Starting phenix.real_space_refine on Tue Mar 19 10:45:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8him_34821/03_2024/8him_34821.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8him_34821/03_2024/8him_34821.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8him_34821/03_2024/8him_34821.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8him_34821/03_2024/8him_34821.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8him_34821/03_2024/8him_34821.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8him_34821/03_2024/8him_34821.pdb" } resolution = 2.8 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= -0.000 sd= 0.005 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 6 6.06 5 P 63 5.49 5 Mg 1 5.21 5 S 141 5.16 5 C 14907 2.51 5 N 4189 2.21 5 O 4641 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 325": "NH1" <-> "NH2" Residue "A ARG 354": "NH1" <-> "NH2" Residue "A ARG 385": "NH1" <-> "NH2" Residue "A ARG 402": "NH1" <-> "NH2" Residue "A ARG 403": "NH1" <-> "NH2" Residue "A ARG 556": "NH1" <-> "NH2" Residue "A GLU 591": "OE1" <-> "OE2" Residue "A ARG 628": "NH1" <-> "NH2" Residue "A ARG 640": "NH1" <-> "NH2" Residue "A GLU 641": "OE1" <-> "OE2" Residue "A GLU 660": "OE1" <-> "OE2" Residue "A TYR 713": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 753": "OE1" <-> "OE2" Residue "A ARG 770": "NH1" <-> "NH2" Residue "A GLU 817": "OE1" <-> "OE2" Residue "A GLU 860": "OE1" <-> "OE2" Residue "A ARG 1019": "NH1" <-> "NH2" Residue "A ARG 1066": "NH1" <-> "NH2" Residue "A ARG 1106": "NH1" <-> "NH2" Residue "A GLU 1117": "OE1" <-> "OE2" Residue "A GLU 1146": "OE1" <-> "OE2" Residue "C ARG 15": "NH1" <-> "NH2" Residue "C ARG 27": "NH1" <-> "NH2" Residue "C ARG 85": "NH1" <-> "NH2" Residue "C ARG 88": "NH1" <-> "NH2" Residue "C ARG 107": "NH1" <-> "NH2" Residue "C ARG 157": "NH1" <-> "NH2" Residue "C PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 227": "NH1" <-> "NH2" Residue "F ARG 59": "NH1" <-> "NH2" Residue "F GLU 99": "OE1" <-> "OE2" Residue "F ARG 106": "NH1" <-> "NH2" Residue "F ARG 108": "NH1" <-> "NH2" Residue "F ARG 116": "NH1" <-> "NH2" Residue "J TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 9": "NH1" <-> "NH2" Residue "K ARG 47": "NH1" <-> "NH2" Residue "L ARG 43": "NH1" <-> "NH2" Residue "H ARG 138": "NH1" <-> "NH2" Residue "I ARG 20": "NH1" <-> "NH2" Residue "I GLU 47": "OE1" <-> "OE2" Residue "I ARG 75": "NH1" <-> "NH2" Residue "I ARG 113": "NH1" <-> "NH2" Residue "E GLU 45": "OE1" <-> "OE2" Residue "E ARG 48": "NH1" <-> "NH2" Residue "E ARG 67": "NH1" <-> "NH2" Residue "E ARG 73": "NH1" <-> "NH2" Residue "E ARG 78": "NH1" <-> "NH2" Residue "E ARG 169": "NH1" <-> "NH2" Residue "B ARG 18": "NH1" <-> "NH2" Residue "B PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 125": "NH1" <-> "NH2" Residue "B GLU 133": "OE1" <-> "OE2" Residue "B ARG 192": "NH1" <-> "NH2" Residue "B GLU 195": "OE1" <-> "OE2" Residue "B ARG 223": "NH1" <-> "NH2" Residue "B ARG 243": "NH1" <-> "NH2" Residue "B ARG 247": "NH1" <-> "NH2" Residue "B ARG 322": "NH1" <-> "NH2" Residue "B ARG 325": "NH1" <-> "NH2" Residue "B ARG 366": "NH1" <-> "NH2" Residue "B ARG 392": "NH1" <-> "NH2" Residue "B ARG 405": "NH1" <-> "NH2" Residue "B ARG 408": "NH1" <-> "NH2" Residue "B ARG 416": "NH1" <-> "NH2" Residue "B ASP 429": "OD1" <-> "OD2" Residue "B GLU 436": "OE1" <-> "OE2" Residue "B ARG 462": "NH1" <-> "NH2" Residue "B ARG 466": "NH1" <-> "NH2" Residue "B ARG 487": "NH1" <-> "NH2" Residue "B ARG 490": "NH1" <-> "NH2" Residue "B ARG 498": "NH1" <-> "NH2" Residue "B ARG 503": "NH1" <-> "NH2" Residue "B ARG 512": "NH1" <-> "NH2" Residue "B ARG 601": "NH1" <-> "NH2" Residue "B GLU 631": "OE1" <-> "OE2" Residue "B GLU 662": "OE1" <-> "OE2" Residue "B GLU 664": "OE1" <-> "OE2" Residue "B PHE 702": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 733": "NH1" <-> "NH2" Residue "B GLU 755": "OE1" <-> "OE2" Residue "B GLU 799": "OE1" <-> "OE2" Residue "B ARG 834": "NH1" <-> "NH2" Residue "B PHE 845": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 859": "NH1" <-> "NH2" Residue "B ARG 876": "NH1" <-> "NH2" Residue "B ARG 899": "NH1" <-> "NH2" Residue "B GLU 924": "OE1" <-> "OE2" Residue "B GLU 927": "OE1" <-> "OE2" Residue "B ARG 1013": "NH1" <-> "NH2" Residue "B TYR 1015": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1018": "NH1" <-> "NH2" Residue "B GLU 1021": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 23948 Number of models: 1 Model: "" Number of chains: 18 Chain: "T" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 529 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "N" Number of atoms: 539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 539 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "P" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 239 Classifications: {'RNA': 11} Modifications used: {'rna3p_pur': 8, 'rna3p_pyr': 3} Link IDs: {'rna3p': 10} Chain: "A" Number of atoms: 6640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 848, 6640 Classifications: {'peptide': 848} Link IDs: {'PTRANS': 27, 'TRANS': 820} Chain breaks: 3 Chain: "C" Number of atoms: 2256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2256 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 10, 'TRANS': 276} Chain breaks: 1 Chain: "F" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 660 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 4, 'TRANS': 75} Chain: "J" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 507 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 1, 'TRANS': 61} Chain: "K" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 890 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} Chain: "L" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 365 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "H" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1129 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 7, 'TRANS': 133} Chain: "I" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 787 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain breaks: 1 Chain: "E" Number of atoms: 1706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1706 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 205} Chain: "B" Number of atoms: 7694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 971, 7694 Classifications: {'peptide': 971} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 36, 'TRANS': 934} Chain breaks: 5 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 6411 SG CYS A 989 128.830 61.009 74.922 1.00131.65 S ATOM 6518 SG CYS A1004 127.128 61.695 78.578 1.00125.74 S ATOM 8652 SG CYS C 90 9.537 90.446 48.460 1.00 74.39 S ATOM 8671 SG CYS C 93 9.634 86.372 50.269 1.00 97.12 S ATOM 8710 SG CYS C 99 8.020 86.719 46.406 1.00 65.02 S ATOM 8736 SG CYS C 102 11.425 87.508 47.370 1.00 60.53 S ATOM 10918 SG CYS J 7 42.506 83.503 38.934 1.00 19.02 S ATOM 10942 SG CYS J 10 40.716 86.503 37.027 1.00 20.13 S ATOM 11208 SG CYS J 44 45.023 86.205 37.500 1.00 22.75 S ATOM 11214 SG CYS J 45 42.706 84.312 34.980 1.00 22.24 S ATOM 12306 SG CYS L 12 29.095 43.429 56.574 1.00 65.81 S ATOM 12324 SG CYS L 15 27.588 41.693 53.802 1.00 71.88 S ATOM 12426 SG CYS L 29 26.637 40.525 57.600 1.00 74.02 S ATOM 12452 SG CYS L 32 30.155 39.384 54.574 1.00 75.69 S ATOM 13795 SG CYS I 7 120.429 30.427 74.025 1.00112.85 S ATOM 13980 SG CYS I 29 118.227 30.994 78.250 1.00122.56 S ATOM 14005 SG CYS I 32 120.449 28.349 77.137 1.00125.28 S Time building chain proxies: 13.55, per 1000 atoms: 0.57 Number of scatterers: 23948 At special positions: 0 Unit cell: (146.73, 158.775, 137.97, 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 6 29.99 S 141 16.00 P 63 15.00 Mg 1 11.99 O 4641 8.00 N 4189 7.00 C 14907 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: 10.57 Conformation dependent library (CDL) restraints added in 4.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A3001 " pdb="ZN ZN A3001 " - pdb=" ND1 HIS A 938 " pdb="ZN ZN A3001 " - pdb=" NE2 HIS A 940 " pdb="ZN ZN A3001 " - pdb=" SG CYS A 989 " pdb="ZN ZN A3001 " - pdb=" SG CYS A1004 " pdb=" ZN C 400 " pdb="ZN ZN C 400 " - pdb=" SG CYS C 102 " pdb="ZN ZN C 400 " - pdb=" SG CYS C 99 " pdb="ZN ZN C 400 " - pdb=" SG CYS C 93 " pdb="ZN ZN C 400 " - pdb=" SG CYS C 90 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 29 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 32 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 7 " pdb=" ZN J 200 " pdb="ZN ZN J 200 " - pdb=" SG CYS J 44 " pdb="ZN ZN J 200 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 200 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 200 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 29 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 15 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 12 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 32 " Number of angles added : 20 5618 Ramachandran restraints generated. 2809 Oldfield, 0 Emsley, 2809 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5364 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 34 sheets defined 35.3% alpha, 19.1% beta 20 base pairs and 38 stacking pairs defined. Time for finding SS restraints: 8.35 Creating SS restraints... Processing helix chain 'A' and resid 343 through 347 Processing helix chain 'A' and resid 359 through 369 removed outlier: 3.566A pdb=" N LEU A 366 " --> pdb=" O TYR A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 441 No H-bonds generated for 'chain 'A' and resid 439 through 441' Processing helix chain 'A' and resid 442 through 447 removed outlier: 3.569A pdb=" N LEU A 446 " --> pdb=" O MET A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 473 Processing helix chain 'A' and resid 492 through 505 removed outlier: 3.665A pdb=" N GLN A 505 " --> pdb=" O VAL A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 518 Processing helix chain 'A' and resid 541 through 546 Processing helix chain 'A' and resid 547 through 549 No H-bonds generated for 'chain 'A' and resid 547 through 549' Processing helix chain 'A' and resid 576 through 591 Processing helix chain 'A' and resid 595 through 613 Proline residue: A 606 - end of helix Processing helix chain 'A' and resid 620 through 624 Processing helix chain 'A' and resid 627 through 650 removed outlier: 5.466A pdb=" N SER A 643 " --> pdb=" O VAL A 639 " (cutoff:3.500A) Proline residue: A 644 - end of helix removed outlier: 3.614A pdb=" N SER A 647 " --> pdb=" O SER A 643 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ARG A 648 " --> pdb=" O PRO A 644 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ARG A 650 " --> pdb=" O VAL A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 675 removed outlier: 3.611A pdb=" N ASN A 661 " --> pdb=" O LEU A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 683 removed outlier: 3.579A pdb=" N ARG A 681 " --> pdb=" O SER A 677 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ASN A 682 " --> pdb=" O TYR A 678 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A 683 " --> pdb=" O SER A 679 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 677 through 683' Processing helix chain 'A' and resid 689 through 700 removed outlier: 3.944A pdb=" N LYS A 694 " --> pdb=" O SER A 690 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU A 695 " --> pdb=" O ALA A 691 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN A 698 " --> pdb=" O LYS A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 729 removed outlier: 4.039A pdb=" N VAL A 718 " --> pdb=" O THR A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 771 removed outlier: 3.534A pdb=" N ALA A 760 " --> pdb=" O ALA A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 787 removed outlier: 3.561A pdb=" N LYS A 780 " --> pdb=" O GLY A 776 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL A 785 " --> pdb=" O ASN A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 847 Proline residue: A 839 - end of helix Processing helix chain 'A' and resid 848 through 863 removed outlier: 3.658A pdb=" N TRP A 855 " --> pdb=" O SER A 851 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL A 861 " --> pdb=" O LEU A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 874 No H-bonds generated for 'chain 'A' and resid 872 through 874' Processing helix chain 'A' and resid 884 through 888 Processing helix chain 'A' and resid 891 through 904 removed outlier: 3.586A pdb=" N SER A 895 " --> pdb=" O CYS A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 911 No H-bonds generated for 'chain 'A' and resid 909 through 911' Processing helix chain 'A' and resid 942 through 949 removed outlier: 3.939A pdb=" N LEU A 946 " --> pdb=" O ASN A 942 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU A 947 " --> pdb=" O LYS A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 952 through 970 removed outlier: 3.606A pdb=" N ILE A 956 " --> pdb=" O SER A 952 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ALA A 963 " --> pdb=" O ARG A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 975 through 979 removed outlier: 4.129A pdb=" N PHE A 978 " --> pdb=" O ALA A 975 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LYS A 979 " --> pdb=" O GLU A 976 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 975 through 979' Processing helix chain 'A' and resid 1017 through 1027 Processing helix chain 'A' and resid 1027 through 1034 removed outlier: 3.536A pdb=" N VAL A1031 " --> pdb=" O THR A1027 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU A1033 " --> pdb=" O TYR A1029 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU A1034 " --> pdb=" O PRO A1030 " (cutoff:3.500A) Processing helix chain 'A' and resid 1085 through 1095 removed outlier: 3.916A pdb=" N ARG A1089 " --> pdb=" O GLY A1085 " (cutoff:3.500A) Processing helix chain 'A' and resid 1111 through 1120 Processing helix chain 'A' and resid 1120 through 1140 removed outlier: 3.664A pdb=" N ALA A1134 " --> pdb=" O GLN A1130 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL A1139 " --> pdb=" O SER A1135 " (cutoff:3.500A) Processing helix chain 'A' and resid 1144 through 1156 removed outlier: 4.086A pdb=" N ILE A1148 " --> pdb=" O LEU A1144 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1176 removed outlier: 3.579A pdb=" N ALA A1171 " --> pdb=" O GLY A1167 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 44 Processing helix chain 'C' and resid 63 through 73 removed outlier: 3.721A pdb=" N LEU C 73 " --> pdb=" O HIS C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 180 Processing helix chain 'C' and resid 196 through 201 Processing helix chain 'C' and resid 204 through 213 Processing helix chain 'C' and resid 241 through 250 Processing helix chain 'C' and resid 276 through 294 removed outlier: 3.948A pdb=" N VAL C 281 " --> pdb=" O ALA C 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 66 through 83 removed outlier: 3.520A pdb=" N ARG F 72 " --> pdb=" O TYR F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 107 Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 30 through 37 Processing helix chain 'J' and resid 42 through 51 removed outlier: 3.723A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 62 removed outlier: 3.658A pdb=" N ASN J 61 " --> pdb=" O GLU J 57 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR J 62 " --> pdb=" O LYS J 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 51 removed outlier: 3.728A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 113 Processing helix chain 'E' and resid 31 through 51 Processing helix chain 'E' and resid 63 through 71 Processing helix chain 'E' and resid 104 through 119 removed outlier: 4.077A pdb=" N ILE E 108 " --> pdb=" O LYS E 104 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N GLU E 119 " --> pdb=" O ILE E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 139 removed outlier: 4.347A pdb=" N LYS E 138 " --> pdb=" O ASP E 134 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA E 139 " --> pdb=" O LYS E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 184 removed outlier: 3.832A pdb=" N GLN E 182 " --> pdb=" O ALA E 178 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE E 183 " --> pdb=" O LEU E 179 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN E 184 " --> pdb=" O LEU E 180 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 204 removed outlier: 3.523A pdb=" N ARG E 201 " --> pdb=" O ASP E 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 40 removed outlier: 3.558A pdb=" N LEU B 25 " --> pdb=" O GLY B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 56 removed outlier: 3.882A pdb=" N SER B 49 " --> pdb=" O HIS B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 65 Processing helix chain 'B' and resid 111 through 118 Processing helix chain 'B' and resid 239 through 242 Processing helix chain 'B' and resid 275 through 283 Processing helix chain 'B' and resid 286 through 295 Processing helix chain 'B' and resid 300 through 315 Processing helix chain 'B' and resid 325 through 336 Processing helix chain 'B' and resid 345 through 354 Processing helix chain 'B' and resid 360 through 380 Processing helix chain 'B' and resid 390 through 392 No H-bonds generated for 'chain 'B' and resid 390 through 392' Processing helix chain 'B' and resid 398 through 428 removed outlier: 3.586A pdb=" N ARG B 405 " --> pdb=" O GLU B 401 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL B 409 " --> pdb=" O ARG B 405 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N HIS B 410 " --> pdb=" O GLU B 406 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS B 420 " --> pdb=" O ARG B 416 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ALA B 421 " --> pdb=" O THR B 417 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N ARG B 424 " --> pdb=" O LYS B 420 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N HIS B 425 " --> pdb=" O ALA B 421 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR B 427 " --> pdb=" O GLN B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 439 removed outlier: 4.124A pdb=" N TYR B 438 " --> pdb=" O PRO B 434 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU B 439 " --> pdb=" O ILE B 435 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 434 through 439' Processing helix chain 'B' and resid 441 through 455 removed outlier: 3.682A pdb=" N THR B 445 " --> pdb=" O ALA B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 486 removed outlier: 3.633A pdb=" N SER B 482 " --> pdb=" O ASN B 478 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU B 486 " --> pdb=" O SER B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 510 removed outlier: 3.679A pdb=" N TRP B 510 " --> pdb=" O PRO B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 552 removed outlier: 4.075A pdb=" N PHE B 549 " --> pdb=" O GLU B 546 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ASP B 550 " --> pdb=" O GLU B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 595 removed outlier: 3.611A pdb=" N PHE B 586 " --> pdb=" O ASP B 582 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N ALA B 588 " --> pdb=" O ASP B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 636 removed outlier: 4.852A pdb=" N HIS B 634 " --> pdb=" O GLU B 631 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS B 635 " --> pdb=" O ASN B 632 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU B 636 " --> pdb=" O LEU B 633 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 631 through 636' Processing helix chain 'B' and resid 645 through 652 Processing helix chain 'B' and resid 660 through 664 removed outlier: 3.748A pdb=" N GLU B 664 " --> pdb=" O ILE B 660 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 660 through 664' Processing helix chain 'B' and resid 672 through 678 removed outlier: 3.519A pdb=" N LEU B 676 " --> pdb=" O THR B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 693 Processing helix chain 'B' and resid 702 through 706 removed outlier: 4.024A pdb=" N ASP B 706 " --> pdb=" O ALA B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 707 through 717 Processing helix chain 'B' and resid 729 through 733 removed outlier: 3.561A pdb=" N ILE B 732 " --> pdb=" O ASN B 729 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG B 733 " --> pdb=" O PRO B 730 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 729 through 733' Processing helix chain 'B' and resid 751 through 758 Processing helix chain 'B' and resid 788 through 793 Processing helix chain 'B' and resid 925 through 929 Processing helix chain 'B' and resid 943 through 945 No H-bonds generated for 'chain 'B' and resid 943 through 945' Processing helix chain 'B' and resid 946 through 951 removed outlier: 3.637A pdb=" N ARG B 950 " --> pdb=" O ALA B 946 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLN B 951 " --> pdb=" O PHE B 947 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 946 through 951' Processing helix chain 'B' and resid 953 through 967 removed outlier: 3.640A pdb=" N GLY B 964 " --> pdb=" O ALA B 960 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N CYS B 967 " --> pdb=" O LYS B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 993 through 1004 Processing helix chain 'B' and resid 1040 through 1044 Processing sheet with id=AA1, first strand: chain 'B' and resid 1046 through 1048 removed outlier: 3.675A pdb=" N SER A 323 " --> pdb=" O ARG B1048 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE A 322 " --> pdb=" O TYR A 459 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 350 through 354 removed outlier: 6.361A pdb=" N ARG A 403 " --> pdb=" O CYS A 372 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N CYS A 372 " --> pdb=" O ARG A 403 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 507 through 508 Processing sheet with id=AA4, first strand: chain 'A' and resid 529 through 531 removed outlier: 5.820A pdb=" N VAL A 529 " --> pdb=" O HIS H 94 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N HIS H 94 " --> pdb=" O VAL A 529 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LYS A 531 " --> pdb=" O VAL H 92 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 529 through 531 removed outlier: 5.820A pdb=" N VAL A 529 " --> pdb=" O HIS H 94 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N HIS H 94 " --> pdb=" O VAL A 529 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LYS A 531 " --> pdb=" O VAL H 92 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N TYR H 113 " --> pdb=" O TYR H 98 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N LEU H 120 " --> pdb=" O ASP H 44 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N THR H 33 " --> pdb=" O VAL H 14 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N VAL H 14 " --> pdb=" O THR H 33 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR H 59 " --> pdb=" O ARG H 144 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG H 144 " --> pdb=" O THR H 59 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 554 through 556 removed outlier: 6.640A pdb=" N GLY A 563 " --> pdb=" O LEU A 567 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N LEU A 567 " --> pdb=" O GLY A 563 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 703 through 704 Processing sheet with id=AA8, first strand: chain 'A' and resid 789 through 791 removed outlier: 6.277A pdb=" N ASN A 799 " --> pdb=" O ILE A 805 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ILE A 805 " --> pdb=" O ASN A 799 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1043 through 1049 removed outlier: 3.844A pdb=" N ASN A1047 " --> pdb=" O ASP A1073 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 906 through 907 removed outlier: 7.325A pdb=" N VAL A 906 " --> pdb=" O ILE A1037 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 982 through 986 removed outlier: 4.098A pdb=" N GLU A 914 " --> pdb=" O HIS A 940 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE A 915 " --> pdb=" O ASN I 46 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N TYR I 44 " --> pdb=" O VAL A 917 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N TYR A 919 " --> pdb=" O CYS I 42 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N CYS I 42 " --> pdb=" O TYR A 919 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1229 through 1230 Processing sheet with id=AB4, first strand: chain 'C' and resid 11 through 18 removed outlier: 5.577A pdb=" N VAL C 12 " --> pdb=" O ARG C 27 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N ARG C 27 " --> pdb=" O VAL C 12 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ILE C 14 " --> pdb=" O GLU C 25 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N GLU C 25 " --> pdb=" O ILE C 14 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU C 270 " --> pdb=" O THR C 184 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N THR C 184 " --> pdb=" O GLU C 270 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 11 through 18 removed outlier: 5.577A pdb=" N VAL C 12 " --> pdb=" O ARG C 27 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N ARG C 27 " --> pdb=" O VAL C 12 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ILE C 14 " --> pdb=" O GLU C 25 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N GLU C 25 " --> pdb=" O ILE C 14 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N GLU C 190 " --> pdb=" O LYS C 261 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 126 through 127 removed outlier: 6.470A pdb=" N GLU C 161 " --> pdb=" O ASN C 58 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ASN C 58 " --> pdb=" O GLU C 161 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LYS C 163 " --> pdb=" O GLU C 56 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N ARG C 169 " --> pdb=" O ILE C 50 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N ILE C 50 " --> pdb=" O ARG C 169 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N GLY C 171 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N VAL C 48 " --> pdb=" O GLY C 171 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 118 through 120 Processing sheet with id=AB8, first strand: chain 'C' and resid 220 through 223 Processing sheet with id=AB9, first strand: chain 'K' and resid 19 through 20 Processing sheet with id=AC1, first strand: chain 'L' and resid 18 through 19 removed outlier: 5.330A pdb=" N VAL B 882 " --> pdb=" O LYS L 39 " (cutoff:3.500A) removed outlier: 9.556A pdb=" N GLY B 877 " --> pdb=" O VAL B 901 " (cutoff:3.500A) removed outlier: 9.211A pdb=" N VAL B 901 " --> pdb=" O GLY B 877 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N VAL B 879 " --> pdb=" O ARG B 899 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ARG B 899 " --> pdb=" O VAL B 879 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYS B 881 " --> pdb=" O SER B 897 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 18 through 19 removed outlier: 5.330A pdb=" N VAL B 882 " --> pdb=" O LYS L 39 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 14 through 16 Processing sheet with id=AC4, first strand: chain 'I' and resid 84 through 89 Processing sheet with id=AC5, first strand: chain 'E' and resid 94 through 96 Processing sheet with id=AC6, first strand: chain 'E' and resid 169 through 170 removed outlier: 3.612A pdb=" N ARG E 169 " --> pdb=" O LYS E 212 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS E 212 " --> pdb=" O ARG E 169 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N TYR E 223 " --> pdb=" O TYR E 215 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 68 through 70 removed outlier: 5.476A pdb=" N VAL B 89 " --> pdb=" O GLU B 133 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N GLU B 133 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N PHE B 91 " --> pdb=" O ASP B 131 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ASP B 131 " --> pdb=" O PHE B 91 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N GLU B 93 " --> pdb=" O ASN B 129 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASN B 129 " --> pdb=" O GLU B 93 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ARG B 125 " --> pdb=" O ASP B 97 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ALA B 124 " --> pdb=" O ARG B 169 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ARG B 169 " --> pdb=" O ALA B 124 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N MET B 126 " --> pdb=" O ILE B 167 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN B 163 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 100 through 101 Processing sheet with id=AC9, first strand: chain 'B' and resid 204 through 206 Processing sheet with id=AD1, first strand: chain 'B' and resid 394 through 397 removed outlier: 6.639A pdb=" N ALA B 215 " --> pdb=" O ARG B 490 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 225 through 226 removed outlier: 3.639A pdb=" N ILE B 245 " --> pdb=" O TYR B 267 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 535 through 536 Processing sheet with id=AD4, first strand: chain 'B' and resid 535 through 536 removed outlier: 3.518A pdb=" N CYS B 685 " --> pdb=" O LEU B 628 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 575 through 580 removed outlier: 5.543A pdb=" N TRP B 576 " --> pdb=" O LEU B 572 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU B 572 " --> pdb=" O TRP B 576 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLY B 578 " --> pdb=" O VAL B 570 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LYS B 569 " --> pdb=" O VAL B 614 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N ILE B 616 " --> pdb=" O LYS B 569 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LEU B 571 " --> pdb=" O ILE B 616 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1011 through 1012 removed outlier: 7.080A pdb=" N ILE B 784 " --> pdb=" O GLY B 921 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ILE B 923 " --> pdb=" O ILE B 784 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N MET B 786 " --> pdb=" O ILE B 923 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N ILE B 940 " --> pdb=" O ASN B 767 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ILE B 769 " --> pdb=" O ILE B 940 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N ILE B 942 " --> pdb=" O ILE B 769 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ALA B 771 " --> pdb=" O ILE B 942 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N PHE B1028 " --> pdb=" O VAL B 772 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 855 through 857 removed outlier: 3.580A pdb=" N ILE B 857 " --> pdb=" O VAL B 869 " (cutoff:3.500A) 878 hydrogen bonds defined for protein. 2436 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 49 hydrogen bonds 94 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 38 stacking parallelities Total time for adding SS restraints: 11.04 Time building geometry restraints manager: 11.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4701 1.32 - 1.45: 5971 1.45 - 1.57: 13493 1.57 - 1.69: 123 1.69 - 1.82: 217 Bond restraints: 24505 Sorted by residual: bond pdb=" N PRO A1053 " pdb=" CD PRO A1053 " ideal model delta sigma weight residual 1.473 1.535 -0.062 1.40e-02 5.10e+03 1.94e+01 bond pdb=" C SER B 229 " pdb=" N PRO B 230 " ideal model delta sigma weight residual 1.333 1.363 -0.029 7.80e-03 1.64e+04 1.42e+01 bond pdb=" C PHE B 110 " pdb=" N LEU B 111 " ideal model delta sigma weight residual 1.327 1.267 0.060 1.71e-02 3.42e+03 1.22e+01 bond pdb=" N VAL B1014 " pdb=" CA VAL B1014 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.14e-02 7.69e+03 1.05e+01 bond pdb=" N VAL A1023 " pdb=" CA VAL A1023 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.21e-02 6.83e+03 8.57e+00 ... (remaining 24500 not shown) Histogram of bond angle deviations from ideal: 98.33 - 105.55: 668 105.55 - 112.78: 12842 112.78 - 120.00: 9140 120.00 - 127.23: 10354 127.23 - 134.45: 324 Bond angle restraints: 33328 Sorted by residual: angle pdb=" N THR B 427 " pdb=" CA THR B 427 " pdb=" C THR B 427 " ideal model delta sigma weight residual 111.71 101.80 9.91 1.15e+00 7.56e-01 7.43e+01 angle pdb=" N VAL A 574 " pdb=" CA VAL A 574 " pdb=" C VAL A 574 " ideal model delta sigma weight residual 113.71 105.89 7.82 9.50e-01 1.11e+00 6.78e+01 angle pdb=" N ARG B 490 " pdb=" CA ARG B 490 " pdb=" C ARG B 490 " ideal model delta sigma weight residual 108.76 120.31 -11.55 1.69e+00 3.50e-01 4.67e+01 angle pdb=" N CYS A 886 " pdb=" CA CYS A 886 " pdb=" CB CYS A 886 " ideal model delta sigma weight residual 112.28 102.63 9.65 1.49e+00 4.50e-01 4.19e+01 angle pdb=" N THR A 898 " pdb=" CA THR A 898 " pdb=" C THR A 898 " ideal model delta sigma weight residual 111.14 104.34 6.80 1.08e+00 8.57e-01 3.96e+01 ... (remaining 33323 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.81: 14200 35.81 - 71.63: 542 71.63 - 107.44: 31 107.44 - 143.25: 0 143.25 - 179.06: 3 Dihedral angle restraints: 14776 sinusoidal: 6493 harmonic: 8283 Sorted by residual: dihedral pdb=" CA GLU E 57 " pdb=" C GLU E 57 " pdb=" N ASP E 58 " pdb=" CA ASP E 58 " ideal model delta harmonic sigma weight residual 180.00 150.68 29.32 0 5.00e+00 4.00e-02 3.44e+01 dihedral pdb=" C CYS A 884 " pdb=" N CYS A 884 " pdb=" CA CYS A 884 " pdb=" CB CYS A 884 " ideal model delta harmonic sigma weight residual -122.60 -137.15 14.55 0 2.50e+00 1.60e-01 3.39e+01 dihedral pdb=" CA GLY H 105 " pdb=" C GLY H 105 " pdb=" N GLN H 106 " pdb=" CA GLN H 106 " ideal model delta harmonic sigma weight residual -180.00 -151.95 -28.05 0 5.00e+00 4.00e-02 3.15e+01 ... (remaining 14773 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.117: 3529 0.117 - 0.234: 209 0.234 - 0.351: 11 0.351 - 0.467: 1 0.467 - 0.584: 2 Chirality restraints: 3752 Sorted by residual: chirality pdb=" CA CYS A 884 " pdb=" N CYS A 884 " pdb=" C CYS A 884 " pdb=" CB CYS A 884 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.54e+00 chirality pdb=" P DT T 12 " pdb=" OP1 DT T 12 " pdb=" OP2 DT T 12 " pdb=" O5' DT T 12 " both_signs ideal model delta sigma weight residual True 2.35 -2.82 -0.48 2.00e-01 2.50e+01 5.73e+00 chirality pdb=" CB ILE H 100 " pdb=" CA ILE H 100 " pdb=" CG1 ILE H 100 " pdb=" CG2 ILE H 100 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.37 2.00e-01 2.50e+01 3.45e+00 ... (remaining 3749 not shown) Planarity restraints: 4062 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 295 " 0.017 2.00e-02 2.50e+03 3.42e-02 1.17e+01 pdb=" C VAL C 295 " -0.059 2.00e-02 2.50e+03 pdb=" O VAL C 295 " 0.023 2.00e-02 2.50e+03 pdb=" N ARG C 296 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN B 478 " -0.051 5.00e-02 4.00e+02 7.72e-02 9.53e+00 pdb=" N PRO B 479 " 0.133 5.00e-02 4.00e+02 pdb=" CA PRO B 479 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 479 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 848 " -0.048 5.00e-02 4.00e+02 7.18e-02 8.25e+00 pdb=" N PRO A 849 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO A 849 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 849 " -0.040 5.00e-02 4.00e+02 ... (remaining 4059 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1365 2.72 - 3.26: 21617 3.26 - 3.81: 38332 3.81 - 4.35: 48012 4.35 - 4.90: 79958 Nonbonded interactions: 189284 Sorted by model distance: nonbonded pdb=" OD1 ASP A 449 " pdb="MG MG A3000 " model vdw 2.173 2.170 nonbonded pdb=" OD1 ASP A 451 " pdb="MG MG A3000 " model vdw 2.185 2.170 nonbonded pdb=" N GLY I 82 " pdb="ZN ZN I 201 " model vdw 2.223 2.310 nonbonded pdb=" O GLY B 430 " pdb=" N LEU B 432 " model vdw 2.291 2.520 nonbonded pdb=" O THR A1056 " pdb=" OG1 THR A1057 " model vdw 2.295 2.440 ... (remaining 189279 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 1.290 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: 7.130 Check model and map are aligned: 0.380 Set scattering table: 0.230 Process input model: 77.040 Find NCS groups from input model: 0.810 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: 0.010 Load rotamer database and sin/cos tables:12.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 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 : 0.008 0.119 24505 Z= 0.505 Angle : 0.994 11.549 33328 Z= 0.586 Chirality : 0.062 0.584 3752 Planarity : 0.007 0.077 4062 Dihedral : 17.535 179.063 9412 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.66 % Favored : 94.23 % Rotamer: Outliers : 0.60 % Allowed : 6.99 % Favored : 92.42 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.49 (0.13), residues: 2809 helix: -2.44 (0.13), residues: 876 sheet: -1.51 (0.21), residues: 524 loop : -2.53 (0.13), residues: 1409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.004 TRP F 126 HIS 0.010 0.002 HIS H 42 PHE 0.040 0.003 PHE B 213 TYR 0.018 0.003 TYR K 87 ARG 0.009 0.001 ARG C 157 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5618 Ramachandran restraints generated. 2809 Oldfield, 0 Emsley, 2809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5618 Ramachandran restraints generated. 2809 Oldfield, 0 Emsley, 2809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 347 time to evaluate : 2.139 Fit side-chains revert: symmetry clash REVERT: A 961 GLU cc_start: 0.7949 (tp30) cc_final: 0.7649 (tp30) REVERT: A 981 MET cc_start: 0.6954 (ptm) cc_final: 0.6680 (ptm) REVERT: A 1066 ARG cc_start: 0.4407 (mtt90) cc_final: 0.4076 (mpp80) REVERT: F 103 LYS cc_start: 0.8209 (mmmt) cc_final: 0.7901 (mtpt) REVERT: F 106 ARG cc_start: 0.7337 (tpp-160) cc_final: 0.7000 (tpp-160) REVERT: F 130 GLU cc_start: 0.8436 (mt-10) cc_final: 0.8202 (mt-10) REVERT: H 31 GLU cc_start: 0.6735 (mm-30) cc_final: 0.6412 (tp30) REVERT: H 39 MET cc_start: 0.4220 (mmt) cc_final: 0.3919 (mtt) REVERT: H 111 GLU cc_start: 0.5863 (pt0) cc_final: 0.5316 (pt0) REVERT: I 17 LYS cc_start: 0.7629 (ttpp) cc_final: 0.7201 (ttpp) REVERT: I 100 PHE cc_start: 0.5066 (m-10) cc_final: 0.4520 (t80) REVERT: E 42 ASN cc_start: 0.8055 (t0) cc_final: 0.7378 (t0) REVERT: E 44 LEU cc_start: 0.7813 (OUTLIER) cc_final: 0.7560 (mt) REVERT: E 130 ASN cc_start: 0.6516 (p0) cc_final: 0.6237 (p0) REVERT: B 243 ARG cc_start: 0.6948 (mtt180) cc_final: 0.6711 (mtm180) REVERT: B 603 MET cc_start: 0.8611 (ttp) cc_final: 0.8272 (ttp) REVERT: B 686 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.7568 (mm-30) REVERT: B 752 MET cc_start: 0.8725 (tpt) cc_final: 0.8456 (tpp) REVERT: B 834 ARG cc_start: 0.6685 (ttt90) cc_final: 0.6217 (ttp80) REVERT: B 950 ARG cc_start: 0.7715 (mmt90) cc_final: 0.7229 (mmt90) outliers start: 15 outliers final: 2 residues processed: 357 average time/residue: 1.6946 time to fit residues: 675.9342 Evaluate side-chains 241 residues out of total 2522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 237 time to evaluate : 2.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1173 THR Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 686 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 240 optimal weight: 1.9990 chunk 216 optimal weight: 6.9990 chunk 119 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 145 optimal weight: 9.9990 chunk 115 optimal weight: 6.9990 chunk 223 optimal weight: 5.9990 chunk 86 optimal weight: 0.5980 chunk 135 optimal weight: 0.9980 chunk 166 optimal weight: 7.9990 chunk 258 optimal weight: 2.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 HIS A 401 HIS A 421 HIS A 424 GLN A 431 HIS A 611 HIS A 693 ASN A 781 ASN A 942 ASN A1011 ASN A1114 GLN A1147 HIS C 279 GLN K 29 ASN K 89 GLN H 46 ASN H 94 HIS ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 46 ASN E 84 HIS B 59 GLN B 163 GLN B 216 GLN B 305 ASN ** B 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 HIS B 596 GLN B 679 GLN B 684 HIS B 705 HIS B 714 GLN B 721 GLN B 745 GLN B 758 GLN B 764 ASN B 767 ASN B 780 GLN B 824 GLN B 892 ASN B 970 GLN B1000 GLN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 24505 Z= 0.242 Angle : 0.626 10.526 33328 Z= 0.340 Chirality : 0.044 0.214 3752 Planarity : 0.005 0.068 4062 Dihedral : 16.662 179.831 3833 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.38 % Favored : 94.59 % Rotamer: Outliers : 2.58 % Allowed : 12.35 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.14), residues: 2809 helix: -0.61 (0.17), residues: 888 sheet: -1.24 (0.22), residues: 517 loop : -2.11 (0.14), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 113 HIS 0.006 0.001 HIS H 42 PHE 0.028 0.002 PHE A 411 TYR 0.015 0.002 TYR B 235 ARG 0.006 0.000 ARG B 325 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5618 Ramachandran restraints generated. 2809 Oldfield, 0 Emsley, 2809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5618 Ramachandran restraints generated. 2809 Oldfield, 0 Emsley, 2809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 253 time to evaluate : 2.849 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 541 PHE cc_start: 0.8094 (OUTLIER) cc_final: 0.7371 (p90) REVERT: A 961 GLU cc_start: 0.7977 (tp30) cc_final: 0.7691 (tp30) REVERT: C 149 ARG cc_start: 0.7042 (OUTLIER) cc_final: 0.6009 (mpt180) REVERT: F 59 ARG cc_start: 0.5849 (mtm-85) cc_final: 0.4963 (pmt170) REVERT: F 92 GLU cc_start: 0.6811 (mp0) cc_final: 0.6591 (mp0) REVERT: F 103 LYS cc_start: 0.8250 (mmmt) cc_final: 0.8011 (mtpt) REVERT: F 115 ARG cc_start: 0.7357 (mtt90) cc_final: 0.7078 (ttm-80) REVERT: K 23 ARG cc_start: 0.7645 (tmm-80) cc_final: 0.7343 (ttp80) REVERT: K 74 ARG cc_start: 0.8025 (ttm-80) cc_final: 0.7786 (ttm170) REVERT: H 7 MET cc_start: 0.6471 (OUTLIER) cc_final: 0.6244 (mtp) REVERT: H 31 GLU cc_start: 0.6546 (mm-30) cc_final: 0.6246 (tp30) REVERT: H 39 MET cc_start: 0.4364 (mmt) cc_final: 0.3544 (mtt) REVERT: I 97 MET cc_start: 0.4892 (OUTLIER) cc_final: 0.4537 (mpp) REVERT: I 100 PHE cc_start: 0.4828 (m-10) cc_final: 0.4411 (t80) REVERT: E 42 ASN cc_start: 0.7976 (t0) cc_final: 0.7332 (t0) REVERT: E 130 ASN cc_start: 0.6525 (p0) cc_final: 0.6189 (p0) REVERT: B 163 GLN cc_start: 0.6898 (tp40) cc_final: 0.6663 (tp40) REVERT: B 333 GLN cc_start: 0.8094 (OUTLIER) cc_final: 0.7700 (tt0) REVERT: B 603 MET cc_start: 0.8609 (ttp) cc_final: 0.8261 (ttp) REVERT: B 686 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7759 (mt-10) REVERT: B 752 MET cc_start: 0.8690 (tpt) cc_final: 0.8443 (tpp) REVERT: B 834 ARG cc_start: 0.6652 (ttt90) cc_final: 0.6174 (ttp80) REVERT: B 950 ARG cc_start: 0.7540 (mmt90) cc_final: 0.6906 (mmm-85) outliers start: 65 outliers final: 26 residues processed: 293 average time/residue: 1.5581 time to fit residues: 515.5605 Evaluate side-chains 250 residues out of total 2522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 218 time to evaluate : 2.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 419 HIS Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 730 VAL Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 1102 ILE Chi-restraints excluded: chain A residue 1135 SER Chi-restraints excluded: chain A residue 1173 THR Chi-restraints excluded: chain C residue 149 ARG Chi-restraints excluded: chain F residue 110 ILE Chi-restraints excluded: chain F residue 126 TRP Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain H residue 7 MET Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain I residue 97 MET Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 333 GLN Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 686 GLU Chi-restraints excluded: chain B residue 840 ASP Chi-restraints excluded: chain B residue 867 HIS Chi-restraints excluded: chain B residue 872 LYS Chi-restraints excluded: chain B residue 919 VAL Chi-restraints excluded: chain B residue 985 HIS Chi-restraints excluded: chain B residue 1042 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 143 optimal weight: 10.0000 chunk 80 optimal weight: 5.9990 chunk 215 optimal weight: 0.9980 chunk 176 optimal weight: 20.0000 chunk 71 optimal weight: 5.9990 chunk 259 optimal weight: 8.9990 chunk 280 optimal weight: 0.7980 chunk 230 optimal weight: 5.9990 chunk 257 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 208 optimal weight: 3.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 46 ASN H 129 HIS ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 34 HIS ** B 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 824 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 24505 Z= 0.237 Angle : 0.596 10.698 33328 Z= 0.321 Chirality : 0.043 0.195 3752 Planarity : 0.005 0.080 4062 Dihedral : 16.432 179.442 3831 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 3.18 % Allowed : 13.82 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.15), residues: 2809 helix: 0.21 (0.18), residues: 889 sheet: -1.00 (0.22), residues: 514 loop : -1.80 (0.15), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 113 HIS 0.007 0.001 HIS H 42 PHE 0.029 0.002 PHE A 411 TYR 0.015 0.002 TYR A 375 ARG 0.009 0.000 ARG B 325 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5618 Ramachandran restraints generated. 2809 Oldfield, 0 Emsley, 2809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5618 Ramachandran restraints generated. 2809 Oldfield, 0 Emsley, 2809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 254 time to evaluate : 2.851 Fit side-chains revert: symmetry clash REVERT: A 541 PHE cc_start: 0.8071 (OUTLIER) cc_final: 0.7462 (p90) REVERT: A 961 GLU cc_start: 0.8001 (tp30) cc_final: 0.7721 (tp30) REVERT: A 1066 ARG cc_start: 0.4565 (mtt90) cc_final: 0.4155 (mpp80) REVERT: C 149 ARG cc_start: 0.7014 (OUTLIER) cc_final: 0.5921 (mpt180) REVERT: C 205 ASP cc_start: 0.5716 (p0) cc_final: 0.5449 (m-30) REVERT: F 59 ARG cc_start: 0.5935 (mtm-85) cc_final: 0.5009 (pmt170) REVERT: F 103 LYS cc_start: 0.8164 (mmmt) cc_final: 0.7887 (mtpt) REVERT: F 106 ARG cc_start: 0.7494 (tpp-160) cc_final: 0.7280 (tpt170) REVERT: F 115 ARG cc_start: 0.7468 (mtt90) cc_final: 0.7256 (ttm-80) REVERT: J 26 GLN cc_start: 0.7188 (tp40) cc_final: 0.6931 (mm-40) REVERT: K 23 ARG cc_start: 0.7720 (tmm-80) cc_final: 0.7435 (ttp80) REVERT: K 74 ARG cc_start: 0.8020 (ttm-80) cc_final: 0.7778 (ttm170) REVERT: H 7 MET cc_start: 0.6481 (OUTLIER) cc_final: 0.6202 (mtp) REVERT: H 8 PHE cc_start: 0.7663 (t80) cc_final: 0.7238 (t80) REVERT: H 31 GLU cc_start: 0.6590 (mm-30) cc_final: 0.6294 (tp30) REVERT: H 39 MET cc_start: 0.4119 (mmt) cc_final: 0.3399 (mtt) REVERT: I 17 LYS cc_start: 0.7716 (tttt) cc_final: 0.7242 (tppt) REVERT: I 97 MET cc_start: 0.4990 (OUTLIER) cc_final: 0.4747 (mpp) REVERT: I 100 PHE cc_start: 0.4708 (m-80) cc_final: 0.4424 (t80) REVERT: E 42 ASN cc_start: 0.7942 (t0) cc_final: 0.7366 (t0) REVERT: E 130 ASN cc_start: 0.6516 (p0) cc_final: 0.6308 (p0) REVERT: B 163 GLN cc_start: 0.6750 (tp40) cc_final: 0.6484 (tp40) REVERT: B 260 LYS cc_start: 0.6874 (ttmm) cc_final: 0.6609 (ptpt) REVERT: B 603 MET cc_start: 0.8596 (ttp) cc_final: 0.8277 (ttp) REVERT: B 752 MET cc_start: 0.8732 (tpt) cc_final: 0.8445 (tpp) REVERT: B 834 ARG cc_start: 0.6598 (ttt90) cc_final: 0.6117 (ttp80) REVERT: B 860 CYS cc_start: 0.7150 (t) cc_final: 0.6758 (p) outliers start: 80 outliers final: 35 residues processed: 307 average time/residue: 1.4643 time to fit residues: 512.0181 Evaluate side-chains 270 residues out of total 2522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 231 time to evaluate : 2.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 419 HIS Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 730 VAL Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 1135 SER Chi-restraints excluded: chain A residue 1173 THR Chi-restraints excluded: chain A residue 1230 LEU Chi-restraints excluded: chain C residue 149 ARG Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain F residue 110 ILE Chi-restraints excluded: chain F residue 126 TRP Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain H residue 7 MET Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain I residue 97 MET Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 670 TRP Chi-restraints excluded: chain B residue 840 ASP Chi-restraints excluded: chain B residue 867 HIS Chi-restraints excluded: chain B residue 872 LYS Chi-restraints excluded: chain B residue 919 VAL Chi-restraints excluded: chain B residue 985 HIS Chi-restraints excluded: chain B residue 1042 GLU Chi-restraints excluded: chain B residue 1047 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 256 optimal weight: 0.9980 chunk 194 optimal weight: 5.9990 chunk 134 optimal weight: 6.9990 chunk 28 optimal weight: 9.9990 chunk 123 optimal weight: 1.9990 chunk 174 optimal weight: 10.0000 chunk 260 optimal weight: 4.9990 chunk 275 optimal weight: 0.0010 chunk 135 optimal weight: 4.9990 chunk 246 optimal weight: 2.9990 chunk 74 optimal weight: 8.9990 overall best weight: 2.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 46 ASN ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 24505 Z= 0.224 Angle : 0.578 9.337 33328 Z= 0.310 Chirality : 0.043 0.231 3752 Planarity : 0.004 0.074 4062 Dihedral : 16.248 178.613 3826 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 3.14 % Allowed : 16.24 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.15), residues: 2809 helix: 0.63 (0.18), residues: 882 sheet: -0.94 (0.23), residues: 507 loop : -1.62 (0.15), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 126 HIS 0.006 0.001 HIS H 42 PHE 0.028 0.002 PHE A 411 TYR 0.014 0.001 TYR K 87 ARG 0.010 0.000 ARG B 325 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5618 Ramachandran restraints generated. 2809 Oldfield, 0 Emsley, 2809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5618 Ramachandran restraints generated. 2809 Oldfield, 0 Emsley, 2809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 242 time to evaluate : 2.719 Fit side-chains revert: symmetry clash REVERT: A 541 PHE cc_start: 0.8110 (OUTLIER) cc_final: 0.7512 (p90) REVERT: A 680 MET cc_start: 0.8294 (mmt) cc_final: 0.7971 (mmt) REVERT: A 961 GLU cc_start: 0.8046 (tp30) cc_final: 0.7778 (tp30) REVERT: A 981 MET cc_start: 0.7124 (OUTLIER) cc_final: 0.6777 (ttp) REVERT: A 1066 ARG cc_start: 0.4643 (mtt90) cc_final: 0.4173 (mpp80) REVERT: C 119 ASP cc_start: 0.8062 (OUTLIER) cc_final: 0.7554 (m-30) REVERT: C 149 ARG cc_start: 0.7048 (OUTLIER) cc_final: 0.5987 (mpt180) REVERT: C 205 ASP cc_start: 0.6216 (p0) cc_final: 0.5966 (m-30) REVERT: F 59 ARG cc_start: 0.6073 (mtm-85) cc_final: 0.5007 (pmt170) REVERT: F 103 LYS cc_start: 0.8155 (mmmt) cc_final: 0.7928 (mtpt) REVERT: F 106 ARG cc_start: 0.7501 (tpp-160) cc_final: 0.7275 (tpt170) REVERT: F 132 ILE cc_start: 0.8163 (mt) cc_final: 0.7887 (mp) REVERT: J 26 GLN cc_start: 0.7225 (tp40) cc_final: 0.7017 (mm-40) REVERT: K 74 ARG cc_start: 0.8002 (ttm-80) cc_final: 0.7784 (ttm170) REVERT: H 7 MET cc_start: 0.6526 (OUTLIER) cc_final: 0.6205 (mtp) REVERT: H 8 PHE cc_start: 0.7411 (t80) cc_final: 0.6822 (t80) REVERT: H 31 GLU cc_start: 0.6592 (mm-30) cc_final: 0.6292 (tp30) REVERT: H 39 MET cc_start: 0.4150 (mmt) cc_final: 0.3434 (mtt) REVERT: H 111 GLU cc_start: 0.5223 (OUTLIER) cc_final: 0.4892 (pt0) REVERT: H 112 MET cc_start: 0.6024 (OUTLIER) cc_final: 0.5797 (mtm) REVERT: I 17 LYS cc_start: 0.7673 (OUTLIER) cc_final: 0.7298 (tppt) REVERT: I 97 MET cc_start: 0.4992 (OUTLIER) cc_final: 0.4750 (mpp) REVERT: I 100 PHE cc_start: 0.4714 (m-80) cc_final: 0.4405 (t80) REVERT: E 42 ASN cc_start: 0.7942 (t0) cc_final: 0.7337 (t0) REVERT: E 47 LEU cc_start: 0.7401 (OUTLIER) cc_final: 0.7071 (mp) REVERT: E 130 ASN cc_start: 0.6422 (p0) cc_final: 0.6201 (p0) REVERT: B 163 GLN cc_start: 0.6625 (tp40) cc_final: 0.6388 (tp40) REVERT: B 603 MET cc_start: 0.8618 (ttp) cc_final: 0.8313 (ttp) REVERT: B 752 MET cc_start: 0.8738 (tpt) cc_final: 0.8446 (tpp) REVERT: B 834 ARG cc_start: 0.6593 (ttt90) cc_final: 0.6125 (ttp80) REVERT: B 860 CYS cc_start: 0.7377 (t) cc_final: 0.6860 (p) outliers start: 79 outliers final: 35 residues processed: 295 average time/residue: 1.3929 time to fit residues: 470.6583 Evaluate side-chains 273 residues out of total 2522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 228 time to evaluate : 2.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 730 VAL Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 981 MET Chi-restraints excluded: chain A residue 1135 SER Chi-restraints excluded: chain A residue 1173 THR Chi-restraints excluded: chain C residue 119 ASP Chi-restraints excluded: chain C residue 149 ARG Chi-restraints excluded: chain F residue 110 ILE Chi-restraints excluded: chain F residue 126 TRP Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain H residue 7 MET Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 111 GLU Chi-restraints excluded: chain H residue 112 MET Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain I residue 17 LYS Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 97 MET Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 670 TRP Chi-restraints excluded: chain B residue 840 ASP Chi-restraints excluded: chain B residue 867 HIS Chi-restraints excluded: chain B residue 872 LYS Chi-restraints excluded: chain B residue 919 VAL Chi-restraints excluded: chain B residue 985 HIS Chi-restraints excluded: chain B residue 1042 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 229 optimal weight: 0.5980 chunk 156 optimal weight: 9.9990 chunk 4 optimal weight: 20.0000 chunk 205 optimal weight: 10.0000 chunk 113 optimal weight: 8.9990 chunk 235 optimal weight: 10.0000 chunk 190 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 140 optimal weight: 5.9990 chunk 247 optimal weight: 0.9990 chunk 69 optimal weight: 6.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 HIS A 982 ASN J 52 HIS H 46 ASN ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 34 HIS ** B 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 333 GLN B 867 HIS B1000 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 24505 Z= 0.346 Angle : 0.642 8.638 33328 Z= 0.343 Chirality : 0.046 0.245 3752 Planarity : 0.005 0.090 4062 Dihedral : 16.278 179.093 3826 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 4.13 % Allowed : 16.32 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.15), residues: 2809 helix: 0.58 (0.18), residues: 887 sheet: -0.91 (0.22), residues: 525 loop : -1.70 (0.15), residues: 1397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A1050 HIS 0.007 0.001 HIS B 985 PHE 0.029 0.002 PHE A 411 TYR 0.017 0.002 TYR K 87 ARG 0.009 0.001 ARG A1067 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5618 Ramachandran restraints generated. 2809 Oldfield, 0 Emsley, 2809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5618 Ramachandran restraints generated. 2809 Oldfield, 0 Emsley, 2809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 238 time to evaluate : 2.720 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 541 PHE cc_start: 0.8189 (OUTLIER) cc_final: 0.7597 (p90) REVERT: A 961 GLU cc_start: 0.8089 (tp30) cc_final: 0.7769 (tp30) REVERT: A 981 MET cc_start: 0.7146 (OUTLIER) cc_final: 0.6801 (ttp) REVERT: A 1066 ARG cc_start: 0.4436 (mtt90) cc_final: 0.4080 (mpp80) REVERT: A 1166 TYR cc_start: 0.6108 (OUTLIER) cc_final: 0.5402 (m-10) REVERT: C 119 ASP cc_start: 0.8048 (OUTLIER) cc_final: 0.7483 (m-30) REVERT: C 149 ARG cc_start: 0.7205 (OUTLIER) cc_final: 0.6079 (mpt180) REVERT: C 203 LEU cc_start: 0.5868 (mt) cc_final: 0.5587 (mt) REVERT: F 59 ARG cc_start: 0.6133 (mtm-85) cc_final: 0.5012 (pmt170) REVERT: F 103 LYS cc_start: 0.8167 (mmmt) cc_final: 0.7892 (mtpt) REVERT: F 132 ILE cc_start: 0.8137 (mt) cc_final: 0.7898 (mp) REVERT: H 7 MET cc_start: 0.6660 (OUTLIER) cc_final: 0.6389 (mtp) REVERT: H 8 PHE cc_start: 0.7340 (t80) cc_final: 0.6902 (t80) REVERT: H 31 GLU cc_start: 0.6596 (mm-30) cc_final: 0.5782 (mm-30) REVERT: H 39 MET cc_start: 0.4220 (mmt) cc_final: 0.3537 (mtt) REVERT: H 112 MET cc_start: 0.6054 (OUTLIER) cc_final: 0.5791 (mtm) REVERT: I 17 LYS cc_start: 0.7650 (OUTLIER) cc_final: 0.7269 (tppt) REVERT: I 100 PHE cc_start: 0.4711 (m-80) cc_final: 0.4376 (t80) REVERT: E 42 ASN cc_start: 0.7967 (t0) cc_final: 0.7412 (t0) REVERT: E 47 LEU cc_start: 0.7411 (OUTLIER) cc_final: 0.7082 (mp) REVERT: E 130 ASN cc_start: 0.6334 (p0) cc_final: 0.6085 (p0) REVERT: B 418 MET cc_start: 0.7500 (OUTLIER) cc_final: 0.6985 (tpt) REVERT: B 603 MET cc_start: 0.8593 (ttp) cc_final: 0.8263 (ttp) REVERT: B 752 MET cc_start: 0.8824 (tpt) cc_final: 0.8550 (tpp) REVERT: B 834 ARG cc_start: 0.6729 (ttt90) cc_final: 0.6299 (ttp80) REVERT: B 860 CYS cc_start: 0.7433 (t) cc_final: 0.6926 (p) REVERT: B 872 LYS cc_start: 0.7618 (OUTLIER) cc_final: 0.7191 (tttt) outliers start: 104 outliers final: 52 residues processed: 310 average time/residue: 1.3649 time to fit residues: 487.2237 Evaluate side-chains 291 residues out of total 2522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 228 time to evaluate : 2.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 419 HIS Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 730 VAL Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 981 MET Chi-restraints excluded: chain A residue 1102 ILE Chi-restraints excluded: chain A residue 1135 SER Chi-restraints excluded: chain A residue 1166 TYR Chi-restraints excluded: chain A residue 1173 THR Chi-restraints excluded: chain A residue 1230 LEU Chi-restraints excluded: chain C residue 119 ASP Chi-restraints excluded: chain C residue 149 ARG Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 110 ILE Chi-restraints excluded: chain F residue 126 TRP Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain H residue 7 MET Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 112 MET Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain I residue 17 LYS Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 418 MET Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 496 THR Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain B residue 670 TRP Chi-restraints excluded: chain B residue 840 ASP Chi-restraints excluded: chain B residue 862 GLU Chi-restraints excluded: chain B residue 872 LYS Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 919 VAL Chi-restraints excluded: chain B residue 985 HIS Chi-restraints excluded: chain B residue 1042 GLU Chi-restraints excluded: chain B residue 1047 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 92 optimal weight: 0.7980 chunk 248 optimal weight: 0.7980 chunk 54 optimal weight: 9.9990 chunk 161 optimal weight: 10.0000 chunk 68 optimal weight: 10.0000 chunk 275 optimal weight: 6.9990 chunk 228 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 144 optimal weight: 4.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 76 HIS H 46 ASN ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 333 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 24505 Z= 0.219 Angle : 0.574 7.933 33328 Z= 0.309 Chirality : 0.043 0.204 3752 Planarity : 0.004 0.080 4062 Dihedral : 16.150 178.749 3826 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 3.57 % Allowed : 17.47 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.16), residues: 2809 helix: 0.82 (0.18), residues: 885 sheet: -0.84 (0.22), residues: 517 loop : -1.58 (0.16), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 126 HIS 0.016 0.001 HIS A 419 PHE 0.030 0.002 PHE F 123 TYR 0.014 0.001 TYR H 113 ARG 0.008 0.000 ARG A1067 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5618 Ramachandran restraints generated. 2809 Oldfield, 0 Emsley, 2809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5618 Ramachandran restraints generated. 2809 Oldfield, 0 Emsley, 2809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 234 time to evaluate : 2.548 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 541 PHE cc_start: 0.8142 (OUTLIER) cc_final: 0.7600 (p90) REVERT: A 680 MET cc_start: 0.8319 (mmt) cc_final: 0.8036 (mmt) REVERT: A 961 GLU cc_start: 0.8099 (tp30) cc_final: 0.7790 (tp30) REVERT: A 981 MET cc_start: 0.7086 (OUTLIER) cc_final: 0.6696 (ttp) REVERT: A 1066 ARG cc_start: 0.4556 (mtt90) cc_final: 0.4089 (mpp80) REVERT: A 1166 TYR cc_start: 0.6075 (OUTLIER) cc_final: 0.5372 (m-10) REVERT: C 119 ASP cc_start: 0.7954 (OUTLIER) cc_final: 0.7361 (m-30) REVERT: C 149 ARG cc_start: 0.6988 (OUTLIER) cc_final: 0.5943 (mpt180) REVERT: C 203 LEU cc_start: 0.5937 (mt) cc_final: 0.5682 (mt) REVERT: C 205 ASP cc_start: 0.5343 (m-30) cc_final: 0.4724 (m-30) REVERT: F 59 ARG cc_start: 0.6101 (mtm-85) cc_final: 0.5003 (pmt170) REVERT: F 92 GLU cc_start: 0.6805 (mp0) cc_final: 0.6519 (mp0) REVERT: F 103 LYS cc_start: 0.8156 (mmmt) cc_final: 0.7910 (mtpt) REVERT: F 132 ILE cc_start: 0.8098 (mt) cc_final: 0.7846 (mp) REVERT: H 7 MET cc_start: 0.6622 (OUTLIER) cc_final: 0.6314 (mtp) REVERT: H 8 PHE cc_start: 0.7137 (t80) cc_final: 0.6657 (t80) REVERT: H 31 GLU cc_start: 0.6623 (mm-30) cc_final: 0.6052 (mm-30) REVERT: H 39 MET cc_start: 0.4097 (mmt) cc_final: 0.3384 (mtt) REVERT: H 112 MET cc_start: 0.6062 (OUTLIER) cc_final: 0.5796 (mtm) REVERT: I 17 LYS cc_start: 0.7607 (OUTLIER) cc_final: 0.7218 (tppt) REVERT: I 100 PHE cc_start: 0.4754 (m-80) cc_final: 0.4408 (t80) REVERT: E 42 ASN cc_start: 0.7972 (t0) cc_final: 0.7471 (t0) REVERT: E 47 LEU cc_start: 0.7398 (OUTLIER) cc_final: 0.7097 (mp) REVERT: E 119 GLU cc_start: 0.5147 (mp0) cc_final: 0.4914 (mp0) REVERT: E 130 ASN cc_start: 0.6424 (p0) cc_final: 0.6183 (p0) REVERT: B 603 MET cc_start: 0.8608 (ttp) cc_final: 0.8290 (ttp) REVERT: B 752 MET cc_start: 0.8793 (tpt) cc_final: 0.8522 (tpp) REVERT: B 834 ARG cc_start: 0.6626 (ttt90) cc_final: 0.6138 (ttp80) REVERT: B 860 CYS cc_start: 0.7415 (t) cc_final: 0.6913 (p) outliers start: 90 outliers final: 47 residues processed: 297 average time/residue: 1.3821 time to fit residues: 470.9000 Evaluate side-chains 278 residues out of total 2522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 222 time to evaluate : 2.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 MET Chi-restraints excluded: chain A residue 419 HIS Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 730 VAL Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 981 MET Chi-restraints excluded: chain A residue 1102 ILE Chi-restraints excluded: chain A residue 1135 SER Chi-restraints excluded: chain A residue 1166 TYR Chi-restraints excluded: chain A residue 1173 THR Chi-restraints excluded: chain A residue 1223 THR Chi-restraints excluded: chain A residue 1230 LEU Chi-restraints excluded: chain C residue 119 ASP Chi-restraints excluded: chain C residue 149 ARG Chi-restraints excluded: chain C residue 222 PHE Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain F residue 110 ILE Chi-restraints excluded: chain F residue 126 TRP Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain K residue 79 SER Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain H residue 7 MET Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 112 MET Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain I residue 17 LYS Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 496 THR Chi-restraints excluded: chain B residue 670 TRP Chi-restraints excluded: chain B residue 679 GLN Chi-restraints excluded: chain B residue 840 ASP Chi-restraints excluded: chain B residue 862 GLU Chi-restraints excluded: chain B residue 867 HIS Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 919 VAL Chi-restraints excluded: chain B residue 985 HIS Chi-restraints excluded: chain B residue 1042 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 265 optimal weight: 0.0970 chunk 31 optimal weight: 4.9990 chunk 157 optimal weight: 9.9990 chunk 201 optimal weight: 7.9990 chunk 156 optimal weight: 0.7980 chunk 232 optimal weight: 0.9980 chunk 153 optimal weight: 0.5980 chunk 274 optimal weight: 4.9990 chunk 171 optimal weight: 9.9990 chunk 167 optimal weight: 40.0000 chunk 126 optimal weight: 5.9990 overall best weight: 1.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 ASN ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 333 GLN B1032 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24505 Z= 0.179 Angle : 0.545 7.749 33328 Z= 0.293 Chirality : 0.042 0.188 3752 Planarity : 0.004 0.061 4062 Dihedral : 15.963 178.099 3826 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 3.45 % Allowed : 17.98 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.16), residues: 2809 helix: 1.10 (0.18), residues: 886 sheet: -0.79 (0.22), residues: 526 loop : -1.49 (0.16), residues: 1397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 113 HIS 0.006 0.001 HIS A 419 PHE 0.031 0.001 PHE F 123 TYR 0.017 0.001 TYR H 113 ARG 0.010 0.000 ARG A1067 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5618 Ramachandran restraints generated. 2809 Oldfield, 0 Emsley, 2809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5618 Ramachandran restraints generated. 2809 Oldfield, 0 Emsley, 2809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 239 time to evaluate : 2.847 Fit side-chains revert: symmetry clash REVERT: A 541 PHE cc_start: 0.8061 (OUTLIER) cc_final: 0.7557 (p90) REVERT: A 680 MET cc_start: 0.8343 (mmt) cc_final: 0.8062 (mmt) REVERT: A 961 GLU cc_start: 0.8145 (tp30) cc_final: 0.7864 (tp30) REVERT: A 981 MET cc_start: 0.7248 (OUTLIER) cc_final: 0.6867 (ttp) REVERT: A 1166 TYR cc_start: 0.5986 (OUTLIER) cc_final: 0.5289 (m-10) REVERT: C 149 ARG cc_start: 0.7032 (OUTLIER) cc_final: 0.5927 (mpt180) REVERT: C 205 ASP cc_start: 0.5438 (m-30) cc_final: 0.4919 (m-30) REVERT: C 222 PHE cc_start: 0.6550 (OUTLIER) cc_final: 0.6273 (t80) REVERT: F 59 ARG cc_start: 0.6121 (mtm-85) cc_final: 0.5088 (pmt170) REVERT: F 63 LYS cc_start: 0.8462 (pttp) cc_final: 0.8218 (ptpp) REVERT: F 103 LYS cc_start: 0.8128 (mmmt) cc_final: 0.7848 (mtpt) REVERT: F 106 ARG cc_start: 0.7479 (tpp-160) cc_final: 0.7262 (tpt170) REVERT: F 123 PHE cc_start: 0.7638 (p90) cc_final: 0.6899 (p90) REVERT: F 132 ILE cc_start: 0.8091 (mt) cc_final: 0.7845 (mp) REVERT: H 8 PHE cc_start: 0.7040 (t80) cc_final: 0.6544 (t80) REVERT: H 31 GLU cc_start: 0.6629 (mm-30) cc_final: 0.6054 (mm-30) REVERT: H 39 MET cc_start: 0.3837 (mmt) cc_final: 0.3390 (mtt) REVERT: H 112 MET cc_start: 0.6024 (OUTLIER) cc_final: 0.5743 (mtm) REVERT: I 5 LYS cc_start: 0.7381 (mttp) cc_final: 0.6811 (mtmm) REVERT: I 17 LYS cc_start: 0.7545 (OUTLIER) cc_final: 0.7177 (tppt) REVERT: I 100 PHE cc_start: 0.4736 (m-80) cc_final: 0.4402 (t80) REVERT: E 119 GLU cc_start: 0.5189 (mp0) cc_final: 0.4945 (mp0) REVERT: E 130 ASN cc_start: 0.6486 (p0) cc_final: 0.6228 (p0) REVERT: E 151 GLN cc_start: 0.7109 (OUTLIER) cc_final: 0.6890 (tp40) REVERT: B 494 LEU cc_start: 0.7331 (OUTLIER) cc_final: 0.6859 (mt) REVERT: B 603 MET cc_start: 0.8593 (ttp) cc_final: 0.8299 (ttp) REVERT: B 752 MET cc_start: 0.8772 (tpt) cc_final: 0.8506 (tpp) REVERT: B 834 ARG cc_start: 0.6587 (ttt90) cc_final: 0.6114 (ttp-110) REVERT: B 872 LYS cc_start: 0.7600 (OUTLIER) cc_final: 0.7190 (tttt) outliers start: 87 outliers final: 46 residues processed: 302 average time/residue: 1.3232 time to fit residues: 462.2470 Evaluate side-chains 273 residues out of total 2522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 217 time to evaluate : 2.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 MET Chi-restraints excluded: chain A residue 419 HIS Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 730 VAL Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 981 MET Chi-restraints excluded: chain A residue 1081 VAL Chi-restraints excluded: chain A residue 1166 TYR Chi-restraints excluded: chain A residue 1223 THR Chi-restraints excluded: chain A residue 1230 LEU Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 149 ARG Chi-restraints excluded: chain C residue 222 PHE Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain F residue 110 ILE Chi-restraints excluded: chain F residue 126 TRP Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain K residue 79 SER Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 112 MET Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain I residue 17 LYS Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 151 GLN Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 496 THR Chi-restraints excluded: chain B residue 670 TRP Chi-restraints excluded: chain B residue 679 GLN Chi-restraints excluded: chain B residue 731 ASN Chi-restraints excluded: chain B residue 840 ASP Chi-restraints excluded: chain B residue 867 HIS Chi-restraints excluded: chain B residue 872 LYS Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 919 VAL Chi-restraints excluded: chain B residue 985 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 169 optimal weight: 10.0000 chunk 109 optimal weight: 0.8980 chunk 164 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 53 optimal weight: 10.0000 chunk 174 optimal weight: 20.0000 chunk 187 optimal weight: 5.9990 chunk 135 optimal weight: 3.9990 chunk 25 optimal weight: 0.3980 chunk 215 optimal weight: 0.7980 chunk 249 optimal weight: 1.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 ASN H 67 ASN ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 333 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 24505 Z= 0.183 Angle : 0.540 8.239 33328 Z= 0.290 Chirality : 0.042 0.191 3752 Planarity : 0.004 0.098 4062 Dihedral : 15.858 177.966 3825 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 3.02 % Allowed : 18.94 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.16), residues: 2809 helix: 1.21 (0.18), residues: 886 sheet: -0.74 (0.22), residues: 530 loop : -1.44 (0.16), residues: 1393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1050 HIS 0.006 0.001 HIS H 42 PHE 0.028 0.001 PHE F 123 TYR 0.018 0.001 TYR H 113 ARG 0.006 0.000 ARG C 259 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5618 Ramachandran restraints generated. 2809 Oldfield, 0 Emsley, 2809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5618 Ramachandran restraints generated. 2809 Oldfield, 0 Emsley, 2809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 228 time to evaluate : 2.534 Fit side-chains revert: symmetry clash REVERT: A 328 ILE cc_start: 0.9185 (OUTLIER) cc_final: 0.8953 (pt) REVERT: A 541 PHE cc_start: 0.8045 (OUTLIER) cc_final: 0.7536 (p90) REVERT: A 680 MET cc_start: 0.8387 (mmt) cc_final: 0.8110 (mmt) REVERT: A 961 GLU cc_start: 0.8146 (tp30) cc_final: 0.7853 (tp30) REVERT: A 981 MET cc_start: 0.7173 (OUTLIER) cc_final: 0.6787 (ttp) REVERT: A 1166 TYR cc_start: 0.5985 (OUTLIER) cc_final: 0.5293 (m-10) REVERT: C 149 ARG cc_start: 0.7018 (OUTLIER) cc_final: 0.5915 (mpt180) REVERT: C 205 ASP cc_start: 0.5585 (m-30) cc_final: 0.5050 (m-30) REVERT: F 59 ARG cc_start: 0.6104 (mtm-85) cc_final: 0.5076 (pmt170) REVERT: F 63 LYS cc_start: 0.8464 (pttp) cc_final: 0.8218 (ptpp) REVERT: F 92 GLU cc_start: 0.6826 (mp0) cc_final: 0.6620 (mp0) REVERT: F 103 LYS cc_start: 0.8130 (mmmt) cc_final: 0.7846 (mtpt) REVERT: F 106 ARG cc_start: 0.7475 (tpp-160) cc_final: 0.7242 (tpt170) REVERT: F 123 PHE cc_start: 0.7665 (p90) cc_final: 0.6963 (p90) REVERT: F 132 ILE cc_start: 0.8126 (mt) cc_final: 0.7876 (mp) REVERT: H 8 PHE cc_start: 0.7034 (t80) cc_final: 0.6536 (t80) REVERT: H 31 GLU cc_start: 0.6631 (mm-30) cc_final: 0.6060 (mm-30) REVERT: H 39 MET cc_start: 0.3940 (mmt) cc_final: 0.3485 (mtt) REVERT: H 112 MET cc_start: 0.5984 (OUTLIER) cc_final: 0.5752 (mtm) REVERT: H 145 LYS cc_start: 0.7034 (OUTLIER) cc_final: 0.6277 (mmtp) REVERT: I 5 LYS cc_start: 0.7428 (mttp) cc_final: 0.6799 (mtmm) REVERT: I 17 LYS cc_start: 0.7597 (OUTLIER) cc_final: 0.7208 (tppt) REVERT: I 100 PHE cc_start: 0.4730 (m-80) cc_final: 0.4401 (t80) REVERT: E 130 ASN cc_start: 0.6388 (p0) cc_final: 0.6116 (p0) REVERT: E 151 GLN cc_start: 0.7032 (OUTLIER) cc_final: 0.6813 (tp40) REVERT: B 420 LYS cc_start: 0.7871 (pttp) cc_final: 0.7374 (mttt) REVERT: B 603 MET cc_start: 0.8594 (ttp) cc_final: 0.8298 (ttp) REVERT: B 752 MET cc_start: 0.8781 (tpt) cc_final: 0.8528 (tpp) REVERT: B 834 ARG cc_start: 0.6610 (ttt90) cc_final: 0.6117 (ttp80) REVERT: B 872 LYS cc_start: 0.7611 (OUTLIER) cc_final: 0.7198 (tttt) outliers start: 76 outliers final: 51 residues processed: 281 average time/residue: 1.3622 time to fit residues: 439.8757 Evaluate side-chains 276 residues out of total 2522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 215 time to evaluate : 2.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 405 MET Chi-restraints excluded: chain A residue 419 HIS Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 730 VAL Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 860 GLU Chi-restraints excluded: chain A residue 981 MET Chi-restraints excluded: chain A residue 1093 ASP Chi-restraints excluded: chain A residue 1166 TYR Chi-restraints excluded: chain A residue 1223 THR Chi-restraints excluded: chain A residue 1230 LEU Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 149 ARG Chi-restraints excluded: chain C residue 222 PHE Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain F residue 107 GLN Chi-restraints excluded: chain F residue 110 ILE Chi-restraints excluded: chain F residue 126 TRP Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain K residue 79 SER Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 112 MET Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain H residue 145 LYS Chi-restraints excluded: chain I residue 17 LYS Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 151 GLN Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 496 THR Chi-restraints excluded: chain B residue 598 GLU Chi-restraints excluded: chain B residue 670 TRP Chi-restraints excluded: chain B residue 679 GLN Chi-restraints excluded: chain B residue 731 ASN Chi-restraints excluded: chain B residue 840 ASP Chi-restraints excluded: chain B residue 867 HIS Chi-restraints excluded: chain B residue 872 LYS Chi-restraints excluded: chain B residue 919 VAL Chi-restraints excluded: chain B residue 985 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 263 optimal weight: 7.9990 chunk 240 optimal weight: 3.9990 chunk 255 optimal weight: 5.9990 chunk 154 optimal weight: 9.9990 chunk 111 optimal weight: 0.8980 chunk 201 optimal weight: 6.9990 chunk 78 optimal weight: 8.9990 chunk 231 optimal weight: 4.9990 chunk 242 optimal weight: 5.9990 chunk 168 optimal weight: 20.0000 chunk 270 optimal weight: 0.9980 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 ASN H 67 ASN ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 333 GLN B 867 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 24505 Z= 0.304 Angle : 0.614 9.106 33328 Z= 0.328 Chirality : 0.045 0.227 3752 Planarity : 0.005 0.100 4062 Dihedral : 15.911 178.485 3825 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 3.22 % Allowed : 19.13 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.16), residues: 2809 helix: 1.01 (0.18), residues: 889 sheet: -0.78 (0.22), residues: 525 loop : -1.52 (0.16), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A1050 HIS 0.005 0.001 HIS B 437 PHE 0.028 0.002 PHE A 411 TYR 0.022 0.002 TYR H 113 ARG 0.006 0.001 ARG C 259 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5618 Ramachandran restraints generated. 2809 Oldfield, 0 Emsley, 2809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5618 Ramachandran restraints generated. 2809 Oldfield, 0 Emsley, 2809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 216 time to evaluate : 2.937 Fit side-chains revert: symmetry clash REVERT: A 328 ILE cc_start: 0.9189 (OUTLIER) cc_final: 0.8965 (pt) REVERT: A 541 PHE cc_start: 0.8149 (OUTLIER) cc_final: 0.7660 (p90) REVERT: A 642 ILE cc_start: 0.8271 (mm) cc_final: 0.8047 (mm) REVERT: A 680 MET cc_start: 0.8472 (mmt) cc_final: 0.8178 (mmt) REVERT: A 961 GLU cc_start: 0.8142 (tp30) cc_final: 0.7840 (tp30) REVERT: A 981 MET cc_start: 0.7150 (OUTLIER) cc_final: 0.6764 (ttp) REVERT: A 1166 TYR cc_start: 0.6055 (OUTLIER) cc_final: 0.5356 (m-10) REVERT: C 149 ARG cc_start: 0.7214 (OUTLIER) cc_final: 0.6130 (mpt180) REVERT: C 205 ASP cc_start: 0.5543 (m-30) cc_final: 0.5107 (m-30) REVERT: F 59 ARG cc_start: 0.6077 (mtm-85) cc_final: 0.5008 (pmt170) REVERT: F 63 LYS cc_start: 0.8471 (pttp) cc_final: 0.8223 (ptpp) REVERT: F 92 GLU cc_start: 0.6809 (mp0) cc_final: 0.6570 (mp0) REVERT: F 103 LYS cc_start: 0.8147 (mmmt) cc_final: 0.7878 (mtpt) REVERT: F 123 PHE cc_start: 0.7663 (p90) cc_final: 0.6933 (p90) REVERT: F 132 ILE cc_start: 0.8220 (mt) cc_final: 0.7975 (mp) REVERT: H 8 PHE cc_start: 0.7026 (t80) cc_final: 0.6592 (t80) REVERT: H 31 GLU cc_start: 0.6624 (mm-30) cc_final: 0.5732 (mm-30) REVERT: H 39 MET cc_start: 0.3976 (mmt) cc_final: 0.3483 (mtt) REVERT: I 5 LYS cc_start: 0.7333 (mttp) cc_final: 0.6786 (mtmm) REVERT: I 17 LYS cc_start: 0.7603 (OUTLIER) cc_final: 0.7205 (tppt) REVERT: I 100 PHE cc_start: 0.4770 (m-80) cc_final: 0.4415 (t80) REVERT: E 130 ASN cc_start: 0.6356 (p0) cc_final: 0.6082 (p0) REVERT: E 151 GLN cc_start: 0.7139 (OUTLIER) cc_final: 0.6880 (tp40) REVERT: B 603 MET cc_start: 0.8603 (ttp) cc_final: 0.8291 (ttp) REVERT: B 752 MET cc_start: 0.8834 (tpt) cc_final: 0.8566 (tpp) REVERT: B 834 ARG cc_start: 0.6728 (ttt90) cc_final: 0.6265 (ttp80) REVERT: B 872 LYS cc_start: 0.7605 (OUTLIER) cc_final: 0.7228 (tttt) outliers start: 81 outliers final: 50 residues processed: 275 average time/residue: 1.3344 time to fit residues: 423.5478 Evaluate side-chains 266 residues out of total 2522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 208 time to evaluate : 2.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 405 MET Chi-restraints excluded: chain A residue 419 HIS Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 730 VAL Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 860 GLU Chi-restraints excluded: chain A residue 981 MET Chi-restraints excluded: chain A residue 1081 VAL Chi-restraints excluded: chain A residue 1093 ASP Chi-restraints excluded: chain A residue 1102 ILE Chi-restraints excluded: chain A residue 1112 ILE Chi-restraints excluded: chain A residue 1135 SER Chi-restraints excluded: chain A residue 1166 TYR Chi-restraints excluded: chain A residue 1223 THR Chi-restraints excluded: chain A residue 1230 LEU Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 149 ARG Chi-restraints excluded: chain C residue 222 PHE Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain F residue 110 ILE Chi-restraints excluded: chain F residue 126 TRP Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain K residue 79 SER Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain I residue 17 LYS Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 151 GLN Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 496 THR Chi-restraints excluded: chain B residue 598 GLU Chi-restraints excluded: chain B residue 670 TRP Chi-restraints excluded: chain B residue 679 GLN Chi-restraints excluded: chain B residue 840 ASP Chi-restraints excluded: chain B residue 872 LYS Chi-restraints excluded: chain B residue 919 VAL Chi-restraints excluded: chain B residue 985 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 165 optimal weight: 4.9990 chunk 128 optimal weight: 0.7980 chunk 188 optimal weight: 4.9990 chunk 283 optimal weight: 2.9990 chunk 261 optimal weight: 1.9990 chunk 226 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 174 optimal weight: 10.0000 chunk 138 optimal weight: 0.9990 chunk 179 optimal weight: 9.9990 chunk 240 optimal weight: 4.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1063 HIS H 46 ASN H 67 ASN ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 333 GLN B 867 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 24505 Z= 0.195 Angle : 0.561 9.281 33328 Z= 0.300 Chirality : 0.042 0.191 3752 Planarity : 0.004 0.092 4062 Dihedral : 15.785 178.191 3825 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 2.62 % Allowed : 19.73 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.16), residues: 2809 helix: 1.18 (0.18), residues: 886 sheet: -0.71 (0.22), residues: 518 loop : -1.45 (0.16), residues: 1405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 113 HIS 0.006 0.001 HIS H 42 PHE 0.027 0.002 PHE A 411 TYR 0.022 0.001 TYR H 113 ARG 0.010 0.000 ARG H 29 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5618 Ramachandran restraints generated. 2809 Oldfield, 0 Emsley, 2809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5618 Ramachandran restraints generated. 2809 Oldfield, 0 Emsley, 2809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 216 time to evaluate : 2.922 Fit side-chains REVERT: A 328 ILE cc_start: 0.9198 (OUTLIER) cc_final: 0.8967 (pt) REVERT: A 541 PHE cc_start: 0.8038 (OUTLIER) cc_final: 0.7602 (p90) REVERT: A 642 ILE cc_start: 0.8217 (mm) cc_final: 0.7993 (mm) REVERT: A 680 MET cc_start: 0.8425 (mmt) cc_final: 0.8150 (mmt) REVERT: A 961 GLU cc_start: 0.8150 (tp30) cc_final: 0.7852 (tp30) REVERT: A 981 MET cc_start: 0.7218 (OUTLIER) cc_final: 0.6809 (ttp) REVERT: A 1066 ARG cc_start: 0.4408 (mtt90) cc_final: 0.3954 (mpp80) REVERT: A 1166 TYR cc_start: 0.5982 (OUTLIER) cc_final: 0.5287 (m-10) REVERT: C 149 ARG cc_start: 0.7008 (OUTLIER) cc_final: 0.5980 (mpt180) REVERT: C 205 ASP cc_start: 0.5517 (m-30) cc_final: 0.5254 (m-30) REVERT: C 259 ARG cc_start: 0.7324 (mtp85) cc_final: 0.6752 (ttp80) REVERT: F 59 ARG cc_start: 0.6015 (mtm-85) cc_final: 0.5007 (pmt170) REVERT: F 63 LYS cc_start: 0.8467 (pttp) cc_final: 0.8221 (ptpp) REVERT: F 103 LYS cc_start: 0.8160 (mmmt) cc_final: 0.7877 (mmmm) REVERT: F 106 ARG cc_start: 0.7482 (tpp-160) cc_final: 0.7276 (tpt170) REVERT: F 123 PHE cc_start: 0.7644 (p90) cc_final: 0.6969 (p90) REVERT: F 132 ILE cc_start: 0.8188 (mt) cc_final: 0.7948 (mp) REVERT: K 23 ARG cc_start: 0.7492 (ttp80) cc_final: 0.7288 (ttp-110) REVERT: H 8 PHE cc_start: 0.6916 (t80) cc_final: 0.6447 (t80) REVERT: H 31 GLU cc_start: 0.6695 (mm-30) cc_final: 0.5785 (mm-30) REVERT: H 39 MET cc_start: 0.3953 (mmt) cc_final: 0.3474 (mtt) REVERT: H 84 THR cc_start: 0.7650 (p) cc_final: 0.7083 (t) REVERT: I 5 LYS cc_start: 0.7328 (mttp) cc_final: 0.6791 (mtmm) REVERT: I 17 LYS cc_start: 0.7524 (OUTLIER) cc_final: 0.7185 (tppt) REVERT: I 100 PHE cc_start: 0.4751 (m-80) cc_final: 0.4414 (t80) REVERT: E 130 ASN cc_start: 0.6412 (p0) cc_final: 0.6188 (p0) REVERT: E 151 GLN cc_start: 0.7011 (OUTLIER) cc_final: 0.6758 (tp40) REVERT: B 603 MET cc_start: 0.8616 (ttp) cc_final: 0.8324 (ttp) REVERT: B 752 MET cc_start: 0.8796 (tpt) cc_final: 0.8527 (tpp) REVERT: B 834 ARG cc_start: 0.6561 (ttt90) cc_final: 0.6075 (ttp80) REVERT: B 872 LYS cc_start: 0.7596 (OUTLIER) cc_final: 0.7229 (tttt) outliers start: 66 outliers final: 47 residues processed: 267 average time/residue: 1.3582 time to fit residues: 418.0597 Evaluate side-chains 266 residues out of total 2522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 211 time to evaluate : 2.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 405 MET Chi-restraints excluded: chain A residue 419 HIS Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 730 VAL Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 860 GLU Chi-restraints excluded: chain A residue 981 MET Chi-restraints excluded: chain A residue 1081 VAL Chi-restraints excluded: chain A residue 1166 TYR Chi-restraints excluded: chain A residue 1223 THR Chi-restraints excluded: chain A residue 1230 LEU Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 149 ARG Chi-restraints excluded: chain C residue 222 PHE Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain F residue 110 ILE Chi-restraints excluded: chain F residue 126 TRP Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain K residue 79 SER Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain I residue 17 LYS Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 151 GLN Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 496 THR Chi-restraints excluded: chain B residue 598 GLU Chi-restraints excluded: chain B residue 670 TRP Chi-restraints excluded: chain B residue 679 GLN Chi-restraints excluded: chain B residue 840 ASP Chi-restraints excluded: chain B residue 872 LYS Chi-restraints excluded: chain B residue 919 VAL Chi-restraints excluded: chain B residue 985 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 69 optimal weight: 10.0000 chunk 208 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 226 optimal weight: 3.9990 chunk 94 optimal weight: 8.9990 chunk 232 optimal weight: 2.9990 chunk 28 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 chunk 198 optimal weight: 3.9990 chunk 12 optimal weight: 7.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 ASN ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 GLN ** B 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 333 GLN B 867 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.138179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.089115 restraints weight = 38515.047| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 2.35 r_work: 0.3026 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 24505 Z= 0.220 Angle : 0.580 15.573 33328 Z= 0.307 Chirality : 0.043 0.193 3752 Planarity : 0.004 0.093 4062 Dihedral : 15.751 178.576 3825 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 2.74 % Allowed : 19.73 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.16), residues: 2809 helix: 1.17 (0.18), residues: 888 sheet: -0.65 (0.22), residues: 518 loop : -1.45 (0.16), residues: 1403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A1050 HIS 0.006 0.001 HIS H 42 PHE 0.027 0.002 PHE A 411 TYR 0.020 0.002 TYR H 113 ARG 0.011 0.000 ARG K 23 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8608.74 seconds wall clock time: 152 minutes 57.43 seconds (9177.43 seconds total)