Starting phenix.real_space_refine on Thu Jun 26 10:09:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ifn_35422/06_2025/8ifn_35422.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ifn_35422/06_2025/8ifn_35422.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ifn_35422/06_2025/8ifn_35422.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ifn_35422/06_2025/8ifn_35422.map" model { file = "/net/cci-nas-00/data/ceres_data/8ifn_35422/06_2025/8ifn_35422.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ifn_35422/06_2025/8ifn_35422.cif" } resolution = 2.81 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 174 5.16 5 C 19290 2.51 5 N 5025 2.21 5 O 5952 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 108 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 30441 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 3, 'TRANS': 124} Chain: "C" Number of atoms: 9124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1180, 9124 Classifications: {'peptide': 1180} Link IDs: {'PTRANS': 58, 'TRANS': 1121} Chain breaks: 4 Chain: "G" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Restraints were copied for chains: I, H, B, E, D, F Time building chain proxies: 25.33, per 1000 atoms: 0.83 Number of scatterers: 30441 At special positions: 0 Unit cell: (155.88, 158.045, 169.953, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 174 16.00 O 5952 8.00 N 5025 7.00 C 19290 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM30367 O5 NAG H 2 .*. O " rejected from bonding due to valence issues. Atom "HETATM30417 O5 NAG I 2 .*. O " rejected from bonding due to valence issues. Atom "HETATM30317 O5 NAG G 2 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=3, symmetry=0 Links applied ALPHA1-3 " BMA G 3 " - " MAN G 4 " " BMA H 3 " - " MAN H 4 " " BMA I 3 " - " MAN I 4 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " NAG-ASN " NAG G 1 " - " ASN B 410 " " NAG H 1 " - " ASN C 410 " " NAG I 1 " - " ASN E 410 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.26 Conformation dependent library (CDL) restraints added in 3.7 seconds 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7254 Finding SS restraints... Secondary structure from input PDB file: 97 helices and 75 sheets defined 23.3% alpha, 27.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.19 Creating SS restraints... Processing helix chain 'B' and resid 37 through 41 removed outlier: 3.906A pdb=" N ASP B 41 " --> pdb=" O THR B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 53 Processing helix chain 'B' and resid 209 through 213 Processing helix chain 'B' and resid 225 through 231 removed outlier: 3.728A pdb=" N TYR B 231 " --> pdb=" O SER B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 307 removed outlier: 3.910A pdb=" N ARG B 307 " --> pdb=" O GLN B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 350 Processing helix chain 'B' and resid 351 through 353 No H-bonds generated for 'chain 'B' and resid 351 through 353' Processing helix chain 'B' and resid 385 through 389 Processing helix chain 'B' and resid 395 through 399 Processing helix chain 'B' and resid 410 through 417 removed outlier: 3.676A pdb=" N LEU B 414 " --> pdb=" O ASN B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 456 removed outlier: 4.931A pdb=" N SER B 454 " --> pdb=" O SER B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 468 Processing helix chain 'B' and resid 524 through 529 removed outlier: 4.248A pdb=" N SER B 528 " --> pdb=" O PRO B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 550 Processing helix chain 'B' and resid 678 through 682 removed outlier: 3.723A pdb=" N ILE B 682 " --> pdb=" O CYS B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 805 through 811 Processing helix chain 'B' and resid 814 through 822 Processing helix chain 'B' and resid 824 through 850 removed outlier: 4.161A pdb=" N CYS B 828 " --> pdb=" O TYR B 824 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER B 829 " --> pdb=" O GLY B 825 " (cutoff:3.500A) Processing helix chain 'B' and resid 888 through 898 removed outlier: 3.629A pdb=" N VAL B 898 " --> pdb=" O LEU B 894 " (cutoff:3.500A) Processing helix chain 'B' and resid 910 through 915 Processing helix chain 'B' and resid 922 through 927 removed outlier: 3.605A pdb=" N GLN B 927 " --> pdb=" O LEU B 923 " (cutoff:3.500A) Processing helix chain 'B' and resid 940 through 953 removed outlier: 3.811A pdb=" N GLU B 944 " --> pdb=" O ASP B 940 " (cutoff:3.500A) Processing helix chain 'B' and resid 954 through 959 Processing helix chain 'B' and resid 971 through 982 Processing helix chain 'B' and resid 987 through 992 Processing helix chain 'B' and resid 995 through 1009 removed outlier: 3.639A pdb=" N ASN B 999 " --> pdb=" O LYS B 995 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN B1009 " --> pdb=" O LEU B1005 " (cutoff:3.500A) Processing helix chain 'B' and resid 1016 through 1039 removed outlier: 3.818A pdb=" N LEU B1036 " --> pdb=" O ALA B1032 " (cutoff:3.500A) Processing helix chain 'B' and resid 1040 through 1042 No H-bonds generated for 'chain 'B' and resid 1040 through 1042' Processing helix chain 'B' and resid 1050 through 1058 Processing helix chain 'B' and resid 1059 through 1107 removed outlier: 4.057A pdb=" N ALA B1065 " --> pdb=" O PRO B1061 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG B1069 " --> pdb=" O ALA B1065 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU B1070 " --> pdb=" O GLN B1066 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU B1094 " --> pdb=" O GLU B1090 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN B1097 " --> pdb=" O ALA B1093 " (cutoff:3.500A) Processing helix chain 'B' and resid 1219 through 1223 Processing helix chain 'A' and resid 87 through 91 removed outlier: 3.594A pdb=" N THR A 91 " --> pdb=" O PRO A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 110 removed outlier: 3.776A pdb=" N LYS A 110 " --> pdb=" O GLY A 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 41 removed outlier: 3.907A pdb=" N ASP C 41 " --> pdb=" O THR C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 53 Processing helix chain 'C' and resid 209 through 213 Processing helix chain 'C' and resid 225 through 231 removed outlier: 3.727A pdb=" N TYR C 231 " --> pdb=" O SER C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 350 Processing helix chain 'C' and resid 351 through 353 No H-bonds generated for 'chain 'C' and resid 351 through 353' Processing helix chain 'C' and resid 385 through 389 Processing helix chain 'C' and resid 395 through 399 Processing helix chain 'C' and resid 410 through 417 removed outlier: 3.676A pdb=" N LEU C 414 " --> pdb=" O ASN C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 456 removed outlier: 4.931A pdb=" N SER C 454 " --> pdb=" O SER C 451 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 468 Processing helix chain 'C' and resid 524 through 529 removed outlier: 4.246A pdb=" N SER C 528 " --> pdb=" O PRO C 525 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 550 Processing helix chain 'C' and resid 678 through 682 removed outlier: 3.724A pdb=" N ILE C 682 " --> pdb=" O CYS C 679 " (cutoff:3.500A) Processing helix chain 'C' and resid 805 through 811 Processing helix chain 'C' and resid 814 through 822 Processing helix chain 'C' and resid 824 through 850 removed outlier: 4.160A pdb=" N CYS C 828 " --> pdb=" O TYR C 824 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER C 829 " --> pdb=" O GLY C 825 " (cutoff:3.500A) Processing helix chain 'C' and resid 888 through 898 removed outlier: 3.629A pdb=" N VAL C 898 " --> pdb=" O LEU C 894 " (cutoff:3.500A) Processing helix chain 'C' and resid 910 through 915 Processing helix chain 'C' and resid 922 through 927 removed outlier: 3.604A pdb=" N GLN C 927 " --> pdb=" O LEU C 923 " (cutoff:3.500A) Processing helix chain 'C' and resid 940 through 953 removed outlier: 3.811A pdb=" N GLU C 944 " --> pdb=" O ASP C 940 " (cutoff:3.500A) Processing helix chain 'C' and resid 954 through 959 Processing helix chain 'C' and resid 971 through 982 Processing helix chain 'C' and resid 987 through 992 Processing helix chain 'C' and resid 995 through 1009 removed outlier: 3.639A pdb=" N ASN C 999 " --> pdb=" O LYS C 995 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN C1009 " --> pdb=" O LEU C1005 " (cutoff:3.500A) Processing helix chain 'C' and resid 1016 through 1039 removed outlier: 3.818A pdb=" N LEU C1036 " --> pdb=" O ALA C1032 " (cutoff:3.500A) Processing helix chain 'C' and resid 1040 through 1042 No H-bonds generated for 'chain 'C' and resid 1040 through 1042' Processing helix chain 'C' and resid 1050 through 1058 Processing helix chain 'C' and resid 1059 through 1107 removed outlier: 4.056A pdb=" N ALA C1065 " --> pdb=" O PRO C1061 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG C1069 " --> pdb=" O ALA C1065 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU C1070 " --> pdb=" O GLN C1066 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU C1094 " --> pdb=" O GLU C1090 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN C1097 " --> pdb=" O ALA C1093 " (cutoff:3.500A) Processing helix chain 'C' and resid 1219 through 1223 Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.595A pdb=" N THR D 91 " --> pdb=" O PRO D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 110 removed outlier: 3.777A pdb=" N LYS D 110 " --> pdb=" O GLY D 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 41 removed outlier: 3.907A pdb=" N ASP E 41 " --> pdb=" O THR E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 53 Processing helix chain 'E' and resid 209 through 213 Processing helix chain 'E' and resid 225 through 231 removed outlier: 3.728A pdb=" N TYR E 231 " --> pdb=" O SER E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 350 Processing helix chain 'E' and resid 351 through 353 No H-bonds generated for 'chain 'E' and resid 351 through 353' Processing helix chain 'E' and resid 385 through 389 Processing helix chain 'E' and resid 395 through 399 Processing helix chain 'E' and resid 410 through 417 removed outlier: 3.676A pdb=" N LEU E 414 " --> pdb=" O ASN E 410 " (cutoff:3.500A) Processing helix chain 'E' and resid 449 through 456 removed outlier: 4.931A pdb=" N SER E 454 " --> pdb=" O SER E 451 " (cutoff:3.500A) Processing helix chain 'E' and resid 463 through 468 Processing helix chain 'E' and resid 524 through 529 removed outlier: 4.246A pdb=" N SER E 528 " --> pdb=" O PRO E 525 " (cutoff:3.500A) Processing helix chain 'E' and resid 546 through 550 Processing helix chain 'E' and resid 678 through 682 removed outlier: 3.724A pdb=" N ILE E 682 " --> pdb=" O CYS E 679 " (cutoff:3.500A) Processing helix chain 'E' and resid 805 through 811 Processing helix chain 'E' and resid 814 through 822 Processing helix chain 'E' and resid 824 through 850 removed outlier: 4.161A pdb=" N CYS E 828 " --> pdb=" O TYR E 824 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER E 829 " --> pdb=" O GLY E 825 " (cutoff:3.500A) Processing helix chain 'E' and resid 888 through 898 removed outlier: 3.629A pdb=" N VAL E 898 " --> pdb=" O LEU E 894 " (cutoff:3.500A) Processing helix chain 'E' and resid 910 through 915 Processing helix chain 'E' and resid 922 through 927 removed outlier: 3.605A pdb=" N GLN E 927 " --> pdb=" O LEU E 923 " (cutoff:3.500A) Processing helix chain 'E' and resid 940 through 953 removed outlier: 3.811A pdb=" N GLU E 944 " --> pdb=" O ASP E 940 " (cutoff:3.500A) Processing helix chain 'E' and resid 954 through 959 Processing helix chain 'E' and resid 971 through 982 Processing helix chain 'E' and resid 987 through 992 Processing helix chain 'E' and resid 995 through 1009 removed outlier: 3.639A pdb=" N ASN E 999 " --> pdb=" O LYS E 995 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN E1009 " --> pdb=" O LEU E1005 " (cutoff:3.500A) Processing helix chain 'E' and resid 1016 through 1039 removed outlier: 3.818A pdb=" N LEU E1036 " --> pdb=" O ALA E1032 " (cutoff:3.500A) Processing helix chain 'E' and resid 1040 through 1042 No H-bonds generated for 'chain 'E' and resid 1040 through 1042' Processing helix chain 'E' and resid 1050 through 1058 Processing helix chain 'E' and resid 1059 through 1107 removed outlier: 4.056A pdb=" N ALA E1065 " --> pdb=" O PRO E1061 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG E1069 " --> pdb=" O ALA E1065 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU E1070 " --> pdb=" O GLN E1066 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU E1094 " --> pdb=" O GLU E1090 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN E1097 " --> pdb=" O ALA E1093 " (cutoff:3.500A) Processing helix chain 'E' and resid 1219 through 1223 Processing helix chain 'F' and resid 87 through 91 removed outlier: 3.594A pdb=" N THR F 91 " --> pdb=" O PRO F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 110 removed outlier: 3.776A pdb=" N LYS F 110 " --> pdb=" O GLY F 106 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 33 through 35 removed outlier: 5.920A pdb=" N ASP B 34 " --> pdb=" O VAL B 102 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS B 99 " --> pdb=" O HIS B 91 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 67 through 75 removed outlier: 4.286A pdb=" N ARG B 335 " --> pdb=" O ASP B 326 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 83 through 85 removed outlier: 5.874A pdb=" N VAL B 263 " --> pdb=" O THR B 283 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N THR B 283 " --> pdb=" O VAL B 263 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LEU B 265 " --> pdb=" O PHE B 281 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 88 through 89 removed outlier: 7.272A pdb=" N SER B 88 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N THR B 206 " --> pdb=" O SER B 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 110 through 111 Processing sheet with id=AA6, first strand: chain 'B' and resid 110 through 111 Processing sheet with id=AA7, first strand: chain 'B' and resid 127 through 129 removed outlier: 3.785A pdb=" N ALA B 309 " --> pdb=" O THR B 139 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 153 through 155 Processing sheet with id=AA9, first strand: chain 'B' and resid 214 through 215 removed outlier: 3.573A pdb=" N SER B 215 " --> pdb=" O ASN B 218 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 689 through 690 removed outlier: 5.787A pdb=" N SER B 362 " --> pdb=" O VAL B 661 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VAL B 661 " --> pdb=" O SER B 362 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N SER B 364 " --> pdb=" O VAL B 659 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N VAL B 659 " --> pdb=" O SER B 364 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N CYS B 713 " --> pdb=" O PHE B 674 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 373 through 375 Processing sheet with id=AB3, first strand: chain 'B' and resid 400 through 404 removed outlier: 6.740A pdb=" N THR B 477 " --> pdb=" O CYS B 425 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N CYS B 425 " --> pdb=" O THR B 477 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU B 479 " --> pdb=" O PHE B 423 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N PHE B 423 " --> pdb=" O LEU B 479 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LEU B 481 " --> pdb=" O ASN B 421 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 408 through 409 Processing sheet with id=AB5, first strand: chain 'B' and resid 513 through 515 removed outlier: 5.191A pdb=" N SER B 498 " --> pdb=" O VAL B 561 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL B 561 " --> pdb=" O SER B 498 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N ILE B 500 " --> pdb=" O SER B 559 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N SER B 559 " --> pdb=" O ILE B 500 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS B 502 " --> pdb=" O SER B 557 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY B 558 " --> pdb=" O ASP B 539 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASP B 539 " --> pdb=" O GLY B 558 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 630 through 632 removed outlier: 6.530A pdb=" N VAL B 631 " --> pdb=" O VAL B 639 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 717 through 724 removed outlier: 6.855A pdb=" N VAL B 718 " --> pdb=" O LEU B 759 " (cutoff:3.500A) removed outlier: 9.008A pdb=" N SER B 761 " --> pdb=" O VAL B 718 " (cutoff:3.500A) removed outlier: 9.900A pdb=" N SER B 720 " --> pdb=" O SER B 761 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N LEU B 735 " --> pdb=" O LEU B 731 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 768 through 769 removed outlier: 5.855A pdb=" N ILE B 768 " --> pdb=" O SER C 858 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 777 through 779 removed outlier: 5.512A pdb=" N VAL B1150 " --> pdb=" O LYS B1174 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N PHE B1172 " --> pdb=" O ALA B1152 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 788 through 790 Processing sheet with id=AC2, first strand: chain 'B' and resid 788 through 790 removed outlier: 5.963A pdb=" N TYR B1141 " --> pdb=" O HIS B1122 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N HIS B1122 " --> pdb=" O TYR B1141 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 802 through 804 Processing sheet with id=AC4, first strand: chain 'B' and resid 857 through 858 Processing sheet with id=AC5, first strand: chain 'B' and resid 1202 through 1205 removed outlier: 4.143A pdb=" N CYS B1164 " --> pdb=" O VAL B1205 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 3 through 7 removed outlier: 4.037A pdb=" N LEU A 81 " --> pdb=" O LEU A 20 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 58 through 60 removed outlier: 6.739A pdb=" N TRP A 36 " --> pdb=" O LEU A 48 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N PHE A 50 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ILE A 34 " --> pdb=" O PHE A 50 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 58 through 60 removed outlier: 6.739A pdb=" N TRP A 36 " --> pdb=" O LEU A 48 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N PHE A 50 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ILE A 34 " --> pdb=" O PHE A 50 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 33 through 35 removed outlier: 5.920A pdb=" N ASP C 34 " --> pdb=" O VAL C 102 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS C 99 " --> pdb=" O HIS C 91 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 67 through 75 removed outlier: 4.287A pdb=" N ARG C 335 " --> pdb=" O ASP C 326 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 83 through 85 removed outlier: 5.875A pdb=" N VAL C 263 " --> pdb=" O THR C 283 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N THR C 283 " --> pdb=" O VAL C 263 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU C 265 " --> pdb=" O PHE C 281 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 88 through 89 removed outlier: 7.273A pdb=" N SER C 88 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N THR C 206 " --> pdb=" O SER C 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'C' and resid 110 through 111 Processing sheet with id=AD5, first strand: chain 'C' and resid 110 through 111 Processing sheet with id=AD6, first strand: chain 'C' and resid 127 through 129 removed outlier: 3.784A pdb=" N ALA C 309 " --> pdb=" O THR C 139 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 153 through 155 Processing sheet with id=AD8, first strand: chain 'C' and resid 214 through 215 removed outlier: 3.574A pdb=" N SER C 215 " --> pdb=" O ASN C 218 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 689 through 690 removed outlier: 5.788A pdb=" N SER C 362 " --> pdb=" O VAL C 661 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N VAL C 661 " --> pdb=" O SER C 362 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N SER C 364 " --> pdb=" O VAL C 659 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N VAL C 659 " --> pdb=" O SER C 364 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N CYS C 713 " --> pdb=" O PHE C 674 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 373 through 375 Processing sheet with id=AE2, first strand: chain 'C' and resid 400 through 404 removed outlier: 6.739A pdb=" N THR C 477 " --> pdb=" O CYS C 425 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N CYS C 425 " --> pdb=" O THR C 477 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LEU C 479 " --> pdb=" O PHE C 423 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N PHE C 423 " --> pdb=" O LEU C 479 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LEU C 481 " --> pdb=" O ASN C 421 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 408 through 409 Processing sheet with id=AE4, first strand: chain 'C' and resid 513 through 515 removed outlier: 5.193A pdb=" N SER C 498 " --> pdb=" O VAL C 561 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL C 561 " --> pdb=" O SER C 498 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N ILE C 500 " --> pdb=" O SER C 559 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N SER C 559 " --> pdb=" O ILE C 500 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS C 502 " --> pdb=" O SER C 557 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY C 558 " --> pdb=" O ASP C 539 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASP C 539 " --> pdb=" O GLY C 558 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 630 through 632 removed outlier: 6.530A pdb=" N VAL C 631 " --> pdb=" O VAL C 639 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 717 through 724 removed outlier: 6.855A pdb=" N VAL C 718 " --> pdb=" O LEU C 759 " (cutoff:3.500A) removed outlier: 9.007A pdb=" N SER C 761 " --> pdb=" O VAL C 718 " (cutoff:3.500A) removed outlier: 9.900A pdb=" N SER C 720 " --> pdb=" O SER C 761 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N LEU C 735 " --> pdb=" O LEU C 731 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 768 through 769 removed outlier: 5.850A pdb=" N ILE C 768 " --> pdb=" O SER E 858 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'C' and resid 777 through 779 removed outlier: 5.513A pdb=" N VAL C1150 " --> pdb=" O LYS C1174 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N PHE C1172 " --> pdb=" O ALA C1152 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 788 through 790 Processing sheet with id=AF1, first strand: chain 'C' and resid 788 through 790 removed outlier: 5.962A pdb=" N TYR C1141 " --> pdb=" O HIS C1122 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N HIS C1122 " --> pdb=" O TYR C1141 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 802 through 804 Processing sheet with id=AF3, first strand: chain 'C' and resid 1202 through 1205 removed outlier: 4.143A pdb=" N CYS C1164 " --> pdb=" O VAL C1205 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 3 through 7 removed outlier: 4.036A pdb=" N LEU D 81 " --> pdb=" O LEU D 20 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 58 through 60 removed outlier: 6.738A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N PHE D 50 " --> pdb=" O ILE D 34 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE D 34 " --> pdb=" O PHE D 50 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 58 through 60 removed outlier: 6.738A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N PHE D 50 " --> pdb=" O ILE D 34 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE D 34 " --> pdb=" O PHE D 50 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 33 through 35 removed outlier: 5.920A pdb=" N ASP E 34 " --> pdb=" O VAL E 102 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS E 99 " --> pdb=" O HIS E 91 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 67 through 75 removed outlier: 4.285A pdb=" N ARG E 335 " --> pdb=" O ASP E 326 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'E' and resid 83 through 85 removed outlier: 5.874A pdb=" N VAL E 263 " --> pdb=" O THR E 283 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N THR E 283 " --> pdb=" O VAL E 263 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU E 265 " --> pdb=" O PHE E 281 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 88 through 89 removed outlier: 7.273A pdb=" N SER E 88 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N THR E 206 " --> pdb=" O SER E 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG1 Processing sheet with id=AG2, first strand: chain 'E' and resid 110 through 111 Processing sheet with id=AG3, first strand: chain 'E' and resid 110 through 111 Processing sheet with id=AG4, first strand: chain 'E' and resid 127 through 129 removed outlier: 3.785A pdb=" N ALA E 309 " --> pdb=" O THR E 139 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'E' and resid 153 through 155 Processing sheet with id=AG6, first strand: chain 'E' and resid 214 through 215 removed outlier: 3.574A pdb=" N SER E 215 " --> pdb=" O ASN E 218 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'E' and resid 689 through 690 removed outlier: 5.787A pdb=" N SER E 362 " --> pdb=" O VAL E 661 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N VAL E 661 " --> pdb=" O SER E 362 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N SER E 364 " --> pdb=" O VAL E 659 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N VAL E 659 " --> pdb=" O SER E 364 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N CYS E 713 " --> pdb=" O PHE E 674 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'E' and resid 373 through 375 Processing sheet with id=AG9, first strand: chain 'E' and resid 400 through 404 removed outlier: 6.740A pdb=" N THR E 477 " --> pdb=" O CYS E 425 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N CYS E 425 " --> pdb=" O THR E 477 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU E 479 " --> pdb=" O PHE E 423 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N PHE E 423 " --> pdb=" O LEU E 479 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LEU E 481 " --> pdb=" O ASN E 421 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'E' and resid 408 through 409 Processing sheet with id=AH2, first strand: chain 'E' and resid 513 through 515 removed outlier: 5.193A pdb=" N SER E 498 " --> pdb=" O VAL E 561 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL E 561 " --> pdb=" O SER E 498 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N ILE E 500 " --> pdb=" O SER E 559 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N SER E 559 " --> pdb=" O ILE E 500 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS E 502 " --> pdb=" O SER E 557 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY E 558 " --> pdb=" O ASP E 539 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASP E 539 " --> pdb=" O GLY E 558 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'E' and resid 630 through 632 removed outlier: 6.531A pdb=" N VAL E 631 " --> pdb=" O VAL E 639 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'E' and resid 717 through 724 removed outlier: 6.855A pdb=" N VAL E 718 " --> pdb=" O LEU E 759 " (cutoff:3.500A) removed outlier: 9.008A pdb=" N SER E 761 " --> pdb=" O VAL E 718 " (cutoff:3.500A) removed outlier: 9.900A pdb=" N SER E 720 " --> pdb=" O SER E 761 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N LEU E 735 " --> pdb=" O LEU E 731 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'E' and resid 777 through 779 removed outlier: 5.514A pdb=" N VAL E1150 " --> pdb=" O LYS E1174 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N PHE E1172 " --> pdb=" O ALA E1152 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'E' and resid 788 through 790 Processing sheet with id=AH7, first strand: chain 'E' and resid 788 through 790 removed outlier: 5.962A pdb=" N TYR E1141 " --> pdb=" O HIS E1122 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N HIS E1122 " --> pdb=" O TYR E1141 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'E' and resid 802 through 804 Processing sheet with id=AH9, first strand: chain 'E' and resid 1202 through 1205 removed outlier: 4.143A pdb=" N CYS E1164 " --> pdb=" O VAL E1205 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'F' and resid 3 through 7 removed outlier: 4.038A pdb=" N LEU F 81 " --> pdb=" O LEU F 20 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'F' and resid 58 through 60 removed outlier: 6.738A pdb=" N TRP F 36 " --> pdb=" O LEU F 48 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N PHE F 50 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ILE F 34 " --> pdb=" O PHE F 50 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'F' and resid 58 through 60 removed outlier: 6.738A pdb=" N TRP F 36 " --> pdb=" O LEU F 48 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N PHE F 50 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ILE F 34 " --> pdb=" O PHE F 50 " (cutoff:3.500A) 1181 hydrogen bonds defined for protein. 3018 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 16.47 Time building geometry restraints manager: 8.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 9785 1.34 - 1.46: 7462 1.46 - 1.58: 13659 1.58 - 1.70: 0 1.70 - 1.83: 234 Bond restraints: 31140 Sorted by residual: bond pdb=" C THR E 283 " pdb=" N LEU E 284 " ideal model delta sigma weight residual 1.331 1.262 0.069 2.07e-02 2.33e+03 1.11e+01 bond pdb=" C THR B 283 " pdb=" N LEU B 284 " ideal model delta sigma weight residual 1.331 1.262 0.069 2.07e-02 2.33e+03 1.10e+01 bond pdb=" C THR C 283 " pdb=" N LEU C 284 " ideal model delta sigma weight residual 1.331 1.262 0.069 2.07e-02 2.33e+03 1.10e+01 bond pdb=" CB ASN E 342 " pdb=" CG ASN E 342 " ideal model delta sigma weight residual 1.516 1.463 0.053 2.50e-02 1.60e+03 4.56e+00 bond pdb=" CB ASN C 342 " pdb=" CG ASN C 342 " ideal model delta sigma weight residual 1.516 1.463 0.053 2.50e-02 1.60e+03 4.54e+00 ... (remaining 31135 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.12: 42181 5.12 - 10.24: 149 10.24 - 15.36: 9 15.36 - 20.48: 3 20.48 - 25.61: 3 Bond angle restraints: 42345 Sorted by residual: angle pdb=" CB MET E 913 " pdb=" CG MET E 913 " pdb=" SD MET E 913 " ideal model delta sigma weight residual 112.70 138.31 -25.61 3.00e+00 1.11e-01 7.28e+01 angle pdb=" CB MET C 913 " pdb=" CG MET C 913 " pdb=" SD MET C 913 " ideal model delta sigma weight residual 112.70 138.25 -25.55 3.00e+00 1.11e-01 7.25e+01 angle pdb=" CB MET B 913 " pdb=" CG MET B 913 " pdb=" SD MET B 913 " ideal model delta sigma weight residual 112.70 138.25 -25.55 3.00e+00 1.11e-01 7.25e+01 angle pdb=" CA MET E 913 " pdb=" CB MET E 913 " pdb=" CG MET E 913 " ideal model delta sigma weight residual 114.10 129.40 -15.30 2.00e+00 2.50e-01 5.86e+01 angle pdb=" CA MET C 913 " pdb=" CB MET C 913 " pdb=" CG MET C 913 " ideal model delta sigma weight residual 114.10 129.35 -15.25 2.00e+00 2.50e-01 5.82e+01 ... (remaining 42340 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.84: 17491 22.84 - 45.69: 892 45.69 - 68.53: 106 68.53 - 91.38: 48 91.38 - 114.22: 12 Dihedral angle restraints: 18549 sinusoidal: 7161 harmonic: 11388 Sorted by residual: dihedral pdb=" CA TYR C 361 " pdb=" C TYR C 361 " pdb=" N SER C 362 " pdb=" CA SER C 362 " ideal model delta harmonic sigma weight residual 180.00 135.77 44.23 0 5.00e+00 4.00e-02 7.83e+01 dihedral pdb=" CA TYR B 361 " pdb=" C TYR B 361 " pdb=" N SER B 362 " pdb=" CA SER B 362 " ideal model delta harmonic sigma weight residual 180.00 135.79 44.21 0 5.00e+00 4.00e-02 7.82e+01 dihedral pdb=" CA TYR E 361 " pdb=" C TYR E 361 " pdb=" N SER E 362 " pdb=" CA SER E 362 " ideal model delta harmonic sigma weight residual 180.00 135.83 44.17 0 5.00e+00 4.00e-02 7.80e+01 ... (remaining 18546 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 4181 0.083 - 0.166: 519 0.166 - 0.249: 28 0.249 - 0.332: 9 0.332 - 0.415: 3 Chirality restraints: 4740 Sorted by residual: chirality pdb=" CA CYS E 237 " pdb=" N CYS E 237 " pdb=" C CYS E 237 " pdb=" CB CYS E 237 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.31e+00 chirality pdb=" CA CYS B 237 " pdb=" N CYS B 237 " pdb=" C CYS B 237 " pdb=" CB CYS B 237 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.24e+00 chirality pdb=" CA CYS C 237 " pdb=" N CYS C 237 " pdb=" C CYS C 237 " pdb=" CB CYS C 237 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.21e+00 ... (remaining 4737 not shown) Planarity restraints: 5493 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN B 815 " 0.016 2.00e-02 2.50e+03 3.18e-02 1.01e+01 pdb=" CD GLN B 815 " -0.055 2.00e-02 2.50e+03 pdb=" OE1 GLN B 815 " 0.021 2.00e-02 2.50e+03 pdb=" NE2 GLN B 815 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN E 815 " -0.016 2.00e-02 2.50e+03 3.17e-02 1.01e+01 pdb=" CD GLN E 815 " 0.055 2.00e-02 2.50e+03 pdb=" OE1 GLN E 815 " -0.021 2.00e-02 2.50e+03 pdb=" NE2 GLN E 815 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN C 815 " 0.016 2.00e-02 2.50e+03 3.17e-02 1.01e+01 pdb=" CD GLN C 815 " -0.055 2.00e-02 2.50e+03 pdb=" OE1 GLN C 815 " 0.021 2.00e-02 2.50e+03 pdb=" NE2 GLN C 815 " 0.019 2.00e-02 2.50e+03 ... (remaining 5490 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.25: 81 2.25 - 2.91: 12966 2.91 - 3.57: 41320 3.57 - 4.24: 73054 4.24 - 4.90: 123997 Nonbonded interactions: 251418 Sorted by model distance: nonbonded pdb=" NH2 ARG B 511 " pdb=" O5 NAG H 2 " model vdw 1.587 2.496 nonbonded pdb=" NH2 ARG C 511 " pdb=" O5 NAG I 2 " model vdw 1.590 2.496 nonbonded pdb=" NH2 ARG E 511 " pdb=" O5 NAG G 2 " model vdw 1.596 2.496 nonbonded pdb=" SG CYS C 727 " pdb=" SG CYS C 736 " model vdw 2.015 3.760 nonbonded pdb=" SG CYS E 727 " pdb=" SG CYS E 736 " model vdw 2.015 3.760 ... (remaining 251413 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.19 Found NCS groups: ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.360 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: 0.030 Extract box with map and model: 1.110 Check model and map are aligned: 0.200 Set scattering table: 0.240 Process input model: 80.070 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.274 31155 Z= 0.401 Angle : 0.939 25.605 42381 Z= 0.498 Chirality : 0.055 0.415 4740 Planarity : 0.005 0.056 5490 Dihedral : 14.513 114.221 11295 Min Nonbonded Distance : 1.587 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.15 % Favored : 93.70 % Rotamer: Outliers : 1.28 % Allowed : 1.07 % Favored : 97.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -1.46 (0.13), residues: 3888 helix: -0.30 (0.19), residues: 732 sheet: -0.53 (0.16), residues: 1047 loop : -1.43 (0.12), residues: 2109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 960 HIS 0.005 0.002 HIS B 194 PHE 0.033 0.002 PHE C 423 TYR 0.048 0.002 TYR B 361 ARG 0.008 0.001 ARG E 46 Details of bonding type rmsd link_NAG-ASN : bond 0.00718 ( 3) link_NAG-ASN : angle 2.61668 ( 9) link_BETA1-4 : bond 0.19307 ( 6) link_BETA1-4 : angle 7.19059 ( 18) link_ALPHA1-3 : bond 0.00051 ( 3) link_ALPHA1-3 : angle 2.02948 ( 9) hydrogen bonds : bond 0.14824 ( 1088) hydrogen bonds : angle 6.84630 ( 3018) covalent geometry : bond 0.00857 (31140) covalent geometry : angle 0.92656 (42345) Misc. bond : bond 0.10973 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 244 time to evaluate : 3.162 Fit side-chains REVERT: B 278 MET cc_start: 0.9119 (mtp) cc_final: 0.8802 (mtm) REVERT: B 757 MET cc_start: 0.8654 (mtp) cc_final: 0.8395 (mtp) REVERT: A 110 LYS cc_start: 0.8615 (mttp) cc_final: 0.8298 (mptt) REVERT: A 116 MET cc_start: 0.8362 (mmt) cc_final: 0.7963 (mmt) REVERT: D 107 MET cc_start: 0.7397 (tmm) cc_final: 0.7080 (tmm) outliers start: 43 outliers final: 0 residues processed: 254 average time/residue: 1.3973 time to fit residues: 420.2124 Evaluate side-chains 175 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 3.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 329 optimal weight: 0.8980 chunk 295 optimal weight: 4.9990 chunk 164 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 chunk 199 optimal weight: 4.9990 chunk 157 optimal weight: 3.9990 chunk 305 optimal weight: 0.0030 chunk 118 optimal weight: 10.0000 chunk 185 optimal weight: 9.9990 chunk 227 optimal weight: 3.9990 chunk 354 optimal weight: 0.7980 overall best weight: 0.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 280 GLN ** B 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 GLN B 842 GLN ** B1146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 77 ASN ** A 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 GLN C 466 GLN C 826 GLN C 842 GLN ** C1146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 GLN E 466 GLN E1031 GLN ** E1146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 57 ASN F 102 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.134276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.098706 restraints weight = 44776.968| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.19 r_work: 0.2994 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.1168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 31155 Z= 0.128 Angle : 0.633 10.202 42381 Z= 0.334 Chirality : 0.045 0.183 4740 Planarity : 0.004 0.051 5490 Dihedral : 7.829 79.854 4497 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.22 % Favored : 94.62 % Rotamer: Outliers : 0.83 % Allowed : 6.86 % Favored : 92.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.06 (0.13), residues: 3888 helix: 0.32 (0.20), residues: 717 sheet: -0.26 (0.16), residues: 1023 loop : -1.29 (0.12), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 36 HIS 0.003 0.001 HIS C 681 PHE 0.013 0.001 PHE A 50 TYR 0.024 0.001 TYR B 361 ARG 0.003 0.000 ARG B 691 Details of bonding type rmsd link_NAG-ASN : bond 0.00628 ( 3) link_NAG-ASN : angle 1.27952 ( 9) link_BETA1-4 : bond 0.00515 ( 6) link_BETA1-4 : angle 3.24387 ( 18) link_ALPHA1-3 : bond 0.00912 ( 3) link_ALPHA1-3 : angle 1.18566 ( 9) hydrogen bonds : bond 0.04732 ( 1088) hydrogen bonds : angle 5.50555 ( 3018) covalent geometry : bond 0.00279 (31140) covalent geometry : angle 0.62933 (42345) Misc. bond : bond 0.00096 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 206 time to evaluate : 3.223 Fit side-chains REVERT: B 278 MET cc_start: 0.9245 (mtp) cc_final: 0.9018 (mtp) REVERT: B 467 PHE cc_start: 0.7923 (m-80) cc_final: 0.7659 (m-80) REVERT: B 943 MET cc_start: 0.8444 (ttp) cc_final: 0.8196 (ttm) REVERT: B 1090 GLU cc_start: 0.8807 (mm-30) cc_final: 0.8602 (mm-30) REVERT: A 77 ASN cc_start: 0.7305 (OUTLIER) cc_final: 0.7056 (p0) REVERT: A 80 TYR cc_start: 0.7421 (m-80) cc_final: 0.7119 (m-10) REVERT: A 110 LYS cc_start: 0.8550 (mttp) cc_final: 0.8115 (mmtt) REVERT: C 569 MET cc_start: 0.7337 (mtp) cc_final: 0.6964 (mtm) REVERT: E 819 GLN cc_start: 0.8432 (pt0) cc_final: 0.8023 (tm130) REVERT: E 943 MET cc_start: 0.8340 (ttp) cc_final: 0.8129 (ttm) outliers start: 28 outliers final: 10 residues processed: 220 average time/residue: 1.2749 time to fit residues: 338.4274 Evaluate side-chains 186 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 175 time to evaluate : 3.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 852 SER Chi-restraints excluded: chain B residue 1216 THR Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 77 ASN Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 852 SER Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 450 LEU Chi-restraints excluded: chain E residue 852 SER Chi-restraints excluded: chain F residue 28 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 69 optimal weight: 5.9990 chunk 379 optimal weight: 30.0000 chunk 54 optimal weight: 0.3980 chunk 333 optimal weight: 0.2980 chunk 99 optimal weight: 2.9990 chunk 223 optimal weight: 3.9990 chunk 60 optimal weight: 8.9990 chunk 272 optimal weight: 8.9990 chunk 58 optimal weight: 4.9990 chunk 184 optimal weight: 20.0000 chunk 79 optimal weight: 0.8980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1146 HIS ** A 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 466 GLN ** C 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1146 HIS ** D 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 466 GLN ** E 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 842 GLN E 848 ASN E1146 HIS ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 77 ASN F 102 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.132915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.095981 restraints weight = 44691.730| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.15 r_work: 0.2967 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 31155 Z= 0.161 Angle : 0.621 10.501 42381 Z= 0.325 Chirality : 0.044 0.177 4740 Planarity : 0.004 0.048 5490 Dihedral : 7.013 63.223 4497 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.40 % Favored : 94.52 % Rotamer: Outliers : 1.01 % Allowed : 9.69 % Favored : 89.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.13), residues: 3888 helix: 0.54 (0.20), residues: 717 sheet: -0.17 (0.16), residues: 1014 loop : -1.32 (0.12), residues: 2157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 36 HIS 0.004 0.001 HIS B 264 PHE 0.014 0.001 PHE E 183 TYR 0.022 0.002 TYR F 118 ARG 0.003 0.000 ARG E 46 Details of bonding type rmsd link_NAG-ASN : bond 0.00433 ( 3) link_NAG-ASN : angle 0.92372 ( 9) link_BETA1-4 : bond 0.00610 ( 6) link_BETA1-4 : angle 2.70618 ( 18) link_ALPHA1-3 : bond 0.00842 ( 3) link_ALPHA1-3 : angle 1.18648 ( 9) hydrogen bonds : bond 0.04798 ( 1088) hydrogen bonds : angle 5.27385 ( 3018) covalent geometry : bond 0.00386 (31140) covalent geometry : angle 0.61852 (42345) Misc. bond : bond 0.00010 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 196 time to evaluate : 3.281 Fit side-chains REVERT: B 361 TYR cc_start: 0.5856 (OUTLIER) cc_final: 0.5651 (m-10) REVERT: B 467 PHE cc_start: 0.7930 (m-80) cc_final: 0.7633 (m-80) REVERT: A 110 LYS cc_start: 0.8619 (mttp) cc_final: 0.8188 (mmtt) REVERT: C 361 TYR cc_start: 0.5965 (OUTLIER) cc_final: 0.5734 (m-10) REVERT: C 1090 GLU cc_start: 0.8770 (mm-30) cc_final: 0.8570 (mm-30) REVERT: E 361 TYR cc_start: 0.5927 (OUTLIER) cc_final: 0.5494 (m-10) REVERT: E 819 GLN cc_start: 0.8448 (pt0) cc_final: 0.8104 (tm130) REVERT: F 77 ASN cc_start: 0.7272 (OUTLIER) cc_final: 0.6997 (p0) outliers start: 34 outliers final: 14 residues processed: 218 average time/residue: 1.6080 time to fit residues: 422.9663 Evaluate side-chains 198 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 180 time to evaluate : 4.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 361 TYR Chi-restraints excluded: chain B residue 669 THR Chi-restraints excluded: chain B residue 784 THR Chi-restraints excluded: chain B residue 852 SER Chi-restraints excluded: chain B residue 1014 THR Chi-restraints excluded: chain B residue 1216 THR Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 361 TYR Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 784 THR Chi-restraints excluded: chain C residue 852 SER Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain E residue 361 TYR Chi-restraints excluded: chain E residue 669 THR Chi-restraints excluded: chain E residue 852 SER Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 77 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 135 optimal weight: 0.2980 chunk 74 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 chunk 379 optimal weight: 30.0000 chunk 303 optimal weight: 0.9980 chunk 332 optimal weight: 1.9990 chunk 187 optimal weight: 10.0000 chunk 373 optimal weight: 4.9990 chunk 132 optimal weight: 5.9990 chunk 314 optimal weight: 0.0870 chunk 337 optimal weight: 3.9990 overall best weight: 1.4762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 792 GLN A 77 ASN ** A 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 ASN C 466 GLN ** C 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 848 ASN ** D 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 792 GLN E1213 ASN F 77 ASN ** F 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.133409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.096482 restraints weight = 44702.035| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.10 r_work: 0.2980 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 31155 Z= 0.143 Angle : 0.593 10.075 42381 Z= 0.311 Chirality : 0.044 0.173 4740 Planarity : 0.004 0.048 5490 Dihedral : 6.359 50.070 4497 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.20 % Favored : 94.73 % Rotamer: Outliers : 1.22 % Allowed : 11.03 % Favored : 87.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -0.89 (0.13), residues: 3888 helix: 0.70 (0.20), residues: 720 sheet: 0.06 (0.16), residues: 966 loop : -1.37 (0.12), residues: 2202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 103 HIS 0.004 0.001 HIS C 681 PHE 0.015 0.001 PHE E 183 TYR 0.021 0.001 TYR F 118 ARG 0.003 0.000 ARG B 614 Details of bonding type rmsd link_NAG-ASN : bond 0.00475 ( 3) link_NAG-ASN : angle 0.88740 ( 9) link_BETA1-4 : bond 0.00482 ( 6) link_BETA1-4 : angle 2.45597 ( 18) link_ALPHA1-3 : bond 0.01123 ( 3) link_ALPHA1-3 : angle 1.21979 ( 9) hydrogen bonds : bond 0.04466 ( 1088) hydrogen bonds : angle 5.08416 ( 3018) covalent geometry : bond 0.00337 (31140) covalent geometry : angle 0.59062 (42345) Misc. bond : bond 0.00019 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 202 time to evaluate : 3.129 Fit side-chains revert: symmetry clash REVERT: B 497 TYR cc_start: 0.6370 (m-80) cc_final: 0.6167 (m-80) REVERT: B 826 GLN cc_start: 0.7883 (mm110) cc_final: 0.7139 (pm20) REVERT: B 1149 VAL cc_start: 0.7079 (t) cc_final: 0.6625 (t) REVERT: C 361 TYR cc_start: 0.6021 (OUTLIER) cc_final: 0.5602 (m-10) REVERT: E 819 GLN cc_start: 0.8518 (pt0) cc_final: 0.8161 (tm130) REVERT: F 102 ASN cc_start: 0.8202 (OUTLIER) cc_final: 0.7938 (t0) REVERT: F 107 MET cc_start: 0.7663 (tmm) cc_final: 0.7457 (tmm) outliers start: 41 outliers final: 25 residues processed: 227 average time/residue: 1.2478 time to fit residues: 344.6869 Evaluate side-chains 210 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 183 time to evaluate : 3.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 361 TYR Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 669 THR Chi-restraints excluded: chain B residue 677 VAL Chi-restraints excluded: chain B residue 784 THR Chi-restraints excluded: chain B residue 852 SER Chi-restraints excluded: chain B residue 1216 THR Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain C residue 361 TYR Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 784 THR Chi-restraints excluded: chain C residue 852 SER Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 361 TYR Chi-restraints excluded: chain E residue 450 LEU Chi-restraints excluded: chain E residue 623 VAL Chi-restraints excluded: chain E residue 677 VAL Chi-restraints excluded: chain E residue 852 SER Chi-restraints excluded: chain E residue 940 ASP Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 102 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 326 optimal weight: 0.9980 chunk 191 optimal weight: 2.9990 chunk 53 optimal weight: 0.4980 chunk 180 optimal weight: 9.9990 chunk 228 optimal weight: 0.7980 chunk 346 optimal weight: 9.9990 chunk 34 optimal weight: 7.9990 chunk 46 optimal weight: 9.9990 chunk 144 optimal weight: 7.9990 chunk 88 optimal weight: 4.9990 chunk 374 optimal weight: 1.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 199 ASN B 466 GLN ** B 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 848 ASN ** A 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 466 GLN ** C 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 792 GLN D 102 ASN E 466 GLN ** E 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.133574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.096831 restraints weight = 44566.717| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.11 r_work: 0.2986 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 31155 Z= 0.140 Angle : 0.580 10.054 42381 Z= 0.305 Chirality : 0.043 0.172 4740 Planarity : 0.004 0.048 5490 Dihedral : 5.719 47.385 4497 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.25 % Favored : 94.68 % Rotamer: Outliers : 1.76 % Allowed : 11.30 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -0.85 (0.13), residues: 3888 helix: 0.84 (0.20), residues: 726 sheet: -0.01 (0.16), residues: 960 loop : -1.34 (0.12), residues: 2202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 103 HIS 0.005 0.001 HIS C 681 PHE 0.015 0.001 PHE E 183 TYR 0.032 0.001 TYR C 499 ARG 0.002 0.000 ARG B 46 Details of bonding type rmsd link_NAG-ASN : bond 0.00458 ( 3) link_NAG-ASN : angle 0.86649 ( 9) link_BETA1-4 : bond 0.00504 ( 6) link_BETA1-4 : angle 2.21254 ( 18) link_ALPHA1-3 : bond 0.01124 ( 3) link_ALPHA1-3 : angle 1.18802 ( 9) hydrogen bonds : bond 0.04345 ( 1088) hydrogen bonds : angle 4.96159 ( 3018) covalent geometry : bond 0.00331 (31140) covalent geometry : angle 0.57781 (42345) Misc. bond : bond 0.00019 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 215 time to evaluate : 4.327 Fit side-chains REVERT: B 467 PHE cc_start: 0.7926 (m-80) cc_final: 0.7677 (m-80) REVERT: B 826 GLN cc_start: 0.7879 (mm110) cc_final: 0.7161 (pm20) REVERT: B 1149 VAL cc_start: 0.6977 (OUTLIER) cc_final: 0.6492 (t) REVERT: C 361 TYR cc_start: 0.5742 (OUTLIER) cc_final: 0.5209 (m-10) REVERT: C 569 MET cc_start: 0.7779 (mtm) cc_final: 0.7365 (mmm) REVERT: C 913 MET cc_start: 0.7485 (pmm) cc_final: 0.5193 (mmp) REVERT: C 1017 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7777 (mp0) REVERT: E 400 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.8196 (tttt) REVERT: E 696 MET cc_start: 0.8795 (ttm) cc_final: 0.8493 (ttp) REVERT: E 727 CYS cc_start: 0.4298 (OUTLIER) cc_final: 0.3924 (p) REVERT: E 819 GLN cc_start: 0.8436 (pt0) cc_final: 0.8162 (tm130) REVERT: E 873 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8479 (mt) REVERT: E 943 MET cc_start: 0.8716 (OUTLIER) cc_final: 0.8422 (ttp) REVERT: E 1149 VAL cc_start: 0.6804 (OUTLIER) cc_final: 0.6411 (t) REVERT: F 102 ASN cc_start: 0.8178 (OUTLIER) cc_final: 0.7923 (t0) outliers start: 59 outliers final: 25 residues processed: 252 average time/residue: 1.3691 time to fit residues: 424.1804 Evaluate side-chains 224 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 191 time to evaluate : 3.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 361 TYR Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 669 THR Chi-restraints excluded: chain B residue 677 VAL Chi-restraints excluded: chain B residue 736 CYS Chi-restraints excluded: chain B residue 784 THR Chi-restraints excluded: chain B residue 852 SER Chi-restraints excluded: chain B residue 985 ILE Chi-restraints excluded: chain B residue 1014 THR Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain C residue 361 TYR Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 784 THR Chi-restraints excluded: chain C residue 852 SER Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 361 TYR Chi-restraints excluded: chain E residue 400 LYS Chi-restraints excluded: chain E residue 623 VAL Chi-restraints excluded: chain E residue 669 THR Chi-restraints excluded: chain E residue 677 VAL Chi-restraints excluded: chain E residue 727 CYS Chi-restraints excluded: chain E residue 852 SER Chi-restraints excluded: chain E residue 873 LEU Chi-restraints excluded: chain E residue 940 ASP Chi-restraints excluded: chain E residue 943 MET Chi-restraints excluded: chain E residue 1149 VAL Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 102 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 302 optimal weight: 8.9990 chunk 157 optimal weight: 0.8980 chunk 183 optimal weight: 0.9990 chunk 51 optimal weight: 9.9990 chunk 385 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 201 optimal weight: 0.9980 chunk 231 optimal weight: 0.5980 chunk 55 optimal weight: 5.9990 chunk 348 optimal weight: 0.0570 chunk 29 optimal weight: 5.9990 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 466 GLN C 566 GLN C1132 ASN ** D 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 199 ASN ** E 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 57 ASN ** F 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.135787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.099278 restraints weight = 44810.076| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.11 r_work: 0.3030 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 31155 Z= 0.105 Angle : 0.542 10.344 42381 Z= 0.285 Chirality : 0.042 0.169 4740 Planarity : 0.004 0.049 5490 Dihedral : 5.183 43.034 4497 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.66 % Favored : 95.27 % Rotamer: Outliers : 1.61 % Allowed : 11.75 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -0.69 (0.13), residues: 3888 helix: 1.06 (0.20), residues: 729 sheet: -0.01 (0.17), residues: 912 loop : -1.19 (0.12), residues: 2247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 103 HIS 0.004 0.001 HIS C 681 PHE 0.015 0.001 PHE E 183 TYR 0.024 0.001 TYR C 499 ARG 0.003 0.000 ARG E 691 Details of bonding type rmsd link_NAG-ASN : bond 0.00542 ( 3) link_NAG-ASN : angle 0.86915 ( 9) link_BETA1-4 : bond 0.00514 ( 6) link_BETA1-4 : angle 1.90479 ( 18) link_ALPHA1-3 : bond 0.01221 ( 3) link_ALPHA1-3 : angle 1.31989 ( 9) hydrogen bonds : bond 0.03688 ( 1088) hydrogen bonds : angle 4.77568 ( 3018) covalent geometry : bond 0.00235 (31140) covalent geometry : angle 0.54009 (42345) Misc. bond : bond 0.00006 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 213 time to evaluate : 2.995 Fit side-chains revert: symmetry clash REVERT: B 467 PHE cc_start: 0.7852 (m-80) cc_final: 0.7578 (m-80) REVERT: B 479 LEU cc_start: 0.7510 (tp) cc_final: 0.7268 (mt) REVERT: B 727 CYS cc_start: 0.4780 (OUTLIER) cc_final: 0.4135 (p) REVERT: B 826 GLN cc_start: 0.7751 (mm110) cc_final: 0.7038 (pm20) REVERT: B 1149 VAL cc_start: 0.6448 (OUTLIER) cc_final: 0.5973 (t) REVERT: A 80 TYR cc_start: 0.6948 (m-80) cc_final: 0.6728 (m-10) REVERT: C 819 GLN cc_start: 0.8226 (OUTLIER) cc_final: 0.7999 (tm-30) REVERT: C 826 GLN cc_start: 0.7833 (mm110) cc_final: 0.7104 (pm20) REVERT: C 912 CYS cc_start: 0.7084 (m) cc_final: 0.5215 (t) REVERT: C 1017 GLU cc_start: 0.8224 (mm-30) cc_final: 0.7650 (mp0) REVERT: C 1059 ASP cc_start: 0.7377 (m-30) cc_final: 0.6949 (m-30) REVERT: C 1149 VAL cc_start: 0.6775 (t) cc_final: 0.6416 (t) REVERT: E 543 LYS cc_start: 0.6558 (tptt) cc_final: 0.5418 (ttpp) REVERT: E 696 MET cc_start: 0.8732 (ttm) cc_final: 0.8471 (ttp) REVERT: E 727 CYS cc_start: 0.4102 (OUTLIER) cc_final: 0.3741 (p) REVERT: E 819 GLN cc_start: 0.8356 (pt0) cc_final: 0.8111 (tm130) REVERT: E 1149 VAL cc_start: 0.6467 (OUTLIER) cc_final: 0.5976 (t) REVERT: F 102 ASN cc_start: 0.8080 (OUTLIER) cc_final: 0.7707 (t0) outliers start: 54 outliers final: 22 residues processed: 248 average time/residue: 1.2896 time to fit residues: 388.0855 Evaluate side-chains 216 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 188 time to evaluate : 3.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 361 TYR Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 677 VAL Chi-restraints excluded: chain B residue 727 CYS Chi-restraints excluded: chain B residue 736 CYS Chi-restraints excluded: chain B residue 784 THR Chi-restraints excluded: chain B residue 852 SER Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1216 THR Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain C residue 361 TYR Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 784 THR Chi-restraints excluded: chain C residue 819 GLN Chi-restraints excluded: chain C residue 852 SER Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 361 TYR Chi-restraints excluded: chain E residue 623 VAL Chi-restraints excluded: chain E residue 669 THR Chi-restraints excluded: chain E residue 727 CYS Chi-restraints excluded: chain E residue 784 THR Chi-restraints excluded: chain E residue 852 SER Chi-restraints excluded: chain E residue 1149 VAL Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 102 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 113 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 218 optimal weight: 7.9990 chunk 332 optimal weight: 0.9990 chunk 371 optimal weight: 7.9990 chunk 189 optimal weight: 2.9990 chunk 259 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 chunk 261 optimal weight: 9.9990 chunk 188 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 981 ASN ** A 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 466 GLN ** C 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 836 HIS ** D 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 102 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.132218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.094916 restraints weight = 44461.366| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.15 r_work: 0.2949 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 31155 Z= 0.196 Angle : 0.627 10.495 42381 Z= 0.328 Chirality : 0.045 0.169 4740 Planarity : 0.004 0.049 5490 Dihedral : 5.462 43.181 4497 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.50 % Favored : 94.42 % Rotamer: Outliers : 1.64 % Allowed : 12.94 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.13), residues: 3888 helix: 0.90 (0.20), residues: 717 sheet: -0.12 (0.16), residues: 1002 loop : -1.26 (0.12), residues: 2169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 103 HIS 0.005 0.001 HIS C1138 PHE 0.015 0.002 PHE E 183 TYR 0.035 0.002 TYR E 499 ARG 0.005 0.000 ARG B 841 Details of bonding type rmsd link_NAG-ASN : bond 0.00304 ( 3) link_NAG-ASN : angle 0.85907 ( 9) link_BETA1-4 : bond 0.00456 ( 6) link_BETA1-4 : angle 2.09805 ( 18) link_ALPHA1-3 : bond 0.00959 ( 3) link_ALPHA1-3 : angle 1.28500 ( 9) hydrogen bonds : bond 0.04865 ( 1088) hydrogen bonds : angle 4.97564 ( 3018) covalent geometry : bond 0.00474 (31140) covalent geometry : angle 0.62518 (42345) Misc. bond : bond 0.00058 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 201 time to evaluate : 3.571 Fit side-chains REVERT: B 467 PHE cc_start: 0.7812 (m-80) cc_final: 0.7555 (m-80) REVERT: B 727 CYS cc_start: 0.4788 (OUTLIER) cc_final: 0.4262 (p) REVERT: B 826 GLN cc_start: 0.7842 (mm110) cc_final: 0.7108 (pm20) REVERT: B 906 MET cc_start: 0.8172 (OUTLIER) cc_final: 0.7886 (tpt) REVERT: B 1149 VAL cc_start: 0.7222 (t) cc_final: 0.6724 (t) REVERT: A 46 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.6878 (pp20) REVERT: A 80 TYR cc_start: 0.6885 (m-80) cc_final: 0.6598 (m-10) REVERT: C 361 TYR cc_start: 0.5915 (OUTLIER) cc_final: 0.5369 (m-10) REVERT: C 699 ARG cc_start: 0.7191 (OUTLIER) cc_final: 0.6321 (mmt180) REVERT: C 819 GLN cc_start: 0.8281 (tm130) cc_final: 0.8063 (tm-30) REVERT: C 826 GLN cc_start: 0.7752 (mm110) cc_final: 0.7187 (pm20) REVERT: C 913 MET cc_start: 0.7448 (pmm) cc_final: 0.5089 (mmp) REVERT: C 1017 GLU cc_start: 0.8371 (mm-30) cc_final: 0.7759 (mp0) REVERT: C 1059 ASP cc_start: 0.7267 (m-30) cc_final: 0.6843 (m-30) REVERT: E 379 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7633 (mp0) REVERT: E 543 LYS cc_start: 0.6182 (tptt) cc_final: 0.5155 (ttpp) REVERT: E 696 MET cc_start: 0.8900 (ttm) cc_final: 0.8691 (ttp) REVERT: E 727 CYS cc_start: 0.4630 (OUTLIER) cc_final: 0.4260 (p) REVERT: E 819 GLN cc_start: 0.8356 (pt0) cc_final: 0.8109 (tm130) REVERT: E 873 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8550 (mt) outliers start: 55 outliers final: 30 residues processed: 235 average time/residue: 1.2978 time to fit residues: 368.1923 Evaluate side-chains 230 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 192 time to evaluate : 3.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 361 TYR Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 614 ARG Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 669 THR Chi-restraints excluded: chain B residue 677 VAL Chi-restraints excluded: chain B residue 727 CYS Chi-restraints excluded: chain B residue 736 CYS Chi-restraints excluded: chain B residue 784 THR Chi-restraints excluded: chain B residue 852 SER Chi-restraints excluded: chain B residue 906 MET Chi-restraints excluded: chain B residue 990 LEU Chi-restraints excluded: chain B residue 1014 THR Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain C residue 361 TYR Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 699 ARG Chi-restraints excluded: chain C residue 784 THR Chi-restraints excluded: chain C residue 852 SER Chi-restraints excluded: chain C residue 989 VAL Chi-restraints excluded: chain C residue 1090 GLU Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 361 TYR Chi-restraints excluded: chain E residue 379 GLU Chi-restraints excluded: chain E residue 484 VAL Chi-restraints excluded: chain E residue 623 VAL Chi-restraints excluded: chain E residue 669 THR Chi-restraints excluded: chain E residue 677 VAL Chi-restraints excluded: chain E residue 727 CYS Chi-restraints excluded: chain E residue 852 SER Chi-restraints excluded: chain E residue 873 LEU Chi-restraints excluded: chain E residue 989 VAL Chi-restraints excluded: chain F residue 28 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 256 optimal weight: 7.9990 chunk 71 optimal weight: 3.9990 chunk 373 optimal weight: 3.9990 chunk 330 optimal weight: 2.9990 chunk 255 optimal weight: 9.9990 chunk 102 optimal weight: 0.7980 chunk 74 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 chunk 173 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 371 optimal weight: 3.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1132 ASN ** D 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.131037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.093674 restraints weight = 44674.578| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 2.14 r_work: 0.2940 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 31155 Z= 0.245 Angle : 0.671 10.562 42381 Z= 0.353 Chirality : 0.047 0.161 4740 Planarity : 0.005 0.051 5490 Dihedral : 5.764 50.362 4497 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.97 % Favored : 93.96 % Rotamer: Outliers : 1.82 % Allowed : 13.21 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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 (0.13), residues: 3888 helix: 0.52 (0.19), residues: 735 sheet: -0.13 (0.16), residues: 969 loop : -1.36 (0.12), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B1184 HIS 0.005 0.001 HIS E1138 PHE 0.017 0.002 PHE E 183 TYR 0.034 0.002 TYR E 499 ARG 0.006 0.001 ARG B 841 Details of bonding type rmsd link_NAG-ASN : bond 0.00169 ( 3) link_NAG-ASN : angle 0.93981 ( 9) link_BETA1-4 : bond 0.00414 ( 6) link_BETA1-4 : angle 2.18177 ( 18) link_ALPHA1-3 : bond 0.00954 ( 3) link_ALPHA1-3 : angle 1.37739 ( 9) hydrogen bonds : bond 0.05305 ( 1088) hydrogen bonds : angle 5.09899 ( 3018) covalent geometry : bond 0.00596 (31140) covalent geometry : angle 0.66973 (42345) Misc. bond : bond 0.00078 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 198 time to evaluate : 3.226 Fit side-chains REVERT: B 258 GLN cc_start: 0.9317 (OUTLIER) cc_final: 0.8441 (tt0) REVERT: B 278 MET cc_start: 0.9346 (mtp) cc_final: 0.8946 (mtm) REVERT: B 727 CYS cc_start: 0.4528 (OUTLIER) cc_final: 0.4022 (p) REVERT: B 826 GLN cc_start: 0.8045 (mm110) cc_final: 0.7280 (pm20) REVERT: A 46 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.6907 (pp20) REVERT: A 80 TYR cc_start: 0.6964 (m-80) cc_final: 0.6701 (m-10) REVERT: C 71 TYR cc_start: 0.9144 (t80) cc_final: 0.8866 (t80) REVERT: C 258 GLN cc_start: 0.9374 (OUTLIER) cc_final: 0.8215 (tt0) REVERT: C 699 ARG cc_start: 0.7302 (OUTLIER) cc_final: 0.6482 (mmt180) REVERT: C 819 GLN cc_start: 0.8344 (tm130) cc_final: 0.8138 (tm-30) REVERT: C 826 GLN cc_start: 0.7829 (mm110) cc_final: 0.7248 (pm20) REVERT: C 913 MET cc_start: 0.7532 (pmm) cc_final: 0.5181 (mmp) REVERT: C 1017 GLU cc_start: 0.8474 (mm-30) cc_final: 0.7890 (mp0) REVERT: E 161 MET cc_start: 0.8198 (mmt) cc_final: 0.7763 (mpp) REVERT: E 379 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7669 (mp0) REVERT: E 563 MET cc_start: 0.6789 (tpt) cc_final: 0.6573 (tpp) REVERT: E 727 CYS cc_start: 0.4593 (OUTLIER) cc_final: 0.4289 (p) REVERT: E 819 GLN cc_start: 0.8403 (pt0) cc_final: 0.8154 (tm130) REVERT: E 873 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8578 (mt) outliers start: 61 outliers final: 33 residues processed: 236 average time/residue: 1.2888 time to fit residues: 369.5919 Evaluate side-chains 234 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 193 time to evaluate : 3.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 258 GLN Chi-restraints excluded: chain B residue 361 TYR Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 614 ARG Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 669 THR Chi-restraints excluded: chain B residue 677 VAL Chi-restraints excluded: chain B residue 727 CYS Chi-restraints excluded: chain B residue 736 CYS Chi-restraints excluded: chain B residue 784 THR Chi-restraints excluded: chain B residue 852 SER Chi-restraints excluded: chain B residue 985 ILE Chi-restraints excluded: chain B residue 990 LEU Chi-restraints excluded: chain B residue 1014 THR Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain C residue 258 GLN Chi-restraints excluded: chain C residue 361 TYR Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 699 ARG Chi-restraints excluded: chain C residue 784 THR Chi-restraints excluded: chain C residue 852 SER Chi-restraints excluded: chain C residue 989 VAL Chi-restraints excluded: chain C residue 1090 GLU Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 361 TYR Chi-restraints excluded: chain E residue 379 GLU Chi-restraints excluded: chain E residue 484 VAL Chi-restraints excluded: chain E residue 623 VAL Chi-restraints excluded: chain E residue 669 THR Chi-restraints excluded: chain E residue 677 VAL Chi-restraints excluded: chain E residue 727 CYS Chi-restraints excluded: chain E residue 852 SER Chi-restraints excluded: chain E residue 873 LEU Chi-restraints excluded: chain E residue 1149 VAL Chi-restraints excluded: chain F residue 28 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 83 optimal weight: 3.9990 chunk 210 optimal weight: 0.2980 chunk 102 optimal weight: 4.9990 chunk 368 optimal weight: 0.9990 chunk 203 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 125 optimal weight: 20.0000 chunk 279 optimal weight: 7.9990 chunk 11 optimal weight: 9.9990 chunk 377 optimal weight: 0.0370 chunk 161 optimal weight: 2.9990 overall best weight: 0.8262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 708 GLN ** B 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 466 GLN C 765 ASN C1132 ASN ** D 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.134673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.097915 restraints weight = 44415.307| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 2.13 r_work: 0.3007 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 31155 Z= 0.111 Angle : 0.563 10.761 42381 Z= 0.297 Chirality : 0.042 0.171 4740 Planarity : 0.004 0.050 5490 Dihedral : 5.220 46.128 4497 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.02 % Favored : 94.91 % Rotamer: Outliers : 1.28 % Allowed : 13.86 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -0.73 (0.13), residues: 3888 helix: 0.97 (0.20), residues: 729 sheet: -0.12 (0.16), residues: 975 loop : -1.18 (0.12), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 103 HIS 0.004 0.001 HIS C 681 PHE 0.015 0.001 PHE E 183 TYR 0.031 0.001 TYR E 497 ARG 0.004 0.000 ARG B 841 Details of bonding type rmsd link_NAG-ASN : bond 0.00523 ( 3) link_NAG-ASN : angle 1.00817 ( 9) link_BETA1-4 : bond 0.00434 ( 6) link_BETA1-4 : angle 1.77203 ( 18) link_ALPHA1-3 : bond 0.01123 ( 3) link_ALPHA1-3 : angle 1.56190 ( 9) hydrogen bonds : bond 0.03906 ( 1088) hydrogen bonds : angle 4.85180 ( 3018) covalent geometry : bond 0.00251 (31140) covalent geometry : angle 0.56166 (42345) Misc. bond : bond 0.00006 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 199 time to evaluate : 3.181 Fit side-chains REVERT: B 278 MET cc_start: 0.9274 (mtp) cc_final: 0.8956 (mtm) REVERT: B 727 CYS cc_start: 0.4917 (OUTLIER) cc_final: 0.4417 (p) REVERT: B 826 GLN cc_start: 0.7820 (mm110) cc_final: 0.7145 (pm20) REVERT: B 1149 VAL cc_start: 0.6773 (OUTLIER) cc_final: 0.6271 (t) REVERT: A 80 TYR cc_start: 0.6889 (m-80) cc_final: 0.6670 (m-10) REVERT: C 819 GLN cc_start: 0.8236 (tm130) cc_final: 0.8032 (tm-30) REVERT: C 826 GLN cc_start: 0.7767 (mm110) cc_final: 0.7220 (pm20) REVERT: C 913 MET cc_start: 0.7676 (pmm) cc_final: 0.5449 (mmp) REVERT: C 1059 ASP cc_start: 0.7275 (m-30) cc_final: 0.6873 (m-30) REVERT: C 1090 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.8225 (tp30) REVERT: C 1149 VAL cc_start: 0.6567 (OUTLIER) cc_final: 0.6146 (t) REVERT: D 102 ASN cc_start: 0.8553 (t160) cc_final: 0.8191 (t0) REVERT: E 543 LYS cc_start: 0.6149 (tptt) cc_final: 0.5142 (ttpp) REVERT: E 727 CYS cc_start: 0.4161 (OUTLIER) cc_final: 0.3794 (p) REVERT: E 819 GLN cc_start: 0.8344 (pt0) cc_final: 0.8117 (tm130) REVERT: E 913 MET cc_start: 0.7665 (OUTLIER) cc_final: 0.7366 (pmm) REVERT: E 1112 LYS cc_start: 0.8597 (mmtm) cc_final: 0.8383 (mmpt) REVERT: E 1149 VAL cc_start: 0.6671 (OUTLIER) cc_final: 0.6311 (t) outliers start: 43 outliers final: 23 residues processed: 229 average time/residue: 1.2799 time to fit residues: 354.2845 Evaluate side-chains 223 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 193 time to evaluate : 3.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 361 TYR Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 669 THR Chi-restraints excluded: chain B residue 677 VAL Chi-restraints excluded: chain B residue 727 CYS Chi-restraints excluded: chain B residue 736 CYS Chi-restraints excluded: chain B residue 784 THR Chi-restraints excluded: chain B residue 852 SER Chi-restraints excluded: chain B residue 990 LEU Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1216 THR Chi-restraints excluded: chain C residue 361 TYR Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 784 THR Chi-restraints excluded: chain C residue 852 SER Chi-restraints excluded: chain C residue 1090 GLU Chi-restraints excluded: chain C residue 1149 VAL Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 361 TYR Chi-restraints excluded: chain E residue 484 VAL Chi-restraints excluded: chain E residue 623 VAL Chi-restraints excluded: chain E residue 669 THR Chi-restraints excluded: chain E residue 677 VAL Chi-restraints excluded: chain E residue 727 CYS Chi-restraints excluded: chain E residue 852 SER Chi-restraints excluded: chain E residue 913 MET Chi-restraints excluded: chain E residue 1149 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 259 optimal weight: 6.9990 chunk 7 optimal weight: 10.0000 chunk 130 optimal weight: 10.0000 chunk 103 optimal weight: 1.9990 chunk 163 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 267 optimal weight: 9.9990 chunk 305 optimal weight: 10.0000 chunk 35 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 245 optimal weight: 0.7980 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 708 GLN ** B 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 981 ASN ** D 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 466 GLN ** E 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 57 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.131868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.094631 restraints weight = 44515.522| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 2.16 r_work: 0.2945 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 31155 Z= 0.207 Angle : 0.639 10.852 42381 Z= 0.335 Chirality : 0.045 0.166 4740 Planarity : 0.004 0.050 5490 Dihedral : 5.479 47.548 4497 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.76 % Favored : 94.16 % Rotamer: Outliers : 1.13 % Allowed : 14.31 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.13), residues: 3888 helix: 0.87 (0.20), residues: 717 sheet: -0.01 (0.16), residues: 966 loop : -1.29 (0.12), residues: 2205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 36 HIS 0.004 0.001 HIS C1138 PHE 0.016 0.002 PHE E 183 TYR 0.029 0.002 TYR E 499 ARG 0.006 0.001 ARG B 841 Details of bonding type rmsd link_NAG-ASN : bond 0.00255 ( 3) link_NAG-ASN : angle 0.95743 ( 9) link_BETA1-4 : bond 0.00453 ( 6) link_BETA1-4 : angle 2.04499 ( 18) link_ALPHA1-3 : bond 0.00849 ( 3) link_ALPHA1-3 : angle 1.34570 ( 9) hydrogen bonds : bond 0.04907 ( 1088) hydrogen bonds : angle 4.97806 ( 3018) covalent geometry : bond 0.00505 (31140) covalent geometry : angle 0.63706 (42345) Misc. bond : bond 0.00054 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 201 time to evaluate : 3.294 Fit side-chains REVERT: B 278 MET cc_start: 0.9364 (mtp) cc_final: 0.8967 (mtm) REVERT: B 727 CYS cc_start: 0.4679 (OUTLIER) cc_final: 0.4149 (p) REVERT: B 826 GLN cc_start: 0.7925 (mm110) cc_final: 0.7165 (pm20) REVERT: B 989 VAL cc_start: 0.8872 (t) cc_final: 0.8669 (t) REVERT: A 46 GLU cc_start: 0.7260 (OUTLIER) cc_final: 0.6776 (pp20) REVERT: A 80 TYR cc_start: 0.6808 (m-80) cc_final: 0.6606 (m-10) REVERT: A 102 ASN cc_start: 0.8343 (t160) cc_final: 0.8086 (t0) REVERT: A 116 MET cc_start: 0.8435 (mmt) cc_final: 0.7915 (mmt) REVERT: C 819 GLN cc_start: 0.8237 (tm130) cc_final: 0.8036 (tm-30) REVERT: C 826 GLN cc_start: 0.7738 (mm110) cc_final: 0.7187 (pm20) REVERT: C 913 MET cc_start: 0.7721 (pmm) cc_final: 0.5420 (mmp) REVERT: C 1059 ASP cc_start: 0.7479 (m-30) cc_final: 0.7002 (m-30) REVERT: D 102 ASN cc_start: 0.8614 (t160) cc_final: 0.8240 (t0) REVERT: E 727 CYS cc_start: 0.4428 (OUTLIER) cc_final: 0.4036 (p) REVERT: E 819 GLN cc_start: 0.8390 (pt0) cc_final: 0.8138 (tm130) REVERT: E 913 MET cc_start: 0.7691 (OUTLIER) cc_final: 0.7407 (pmm) outliers start: 38 outliers final: 24 residues processed: 226 average time/residue: 1.5495 time to fit residues: 427.7878 Evaluate side-chains 223 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 195 time to evaluate : 4.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 361 TYR Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 669 THR Chi-restraints excluded: chain B residue 677 VAL Chi-restraints excluded: chain B residue 727 CYS Chi-restraints excluded: chain B residue 736 CYS Chi-restraints excluded: chain B residue 784 THR Chi-restraints excluded: chain B residue 852 SER Chi-restraints excluded: chain B residue 990 LEU Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain C residue 361 TYR Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 784 THR Chi-restraints excluded: chain C residue 852 SER Chi-restraints excluded: chain C residue 1090 GLU Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 361 TYR Chi-restraints excluded: chain E residue 484 VAL Chi-restraints excluded: chain E residue 623 VAL Chi-restraints excluded: chain E residue 669 THR Chi-restraints excluded: chain E residue 677 VAL Chi-restraints excluded: chain E residue 727 CYS Chi-restraints excluded: chain E residue 852 SER Chi-restraints excluded: chain E residue 913 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 186 optimal weight: 3.9990 chunk 351 optimal weight: 0.9990 chunk 163 optimal weight: 0.9980 chunk 247 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 291 optimal weight: 0.8980 chunk 187 optimal weight: 0.9990 chunk 89 optimal weight: 0.5980 chunk 326 optimal weight: 0.9990 chunk 56 optimal weight: 8.9990 chunk 204 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 57 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.134639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.097771 restraints weight = 44607.808| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.16 r_work: 0.2999 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 31155 Z= 0.113 Angle : 0.564 11.188 42381 Z= 0.296 Chirality : 0.042 0.169 4740 Planarity : 0.004 0.049 5490 Dihedral : 5.088 42.214 4497 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.96 % Favored : 94.96 % Rotamer: Outliers : 1.04 % Allowed : 14.52 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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 (0.13), residues: 3888 helix: 1.05 (0.20), residues: 729 sheet: -0.15 (0.16), residues: 984 loop : -1.13 (0.12), residues: 2175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 36 HIS 0.004 0.001 HIS C 681 PHE 0.015 0.001 PHE E 183 TYR 0.026 0.001 TYR E 499 ARG 0.004 0.000 ARG B 841 Details of bonding type rmsd link_NAG-ASN : bond 0.00458 ( 3) link_NAG-ASN : angle 1.04196 ( 9) link_BETA1-4 : bond 0.00447 ( 6) link_BETA1-4 : angle 1.76163 ( 18) link_ALPHA1-3 : bond 0.01070 ( 3) link_ALPHA1-3 : angle 1.47052 ( 9) hydrogen bonds : bond 0.03908 ( 1088) hydrogen bonds : angle 4.77843 ( 3018) covalent geometry : bond 0.00258 (31140) covalent geometry : angle 0.56241 (42345) Misc. bond : bond 0.00015 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 26439.31 seconds wall clock time: 464 minutes 54.13 seconds (27894.13 seconds total)