: N 109 TYR cc_start: 0.5318 (m-10) cc_final: 0.4720 (t80) REVERT: N 132 MET cc_start: 0.3587 (tmm) cc_final: 0.3359 (tmm) outliers start: 79 outliers final: 48 residues processed: 156 average time/residue: 0.2690 time to fit residues: 69.8763 Evaluate side-chains 135 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 80 time to evaluate : 2.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 731 ASP Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 759 VAL Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 837 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 934 ASN Chi-restraints excluded: chain A residue 975 ASN Chi-restraints excluded: chain C residue 414 GLN Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 559 TYR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 633 HIS Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 731 ASP Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 810 LEU Chi-restraints excluded: chain C residue 812 ILE Chi-restraints excluded: chain C residue 833 LEU Chi-restraints excluded: chain C residue 887 LEU Chi-restraints excluded: chain C residue 906 LEU Chi-restraints excluded: chain C residue 921 SER Chi-restraints excluded: chain C residue 975 ASN Chi-restraints excluded: chain C residue 1001 LYS Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 146 TYR Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 287 CYS Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 313 HIS Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 65 ASP Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 151 SER Chi-restraints excluded: chain D residue 162 MET Chi-restraints excluded: chain D residue 191 CYS Chi-restraints excluded: chain D residue 310 ASP Chi-restraints excluded: chain D residue 324 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 173 optimal weight: 10.0000 chunk 117 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 154 optimal weight: 7.9990 chunk 85 optimal weight: 0.0270 chunk 177 optimal weight: 6.9990 chunk 143 optimal weight: 10.0000 chunk 0 optimal weight: 30.0000 chunk 106 optimal weight: 2.9990 chunk 186 optimal weight: 7.9990 chunk 52 optimal weight: 10.0000 overall best weight: 4.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 HIS ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 GLN ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.4337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 20558 Z= 0.318 Angle : 0.659 14.714 28708 Z= 0.355 Chirality : 0.042 0.163 3185 Planarity : 0.004 0.047 2980 Dihedral : 25.641 174.446 4432 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer: Outliers : 5.42 % Allowed : 15.04 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % 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: -1.37 (0.19), residues: 1978 helix: 0.58 (0.19), residues: 759 sheet: -0.80 (0.29), residues: 334 loop : -2.34 (0.19), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 893 HIS 0.008 0.001 HIS C 991 PHE 0.025 0.002 PHE B 29 TYR 0.013 0.002 TYR D 234 ARG 0.004 0.001 ARG C 556 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 82 time to evaluate : 1.808 Fit side-chains revert: symmetry clash REVERT: A 402 ARG cc_start: 0.5900 (OUTLIER) cc_final: 0.5390 (ttp-170) REVERT: A 510 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8738 (tt) REVERT: A 731 ASP cc_start: 0.8870 (OUTLIER) cc_final: 0.8661 (p0) REVERT: C 559 TYR cc_start: 0.8134 (OUTLIER) cc_final: 0.7860 (m-80) REVERT: C 858 MET cc_start: 0.7671 (mmm) cc_final: 0.7209 (mmm) REVERT: C 883 MET cc_start: 0.8155 (tpt) cc_final: 0.7545 (tpt) REVERT: C 887 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8456 (mm) REVERT: C 1001 LYS cc_start: 0.9268 (OUTLIER) cc_final: 0.8994 (ttpp) REVERT: B 162 MET cc_start: 0.7885 (mmm) cc_final: 0.7683 (mmt) REVERT: B 294 ASP cc_start: 0.6600 (OUTLIER) cc_final: 0.5622 (m-30) REVERT: B 304 THR cc_start: 0.7927 (OUTLIER) cc_final: 0.7718 (p) REVERT: D 65 ASP cc_start: 0.8380 (OUTLIER) cc_final: 0.8063 (p0) REVERT: D 189 PHE cc_start: 0.8148 (m-80) cc_final: 0.7720 (t80) REVERT: D 217 TYR cc_start: 0.8187 (m-80) cc_final: 0.7755 (m-80) REVERT: N 109 TYR cc_start: 0.5494 (m-10) cc_final: 0.4862 (t80) outliers start: 89 outliers final: 56 residues processed: 165 average time/residue: 0.2727 time to fit residues: 74.5844 Evaluate side-chains 144 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 79 time to evaluate : 2.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 ARG Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 731 ASP Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 759 VAL Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 837 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 934 ASN Chi-restraints excluded: chain A residue 975 ASN Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 559 TYR Chi-restraints excluded: chain C residue 597 GLU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 633 HIS Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 731 ASP Chi-restraints excluded: chain C residue 752 GLU Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 807 ILE Chi-restraints excluded: chain C residue 810 LEU Chi-restraints excluded: chain C residue 812 ILE Chi-restraints excluded: chain C residue 833 LEU Chi-restraints excluded: chain C residue 850 ASN Chi-restraints excluded: chain C residue 887 LEU Chi-restraints excluded: chain C residue 906 LEU Chi-restraints excluded: chain C residue 921 SER Chi-restraints excluded: chain C residue 975 ASN Chi-restraints excluded: chain C residue 1001 LYS Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 146 TYR Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 287 CYS Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 313 HIS Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 65 ASP Chi-restraints excluded: chain D residue 151 SER Chi-restraints excluded: chain D residue 162 MET Chi-restraints excluded: chain D residue 191 CYS Chi-restraints excluded: chain D residue 310 ASP Chi-restraints excluded: chain D residue 324 ASN Chi-restraints excluded: chain N residue 136 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 69 optimal weight: 2.9990 chunk 187 optimal weight: 0.9980 chunk 41 optimal weight: 5.9990 chunk 122 optimal weight: 0.1980 chunk 51 optimal weight: 0.8980 chunk 208 optimal weight: 9.9990 chunk 172 optimal weight: 10.0000 chunk 96 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 109 optimal weight: 0.8980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 480 GLN C 750 HIS B 181 HIS ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 222 HIS D 265 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.4162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20558 Z= 0.164 Angle : 0.576 9.847 28708 Z= 0.308 Chirality : 0.039 0.165 3185 Planarity : 0.004 0.045 2980 Dihedral : 25.450 177.374 4430 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 2.86 % Allowed : 17.30 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % 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 (0.19), residues: 1978 helix: 1.16 (0.19), residues: 745 sheet: -0.66 (0.28), residues: 342 loop : -2.02 (0.20), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 317 HIS 0.004 0.001 HIS A 744 PHE 0.018 0.001 PHE A 971 TYR 0.013 0.001 TYR C 998 ARG 0.004 0.000 ARG B 284 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 87 time to evaluate : 2.088 Fit side-chains REVERT: A 645 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8532 (ptmm) REVERT: C 568 MET cc_start: 0.8412 (mmm) cc_final: 0.8197 (mmm) REVERT: C 658 MET cc_start: 0.8858 (pmm) cc_final: 0.8335 (pmm) REVERT: C 858 MET cc_start: 0.7445 (mmm) cc_final: 0.6982 (mmm) REVERT: C 883 MET cc_start: 0.8175 (tpt) cc_final: 0.7732 (tpt) REVERT: C 887 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8471 (mm) REVERT: B 5 MET cc_start: 0.8436 (tmm) cc_final: 0.7996 (tmm) REVERT: B 219 LEU cc_start: 0.8461 (mm) cc_final: 0.7426 (tt) REVERT: D 189 PHE cc_start: 0.8028 (m-80) cc_final: 0.7696 (t80) REVERT: N 109 TYR cc_start: 0.5488 (m-10) cc_final: 0.4880 (t80) outliers start: 47 outliers final: 32 residues processed: 129 average time/residue: 0.2749 time to fit residues: 59.7596 Evaluate side-chains 116 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 82 time to evaluate : 2.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 645 LYS Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 837 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 983 GLU Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 633 HIS Chi-restraints excluded: chain C residue 715 VAL Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 731 ASP Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 807 ILE Chi-restraints excluded: chain C residue 810 LEU Chi-restraints excluded: chain C residue 833 LEU Chi-restraints excluded: chain C residue 850 ASN Chi-restraints excluded: chain C residue 887 LEU Chi-restraints excluded: chain C residue 906 LEU Chi-restraints excluded: chain C residue 975 ASN Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 146 TYR Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain D residue 151 SER Chi-restraints excluded: chain D residue 219 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 200 optimal weight: 10.0000 chunk 23 optimal weight: 8.9990 chunk 118 optimal weight: 2.9990 chunk 151 optimal weight: 5.9990 chunk 117 optimal weight: 7.9990 chunk 175 optimal weight: 0.9980 chunk 116 optimal weight: 0.9980 chunk 207 optimal weight: 5.9990 chunk 129 optimal weight: 10.0000 chunk 126 optimal weight: 7.9990 chunk 95 optimal weight: 10.0000 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 GLN D 265 GLN ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.4392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20558 Z= 0.257 Angle : 0.604 9.246 28708 Z= 0.327 Chirality : 0.040 0.182 3185 Planarity : 0.004 0.045 2980 Dihedral : 25.527 175.745 4430 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 3.53 % Allowed : 16.87 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % 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: -0.90 (0.19), residues: 1978 helix: 1.07 (0.19), residues: 758 sheet: -0.60 (0.30), residues: 322 loop : -2.14 (0.20), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 893 HIS 0.005 0.001 HIS C 991 PHE 0.015 0.002 PHE B 29 TYR 0.016 0.001 TYR D 217 ARG 0.003 0.000 ARG A 402 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 79 time to evaluate : 2.160 Fit side-chains REVERT: C 658 MET cc_start: 0.8950 (pmm) cc_final: 0.8433 (pmm) REVERT: C 858 MET cc_start: 0.7568 (mmm) cc_final: 0.7082 (mmm) REVERT: C 883 MET cc_start: 0.8147 (tpt) cc_final: 0.7610 (tpt) REVERT: C 887 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8448 (mm) REVERT: C 1001 LYS cc_start: 0.9221 (OUTLIER) cc_final: 0.8975 (ttpp) REVERT: B 5 MET cc_start: 0.8461 (tmm) cc_final: 0.8009 (tmm) REVERT: B 294 ASP cc_start: 0.6581 (OUTLIER) cc_final: 0.5737 (m-30) REVERT: D 189 PHE cc_start: 0.8091 (m-80) cc_final: 0.7750 (t80) REVERT: N 109 TYR cc_start: 0.5668 (m-10) cc_final: 0.5021 (t80) outliers start: 58 outliers final: 48 residues processed: 132 average time/residue: 0.2510 time to fit residues: 56.7680 Evaluate side-chains 129 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 78 time to evaluate : 1.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 759 VAL Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 837 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain C residue 518 GLU Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 597 GLU Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 633 HIS Chi-restraints excluded: chain C residue 691 MET Chi-restraints excluded: chain C residue 715 VAL Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 731 ASP Chi-restraints excluded: chain C residue 752 GLU Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 807 ILE Chi-restraints excluded: chain C residue 810 LEU Chi-restraints excluded: chain C residue 833 LEU Chi-restraints excluded: chain C residue 850 ASN Chi-restraints excluded: chain C residue 887 LEU Chi-restraints excluded: chain C residue 906 LEU Chi-restraints excluded: chain C residue 921 SER Chi-restraints excluded: chain C residue 975 ASN Chi-restraints excluded: chain C residue 1001 LYS Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 287 CYS Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 313 HIS Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 191 CYS Chi-restraints excluded: chain D residue 310 ASP Chi-restraints excluded: chain D residue 324 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 128 optimal weight: 0.9980 chunk 82 optimal weight: 0.6980 chunk 123 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 131 optimal weight: 6.9990 chunk 141 optimal weight: 6.9990 chunk 102 optimal weight: 8.9990 chunk 19 optimal weight: 3.9990 chunk 162 optimal weight: 0.0570 chunk 188 optimal weight: 10.0000 overall best weight: 1.7502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.4356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20558 Z= 0.173 Angle : 0.578 16.397 28708 Z= 0.307 Chirality : 0.039 0.168 3185 Planarity : 0.003 0.045 2980 Dihedral : 25.495 178.462 4430 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 3.11 % Allowed : 17.48 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % 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: -0.58 (0.19), residues: 1978 helix: 1.37 (0.19), residues: 745 sheet: -0.51 (0.29), residues: 342 loop : -1.93 (0.20), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 893 HIS 0.004 0.001 HIS A 744 PHE 0.015 0.001 PHE C 641 TYR 0.017 0.001 TYR D 217 ARG 0.003 0.000 ARG A 696 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 82 time to evaluate : 2.008 Fit side-chains REVERT: C 658 MET cc_start: 0.8924 (pmm) cc_final: 0.8417 (pmm) REVERT: C 858 MET cc_start: 0.7548 (mmm) cc_final: 0.7086 (mmm) REVERT: C 883 MET cc_start: 0.8187 (tpt) cc_final: 0.7743 (tpt) REVERT: C 887 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8475 (mm) REVERT: C 889 MET cc_start: 0.8040 (mmt) cc_final: 0.7819 (mmp) REVERT: C 1001 LYS cc_start: 0.9182 (OUTLIER) cc_final: 0.8967 (ttpp) REVERT: B 5 MET cc_start: 0.8466 (tmm) cc_final: 0.7978 (tmm) REVERT: B 294 ASP cc_start: 0.6511 (OUTLIER) cc_final: 0.5842 (m-30) REVERT: D 189 PHE cc_start: 0.8046 (m-80) cc_final: 0.7741 (t80) REVERT: N 109 TYR cc_start: 0.5446 (m-10) cc_final: 0.4866 (t80) outliers start: 51 outliers final: 43 residues processed: 127 average time/residue: 0.2552 time to fit residues: 55.1896 Evaluate side-chains 128 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 82 time to evaluate : 1.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain C residue 518 GLU Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 597 GLU Chi-restraints excluded: chain C residue 633 HIS Chi-restraints excluded: chain C residue 715 VAL Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 731 ASP Chi-restraints excluded: chain C residue 752 GLU Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 807 ILE Chi-restraints excluded: chain C residue 810 LEU Chi-restraints excluded: chain C residue 833 LEU Chi-restraints excluded: chain C residue 850 ASN Chi-restraints excluded: chain C residue 887 LEU Chi-restraints excluded: chain C residue 906 LEU Chi-restraints excluded: chain C residue 921 SER Chi-restraints excluded: chain C residue 975 ASN Chi-restraints excluded: chain C residue 1001 LYS Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 151 SER Chi-restraints excluded: chain D residue 162 MET Chi-restraints excluded: chain D residue 191 CYS Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 324 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 198 optimal weight: 20.0000 chunk 181 optimal weight: 0.8980 chunk 193 optimal weight: 8.9990 chunk 116 optimal weight: 8.9990 chunk 84 optimal weight: 9.9990 chunk 151 optimal weight: 0.0670 chunk 59 optimal weight: 0.9980 chunk 174 optimal weight: 3.9990 chunk 182 optimal weight: 1.9990 chunk 192 optimal weight: 7.9990 chunk 126 optimal weight: 4.9990 overall best weight: 1.5922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.4382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20558 Z= 0.169 Angle : 0.566 10.257 28708 Z= 0.303 Chirality : 0.039 0.167 3185 Planarity : 0.003 0.044 2980 Dihedral : 25.459 178.927 4430 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 3.17 % Allowed : 17.66 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % 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: -0.45 (0.19), residues: 1978 helix: 1.44 (0.19), residues: 747 sheet: -0.35 (0.29), residues: 338 loop : -1.86 (0.20), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 893 HIS 0.004 0.001 HIS A 744 PHE 0.014 0.001 PHE C 641 TYR 0.015 0.001 TYR D 217 ARG 0.003 0.000 ARG C 621 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 81 time to evaluate : 2.215 Fit side-chains REVERT: C 658 MET cc_start: 0.8932 (pmm) cc_final: 0.8420 (pmm) REVERT: C 883 MET cc_start: 0.8190 (tpt) cc_final: 0.7986 (tpt) REVERT: C 887 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8512 (mm) REVERT: C 1001 LYS cc_start: 0.9197 (OUTLIER) cc_final: 0.8924 (ttpp) REVERT: B 5 MET cc_start: 0.8464 (tmm) cc_final: 0.7967 (tmm) REVERT: B 280 GLU cc_start: 0.7381 (pm20) cc_final: 0.7042 (pm20) REVERT: B 294 ASP cc_start: 0.6284 (OUTLIER) cc_final: 0.5741 (m-30) REVERT: D 189 PHE cc_start: 0.8038 (m-80) cc_final: 0.7727 (t80) REVERT: N 109 TYR cc_start: 0.5435 (m-10) cc_final: 0.4873 (t80) outliers start: 52 outliers final: 46 residues processed: 128 average time/residue: 0.2597 time to fit residues: 56.3938 Evaluate side-chains 129 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 80 time to evaluate : 2.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 759 VAL Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain C residue 518 GLU Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 597 GLU Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 633 HIS Chi-restraints excluded: chain C residue 691 MET Chi-restraints excluded: chain C residue 715 VAL Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 731 ASP Chi-restraints excluded: chain C residue 752 GLU Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 807 ILE Chi-restraints excluded: chain C residue 810 LEU Chi-restraints excluded: chain C residue 833 LEU Chi-restraints excluded: chain C residue 850 ASN Chi-restraints excluded: chain C residue 887 LEU Chi-restraints excluded: chain C residue 906 LEU Chi-restraints excluded: chain C residue 921 SER Chi-restraints excluded: chain C residue 975 ASN Chi-restraints excluded: chain C residue 1001 LYS Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 287 CYS Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 151 SER Chi-restraints excluded: chain D residue 191 CYS Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 324 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 204 optimal weight: 10.0000 chunk 124 optimal weight: 0.5980 chunk 96 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 214 optimal weight: 6.9990 chunk 197 optimal weight: 10.0000 chunk 170 optimal weight: 4.9990 chunk 17 optimal weight: 9.9990 chunk 131 optimal weight: 6.9990 chunk 104 optimal weight: 1.9990 chunk 135 optimal weight: 0.0870 overall best weight: 1.5364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.4409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20558 Z= 0.166 Angle : 0.563 7.730 28708 Z= 0.300 Chirality : 0.039 0.174 3185 Planarity : 0.003 0.044 2980 Dihedral : 25.436 179.745 4430 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 3.23 % Allowed : 17.54 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % 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: -0.36 (0.19), residues: 1978 helix: 1.54 (0.19), residues: 747 sheet: -0.27 (0.30), residues: 328 loop : -1.83 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 893 HIS 0.004 0.001 HIS C 515 PHE 0.013 0.001 PHE A 911 TYR 0.015 0.001 TYR D 217 ARG 0.003 0.000 ARG A 696 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 82 time to evaluate : 2.083 Fit side-chains REVERT: C 658 MET cc_start: 0.8909 (pmm) cc_final: 0.8399 (pmm) REVERT: C 858 MET cc_start: 0.7490 (mmm) cc_final: 0.7215 (mmm) REVERT: C 887 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8441 (mm) REVERT: C 1001 LYS cc_start: 0.9201 (OUTLIER) cc_final: 0.8971 (ttpp) REVERT: B 5 MET cc_start: 0.8454 (tmm) cc_final: 0.7955 (tmm) REVERT: B 126 GLU cc_start: 0.7828 (pm20) cc_final: 0.7558 (pm20) REVERT: B 280 GLU cc_start: 0.7567 (pm20) cc_final: 0.7146 (pm20) REVERT: B 294 ASP cc_start: 0.6330 (OUTLIER) cc_final: 0.5820 (m-30) REVERT: D 189 PHE cc_start: 0.8013 (m-80) cc_final: 0.7704 (t80) REVERT: N 109 TYR cc_start: 0.5293 (m-10) cc_final: 0.4736 (t80) outliers start: 53 outliers final: 47 residues processed: 129 average time/residue: 0.2658 time to fit residues: 58.2286 Evaluate side-chains 129 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 79 time to evaluate : 1.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 645 LYS Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 759 VAL Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain C residue 518 GLU Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 597 GLU Chi-restraints excluded: chain C residue 633 HIS Chi-restraints excluded: chain C residue 715 VAL Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 731 ASP Chi-restraints excluded: chain C residue 752 GLU Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 807 ILE Chi-restraints excluded: chain C residue 810 LEU Chi-restraints excluded: chain C residue 833 LEU Chi-restraints excluded: chain C residue 850 ASN Chi-restraints excluded: chain C residue 887 LEU Chi-restraints excluded: chain C residue 906 LEU Chi-restraints excluded: chain C residue 921 SER Chi-restraints excluded: chain C residue 975 ASN Chi-restraints excluded: chain C residue 1001 LYS Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 287 CYS Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 151 SER Chi-restraints excluded: chain D residue 162 MET Chi-restraints excluded: chain D residue 191 CYS Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 310 ASP Chi-restraints excluded: chain D residue 324 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 181 optimal weight: 0.0670 chunk 52 optimal weight: 3.9990 chunk 157 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 47 optimal weight: 6.9990 chunk 170 optimal weight: 0.0670 chunk 71 optimal weight: 1.9990 chunk 175 optimal weight: 1.9990 chunk 21 optimal weight: 8.9990 chunk 31 optimal weight: 2.9990 chunk 149 optimal weight: 0.7980 overall best weight: 0.9860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.064686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.050092 restraints weight = 124016.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.050972 restraints weight = 63211.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.051468 restraints weight = 40589.206| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.4419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20558 Z= 0.151 Angle : 0.555 8.139 28708 Z= 0.295 Chirality : 0.038 0.167 3185 Planarity : 0.003 0.045 2980 Dihedral : 25.399 179.588 4430 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 2.86 % Allowed : 18.21 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % 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 (0.20), residues: 1978 helix: 1.62 (0.19), residues: 749 sheet: -0.32 (0.30), residues: 336 loop : -1.73 (0.21), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 893 HIS 0.006 0.001 HIS C 515 PHE 0.013 0.001 PHE A 911 TYR 0.015 0.001 TYR D 217 ARG 0.002 0.000 ARG A 696 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2971.01 seconds wall clock time: 55 minutes 45.59 seconds (3345.59 seconds total)