Starting phenix.real_space_refine on Mon Aug 25 20:12:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ifn_35422/08_2025/8ifn_35422.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ifn_35422/08_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_35422/08_2025/8ifn_35422.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ifn_35422/08_2025/8ifn_35422.map" model { file = "/net/cci-nas-00/data/ceres_data/8ifn_35422/08_2025/8ifn_35422.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ifn_35422/08_2025/8ifn_35422.cif" } resolution = 2.81 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30441 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" 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: "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: "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: C, E, D, F, H, I Time building chain proxies: 9.15, per 1000 atoms: 0.30 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=57, symmetry=0 Simple disulfide: pdb=" SG CYS B 30 " - pdb=" SG CYS B 195 " distance=2.03 Simple disulfide: pdb=" SG CYS B 176 " - pdb=" SG CYS B 214 " distance=2.03 Simple disulfide: pdb=" SG CYS B 185 " - pdb=" SG CYS B 237 " distance=2.06 Simple disulfide: pdb=" SG CYS B 339 " - pdb=" SG CYS B 349 " distance=2.02 Simple disulfide: pdb=" SG CYS B 383 " - pdb=" SG CYS B 407 " distance=2.03 Simple disulfide: pdb=" SG CYS B 425 " - pdb=" SG CYS B 478 " distance=2.03 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 585 " distance=2.03 Simple disulfide: pdb=" SG CYS B 503 " - pdb=" SG CYS B 526 " distance=2.03 Simple disulfide: pdb=" SG CYS B 603 " - pdb=" SG CYS B 654 " distance=2.03 Simple disulfide: pdb=" SG CYS B 620 " - pdb=" SG CYS B 650 " distance=2.05 Simple disulfide: pdb=" SG CYS B 679 " - pdb=" SG CYS B 713 " distance=2.03 Simple disulfide: pdb=" SG CYS B 727 " - pdb=" SG CYS B 736 " distance=2.02 Simple disulfide: pdb=" SG CYS B 806 " - pdb=" SG CYS B 828 " distance=2.04 Simple disulfide: pdb=" SG CYS B 811 " - pdb=" SG CYS B 817 " distance=2.03 Simple disulfide: pdb=" SG CYS B 912 " - pdb=" SG CYS B 925 " distance=2.04 Simple disulfide: pdb=" SG CYS B1106 " - pdb=" SG CYS B1117 " distance=2.03 Simple disulfide: pdb=" SG CYS B1156 " - pdb=" SG CYS B1164 " distance=2.03 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 33 " - pdb=" SG CYS A 105 " distance=2.03 Simple disulfide: pdb=" SG CYS C 30 " - pdb=" SG CYS C 195 " distance=2.03 Simple disulfide: pdb=" SG CYS E 30 " - pdb=" SG CYS E 195 " distance=2.03 Simple disulfide: pdb=" SG CYS C 176 " - pdb=" SG CYS C 214 " distance=2.03 Simple disulfide: pdb=" SG CYS E 176 " - pdb=" SG CYS E 214 " distance=2.03 Simple disulfide: pdb=" SG CYS C 185 " - pdb=" SG CYS C 237 " distance=2.06 Simple disulfide: pdb=" SG CYS E 185 " - pdb=" SG CYS E 237 " distance=2.06 Simple disulfide: pdb=" SG CYS C 339 " - pdb=" SG CYS C 349 " distance=2.02 Simple disulfide: pdb=" SG CYS E 339 " - pdb=" SG CYS E 349 " distance=2.02 Simple disulfide: pdb=" SG CYS C 383 " - pdb=" SG CYS C 407 " distance=2.03 Simple disulfide: pdb=" SG CYS E 383 " - pdb=" SG CYS E 407 " distance=2.03 Simple disulfide: pdb=" SG CYS C 425 " - pdb=" SG CYS C 478 " distance=2.03 Simple disulfide: pdb=" SG CYS E 425 " - pdb=" SG CYS E 478 " distance=2.03 Simple disulfide: pdb=" SG CYS C 437 " - pdb=" SG CYS C 585 " distance=2.03 Simple disulfide: pdb=" SG CYS E 437 " - pdb=" SG CYS E 585 " distance=2.03 Simple disulfide: pdb=" SG CYS C 503 " - pdb=" SG CYS C 526 " distance=2.03 Simple disulfide: pdb=" SG CYS E 503 " - pdb=" SG CYS E 526 " distance=2.03 Simple disulfide: pdb=" SG CYS C 603 " - pdb=" SG CYS C 654 " distance=2.03 Simple disulfide: pdb=" SG CYS E 603 " - pdb=" SG CYS E 654 " distance=2.03 Simple disulfide: pdb=" SG CYS C 620 " - pdb=" SG CYS C 650 " distance=2.05 Simple disulfide: pdb=" SG CYS E 620 " - pdb=" SG CYS E 650 " distance=2.05 Simple disulfide: pdb=" SG CYS C 679 " - pdb=" SG CYS C 713 " distance=2.03 Simple disulfide: pdb=" SG CYS E 679 " - pdb=" SG CYS E 713 " distance=2.03 Simple disulfide: pdb=" SG CYS C 727 " - pdb=" SG CYS C 736 " distance=2.01 Simple disulfide: pdb=" SG CYS E 727 " - pdb=" SG CYS E 736 " distance=2.02 Simple disulfide: pdb=" SG CYS C 806 " - pdb=" SG CYS C 828 " distance=2.04 Simple disulfide: pdb=" SG CYS E 806 " - pdb=" SG CYS E 828 " distance=2.03 Simple disulfide: pdb=" SG CYS C 811 " - pdb=" SG CYS C 817 " distance=2.03 Simple disulfide: pdb=" SG CYS E 811 " - pdb=" SG CYS E 817 " distance=2.03 Simple disulfide: pdb=" SG CYS C 912 " - pdb=" SG CYS C 925 " distance=2.03 Simple disulfide: pdb=" SG CYS E 912 " - pdb=" SG CYS E 925 " distance=2.04 Simple disulfide: pdb=" SG CYS C1106 " - pdb=" SG CYS C1117 " distance=2.03 Simple disulfide: pdb=" SG CYS E1106 " - pdb=" SG CYS E1117 " distance=2.03 Simple disulfide: pdb=" SG CYS C1156 " - pdb=" SG CYS C1164 " distance=2.03 Simple disulfide: pdb=" SG CYS E1156 " - pdb=" SG CYS E1164 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 33 " - pdb=" SG CYS D 105 " distance=2.03 Simple disulfide: pdb=" SG CYS F 33 " - pdb=" SG CYS F 105 " distance=2.03 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: 2.28 Conformation dependent library (CDL) restraints added in 973.3 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.53 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: 7.30 Time building geometry restraints manager: 3.11 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: 17590 22.84 - 45.69: 955 45.69 - 68.53: 109 68.53 - 91.38: 54 91.38 - 114.22: 12 Dihedral angle restraints: 18720 sinusoidal: 7332 harmonic: 11388 Sorted by residual: dihedral pdb=" CB CYS C 185 " pdb=" SG CYS C 185 " pdb=" SG CYS C 237 " pdb=" CB CYS C 237 " ideal model delta sinusoidal sigma weight residual -86.00 2.19 -88.19 1 1.00e+01 1.00e-02 9.30e+01 dihedral pdb=" CB CYS E 185 " pdb=" SG CYS E 185 " pdb=" SG CYS E 237 " pdb=" CB CYS E 237 " ideal model delta sinusoidal sigma weight residual -86.00 2.18 -88.18 1 1.00e+01 1.00e-02 9.30e+01 dihedral pdb=" CB CYS B 185 " pdb=" SG CYS B 185 " pdb=" SG CYS B 237 " pdb=" CB CYS B 237 " ideal model delta sinusoidal sigma weight residual -86.00 2.18 -88.18 1 1.00e+01 1.00e-02 9.30e+01 ... (remaining 18717 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: 24 2.25 - 2.91: 12957 2.91 - 3.57: 41215 3.57 - 4.24: 73054 4.24 - 4.90: 123997 Nonbonded interactions: 251247 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=" NH2 ARG C 511 " pdb=" C4 NAG I 2 " model vdw 2.178 2.840 nonbonded pdb=" O ALA B 92 " pdb=" NE2 GLN B 304 " model vdw 2.180 3.120 ... (remaining 251242 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: 0.08 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } 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: 1.470 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: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 29.430 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.050 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:5.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.320 ------------------------------------------------------------------------------- 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 31212 Z= 0.401 Angle : 0.950 25.605 42495 Z= 0.502 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.008 0.001 ARG E 46 TYR 0.048 0.002 TYR B 361 PHE 0.033 0.002 PHE C 423 TRP 0.009 0.002 TRP B 960 HIS 0.005 0.002 HIS B 194 Details of bonding type rmsd covalent geometry : bond 0.00857 (31140) covalent geometry : angle 0.92656 (42345) SS BOND : bond 0.00925 ( 57) SS BOND : angle 2.95436 ( 114) hydrogen bonds : bond 0.14824 ( 1088) hydrogen bonds : angle 6.84630 ( 3018) Misc. bond : bond 0.10973 ( 3) link_ALPHA1-3 : bond 0.00051 ( 3) link_ALPHA1-3 : angle 2.02948 ( 9) link_BETA1-4 : bond 0.19307 ( 6) link_BETA1-4 : angle 7.19059 ( 18) link_NAG-ASN : bond 0.00718 ( 3) link_NAG-ASN : angle 2.61668 ( 9) *********************** 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 : 1.151 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: 0.6740 time to fit residues: 200.6972 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 : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 0.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 0.5980 chunk 183 optimal weight: 4.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 199 ASN B 280 GLN ** B 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 GLN B 842 GLN B1146 HIS A 77 ASN ** A 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 ASN C 280 GLN C 826 GLN C 842 GLN C1146 HIS D 102 ASN E 280 GLN E 466 GLN E1031 GLN ** E1146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 57 ASN F 77 ASN F 102 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.134370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.097016 restraints weight = 44468.516| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 2.14 r_work: 0.2990 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.1027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 31212 Z= 0.135 Angle : 0.658 10.275 42495 Z= 0.345 Chirality : 0.045 0.195 4740 Planarity : 0.004 0.052 5490 Dihedral : 7.918 80.842 4497 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.56 % Favored : 94.29 % Rotamer: Outliers : 0.81 % Allowed : 6.98 % Favored : 92.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.10 (0.13), residues: 3888 helix: 0.24 (0.19), residues: 726 sheet: -0.30 (0.16), residues: 1044 loop : -1.31 (0.12), residues: 2118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 691 TYR 0.025 0.001 TYR B 361 PHE 0.011 0.001 PHE C 778 TRP 0.007 0.001 TRP A 103 HIS 0.004 0.001 HIS E 681 Details of bonding type rmsd covalent geometry : bond 0.00306 (31140) covalent geometry : angle 0.64859 (42345) SS BOND : bond 0.00331 ( 57) SS BOND : angle 1.82871 ( 114) hydrogen bonds : bond 0.04818 ( 1088) hydrogen bonds : angle 5.47518 ( 3018) Misc. bond : bond 0.00081 ( 3) link_ALPHA1-3 : bond 0.01010 ( 3) link_ALPHA1-3 : angle 1.27665 ( 9) link_BETA1-4 : bond 0.00164 ( 6) link_BETA1-4 : angle 3.14795 ( 18) link_NAG-ASN : bond 0.00668 ( 3) link_NAG-ASN : angle 1.09423 ( 9) *********************** 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 225 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 198 time to evaluate : 1.158 Fit side-chains REVERT: B 467 PHE cc_start: 0.7986 (m-80) cc_final: 0.7732 (m-80) REVERT: A 77 ASN cc_start: 0.7355 (OUTLIER) cc_final: 0.7086 (p0) REVERT: A 80 TYR cc_start: 0.7385 (m-80) cc_final: 0.7030 (m-10) REVERT: A 110 LYS cc_start: 0.8535 (mttp) cc_final: 0.8123 (mmtt) REVERT: A 116 MET cc_start: 0.8344 (mmt) cc_final: 0.7964 (mmt) REVERT: C 569 MET cc_start: 0.7373 (mtp) cc_final: 0.6922 (mtm) REVERT: D 107 MET cc_start: 0.7435 (tmm) cc_final: 0.7149 (tmm) REVERT: E 819 GLN cc_start: 0.8427 (pt0) cc_final: 0.7994 (tm130) REVERT: E 891 GLU cc_start: 0.8423 (tt0) cc_final: 0.8129 (tt0) REVERT: E 943 MET cc_start: 0.8374 (ttp) cc_final: 0.8149 (ttm) REVERT: F 77 ASN cc_start: 0.7221 (OUTLIER) cc_final: 0.6992 (p0) outliers start: 27 outliers final: 9 residues processed: 212 average time/residue: 0.5749 time to fit residues: 145.7440 Evaluate side-chains 185 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 174 time to evaluate : 1.133 ------------------------------------------------------------------------------- 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 450 LEU 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 59 optimal weight: 1.9990 chunk 176 optimal weight: 5.9990 chunk 50 optimal weight: 7.9990 chunk 196 optimal weight: 7.9990 chunk 234 optimal weight: 0.9980 chunk 296 optimal weight: 6.9990 chunk 157 optimal weight: 0.9990 chunk 112 optimal weight: 7.9990 chunk 185 optimal weight: 3.9990 chunk 166 optimal weight: 5.9990 chunk 52 optimal weight: 8.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 792 GLN B 987 GLN ** A 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 466 GLN C 826 GLN C 848 ASN D 102 ASN E 466 GLN ** E 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 792 GLN E 848 ASN E1146 HIS ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 102 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.131892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.094511 restraints weight = 44421.702| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 2.09 r_work: 0.2944 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.1138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 31212 Z= 0.225 Angle : 0.704 12.710 42495 Z= 0.367 Chirality : 0.047 0.304 4740 Planarity : 0.005 0.048 5490 Dihedral : 7.387 67.144 4497 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.04 % Favored : 93.88 % Rotamer: Outliers : 1.34 % Allowed : 9.66 % Favored : 89.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.14 (0.13), residues: 3888 helix: 0.24 (0.19), residues: 726 sheet: -0.11 (0.17), residues: 960 loop : -1.44 (0.12), residues: 2202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 46 TYR 0.025 0.002 TYR F 118 PHE 0.014 0.002 PHE E 183 TRP 0.006 0.001 TRP F 36 HIS 0.005 0.001 HIS B 264 Details of bonding type rmsd covalent geometry : bond 0.00545 (31140) covalent geometry : angle 0.69332 (42345) SS BOND : bond 0.00417 ( 57) SS BOND : angle 2.12460 ( 114) hydrogen bonds : bond 0.05446 ( 1088) hydrogen bonds : angle 5.35414 ( 3018) Misc. bond : bond 0.00058 ( 3) link_ALPHA1-3 : bond 0.00917 ( 3) link_ALPHA1-3 : angle 1.28871 ( 9) link_BETA1-4 : bond 0.00642 ( 6) link_BETA1-4 : angle 2.88710 ( 18) link_NAG-ASN : bond 0.00403 ( 3) link_NAG-ASN : angle 0.79662 ( 9) *********************** 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 244 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 199 time to evaluate : 1.198 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 361 TYR cc_start: 0.6039 (OUTLIER) cc_final: 0.5809 (m-10) REVERT: A 110 LYS cc_start: 0.8576 (mttp) cc_final: 0.8172 (mmtt) REVERT: C 361 TYR cc_start: 0.6060 (OUTLIER) cc_final: 0.5673 (m-10) REVERT: C 569 MET cc_start: 0.7331 (mtp) cc_final: 0.7053 (mtm) REVERT: C 1090 GLU cc_start: 0.8781 (mm-30) cc_final: 0.8517 (mm-30) REVERT: E 361 TYR cc_start: 0.5990 (OUTLIER) cc_final: 0.5778 (m-10) REVERT: E 819 GLN cc_start: 0.8453 (pt0) cc_final: 0.8043 (tm130) REVERT: F 116 MET cc_start: 0.8157 (mmm) cc_final: 0.7787 (mmt) outliers start: 45 outliers final: 22 residues processed: 226 average time/residue: 0.5938 time to fit residues: 160.7656 Evaluate side-chains 208 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 183 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 361 TYR Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 669 THR 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 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 623 VAL Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 736 CYS 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 623 VAL Chi-restraints excluded: chain E residue 669 THR Chi-restraints excluded: chain E residue 736 CYS Chi-restraints excluded: chain E residue 852 SER Chi-restraints excluded: chain F residue 28 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 263 optimal weight: 0.9980 chunk 174 optimal weight: 10.0000 chunk 12 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 143 optimal weight: 1.9990 chunk 54 optimal weight: 20.0000 chunk 60 optimal weight: 0.9990 chunk 346 optimal weight: 0.9990 chunk 311 optimal weight: 0.0980 chunk 135 optimal weight: 1.9990 chunk 120 optimal weight: 10.0000 overall best weight: 1.0186 ------------------------------------------------------------------------------- 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 466 GLN ** B 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 77 ASN ** A 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 466 GLN C 792 GLN C 826 GLN D 102 ASN ** E 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 842 GLN F 77 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.134617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.097479 restraints weight = 44158.920| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 2.09 r_work: 0.2999 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 31212 Z= 0.120 Angle : 0.600 10.163 42495 Z= 0.314 Chirality : 0.043 0.176 4740 Planarity : 0.004 0.050 5490 Dihedral : 6.405 50.940 4497 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.17 % Favored : 94.75 % Rotamer: Outliers : 1.52 % Allowed : 11.15 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.94 (0.13), residues: 3888 helix: 0.57 (0.20), residues: 732 sheet: -0.13 (0.17), residues: 969 loop : -1.29 (0.12), residues: 2187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 691 TYR 0.021 0.001 TYR F 118 PHE 0.013 0.001 PHE C 827 TRP 0.007 0.001 TRP A 103 HIS 0.003 0.001 HIS C 681 Details of bonding type rmsd covalent geometry : bond 0.00271 (31140) covalent geometry : angle 0.59243 (42345) SS BOND : bond 0.00234 ( 57) SS BOND : angle 1.68021 ( 114) hydrogen bonds : bond 0.04268 ( 1088) hydrogen bonds : angle 5.07500 ( 3018) Misc. bond : bond 0.00006 ( 3) link_ALPHA1-3 : bond 0.01118 ( 3) link_ALPHA1-3 : angle 1.20501 ( 9) link_BETA1-4 : bond 0.00495 ( 6) link_BETA1-4 : angle 2.49051 ( 18) link_NAG-ASN : bond 0.00573 ( 3) link_NAG-ASN : angle 0.79647 ( 9) *********************** 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 252 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 201 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 240 MET cc_start: 0.9039 (tpp) cc_final: 0.8811 (ttt) REVERT: B 467 PHE cc_start: 0.7893 (m-80) cc_final: 0.7582 (m-80) REVERT: B 826 GLN cc_start: 0.7927 (mm110) cc_final: 0.7185 (pm20) REVERT: B 1149 VAL cc_start: 0.6994 (OUTLIER) cc_final: 0.6453 (t) REVERT: A 77 ASN cc_start: 0.7371 (OUTLIER) cc_final: 0.7028 (p0) REVERT: C 361 TYR cc_start: 0.5973 (OUTLIER) cc_final: 0.5431 (m-10) REVERT: C 569 MET cc_start: 0.7223 (mtp) cc_final: 0.7018 (mtm) REVERT: C 826 GLN cc_start: 0.7898 (mm-40) cc_final: 0.7290 (pm20) REVERT: E 819 GLN cc_start: 0.8505 (pt0) cc_final: 0.8140 (tm130) REVERT: E 1149 VAL cc_start: 0.6712 (OUTLIER) cc_final: 0.6291 (t) REVERT: F 77 ASN cc_start: 0.7335 (OUTLIER) cc_final: 0.6997 (p0) outliers start: 51 outliers final: 21 residues processed: 235 average time/residue: 0.6077 time to fit residues: 171.8005 Evaluate side-chains 210 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 184 time to evaluate : 1.084 ------------------------------------------------------------------------------- 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 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 1149 VAL 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 361 TYR Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 736 CYS 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 450 LEU Chi-restraints excluded: chain E residue 677 VAL Chi-restraints excluded: chain E residue 736 CYS Chi-restraints excluded: chain E residue 852 SER Chi-restraints excluded: chain E residue 940 ASP Chi-restraints excluded: chain E residue 1149 VAL Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 77 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 235 optimal weight: 0.5980 chunk 188 optimal weight: 7.9990 chunk 245 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 109 optimal weight: 4.9990 chunk 174 optimal weight: 20.0000 chunk 71 optimal weight: 4.9990 chunk 300 optimal weight: 2.9990 chunk 309 optimal weight: 20.0000 chunk 20 optimal weight: 5.9990 chunk 260 optimal weight: 5.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- 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 501 ASN B 848 ASN B 981 ASN A 77 ASN ** A 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 466 GLN ** E 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 57 ASN F 77 ASN ** 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 = 0.3672 r_free = 0.3672 target = 0.131435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.093844 restraints weight = 44013.690| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 2.05 r_work: 0.2935 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 31212 Z= 0.256 Angle : 0.705 12.349 42495 Z= 0.368 Chirality : 0.048 0.295 4740 Planarity : 0.005 0.049 5490 Dihedral : 6.414 51.603 4497 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.15 % Favored : 93.78 % Rotamer: Outliers : 2.24 % Allowed : 11.69 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.12 (0.13), residues: 3888 helix: 0.36 (0.19), residues: 735 sheet: -0.19 (0.16), residues: 981 loop : -1.43 (0.12), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 46 TYR 0.032 0.002 TYR C 499 PHE 0.016 0.002 PHE C 266 TRP 0.007 0.001 TRP B1184 HIS 0.006 0.001 HIS C1138 Details of bonding type rmsd covalent geometry : bond 0.00622 (31140) covalent geometry : angle 0.69556 (42345) SS BOND : bond 0.00405 ( 57) SS BOND : angle 2.13282 ( 114) hydrogen bonds : bond 0.05478 ( 1088) hydrogen bonds : angle 5.21100 ( 3018) Misc. bond : bond 0.00081 ( 3) link_ALPHA1-3 : bond 0.00719 ( 3) link_ALPHA1-3 : angle 1.25447 ( 9) link_BETA1-4 : bond 0.00518 ( 6) link_BETA1-4 : angle 2.59431 ( 18) link_NAG-ASN : bond 0.00289 ( 3) link_NAG-ASN : angle 0.83467 ( 9) *********************** 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 272 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 197 time to evaluate : 1.189 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 258 GLN cc_start: 0.9342 (OUTLIER) cc_final: 0.8389 (tt0) REVERT: B 467 PHE cc_start: 0.7881 (m-80) cc_final: 0.7556 (m-80) REVERT: B 614 ARG cc_start: 0.8937 (ttm170) cc_final: 0.8560 (ttm-80) REVERT: B 826 GLN cc_start: 0.8054 (mm110) cc_final: 0.7246 (pm20) REVERT: B 906 MET cc_start: 0.8084 (tpt) cc_final: 0.7723 (tpt) REVERT: B 940 ASP cc_start: 0.8509 (OUTLIER) cc_final: 0.8258 (m-30) REVERT: C 361 TYR cc_start: 0.5869 (OUTLIER) cc_final: 0.5287 (m-10) REVERT: C 699 ARG cc_start: 0.7248 (OUTLIER) cc_final: 0.6383 (mmt180) REVERT: C 819 GLN cc_start: 0.8218 (tm130) cc_final: 0.7982 (tm-30) REVERT: C 826 GLN cc_start: 0.7941 (mm-40) cc_final: 0.7331 (pm20) REVERT: C 913 MET cc_start: 0.7562 (pmm) cc_final: 0.5333 (mmp) REVERT: C 1059 ASP cc_start: 0.7645 (m-30) cc_final: 0.7220 (m-30) REVERT: C 1090 GLU cc_start: 0.8757 (mm-30) cc_final: 0.8527 (mm-30) REVERT: E 696 MET cc_start: 0.8965 (ttm) cc_final: 0.8719 (ttp) REVERT: E 819 GLN cc_start: 0.8494 (pt0) cc_final: 0.8162 (tm130) REVERT: E 873 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8541 (mt) REVERT: F 39 GLN cc_start: 0.5500 (tp40) cc_final: 0.5239 (tp40) REVERT: F 102 ASN cc_start: 0.8236 (OUTLIER) cc_final: 0.7921 (t0) outliers start: 75 outliers final: 34 residues processed: 250 average time/residue: 0.5547 time to fit residues: 168.9565 Evaluate side-chains 228 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 188 time to evaluate : 1.380 ------------------------------------------------------------------------------- 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 623 VAL Chi-restraints excluded: chain B residue 650 CYS 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 940 ASP Chi-restraints excluded: chain B residue 943 MET Chi-restraints excluded: chain B residue 985 ILE Chi-restraints excluded: chain B residue 1014 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 650 CYS Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 699 ARG Chi-restraints excluded: chain C residue 736 CYS 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 D residue 28 THR Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain E residue 238 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 677 VAL Chi-restraints excluded: chain E residue 736 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 F residue 28 THR Chi-restraints excluded: chain F residue 83 MET 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 360 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 289 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 308 optimal weight: 5.9990 chunk 336 optimal weight: 0.8980 chunk 271 optimal weight: 0.3980 chunk 341 optimal weight: 0.7980 chunk 69 optimal weight: 0.2980 chunk 238 optimal weight: 0.0770 overall best weight: 0.4938 ------------------------------------------------------------------------------- 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** ** A 102 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.135546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.098572 restraints weight = 44323.566| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.10 r_work: 0.3021 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 31212 Z= 0.105 Angle : 0.571 10.026 42495 Z= 0.300 Chirality : 0.042 0.172 4740 Planarity : 0.004 0.050 5490 Dihedral : 5.568 49.638 4497 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.68 % Favored : 95.24 % Rotamer: Outliers : 1.55 % Allowed : 12.79 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.83 (0.13), residues: 3888 helix: 0.85 (0.20), residues: 732 sheet: -0.22 (0.16), residues: 966 loop : -1.21 (0.12), residues: 2190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 691 TYR 0.023 0.001 TYR C 499 PHE 0.012 0.001 PHE E 183 TRP 0.009 0.001 TRP A 103 HIS 0.004 0.001 HIS C 681 Details of bonding type rmsd covalent geometry : bond 0.00228 (31140) covalent geometry : angle 0.56411 (42345) SS BOND : bond 0.00208 ( 57) SS BOND : angle 1.60296 ( 114) hydrogen bonds : bond 0.03882 ( 1088) hydrogen bonds : angle 4.88040 ( 3018) Misc. bond : bond 0.00008 ( 3) link_ALPHA1-3 : bond 0.01203 ( 3) link_ALPHA1-3 : angle 1.28247 ( 9) link_BETA1-4 : bond 0.00401 ( 6) link_BETA1-4 : angle 2.05534 ( 18) link_NAG-ASN : bond 0.00506 ( 3) link_NAG-ASN : angle 0.90588 ( 9) *********************** 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 265 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 213 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 826 GLN cc_start: 0.7868 (mm110) cc_final: 0.7157 (pm20) REVERT: B 906 MET cc_start: 0.8021 (tpt) cc_final: 0.7692 (tpt) REVERT: B 1090 GLU cc_start: 0.8730 (mm-30) cc_final: 0.8501 (mm-30) REVERT: B 1149 VAL cc_start: 0.6675 (OUTLIER) cc_final: 0.6143 (t) REVERT: C 826 GLN cc_start: 0.7814 (mm-40) cc_final: 0.7256 (pm20) REVERT: C 912 CYS cc_start: 0.7056 (OUTLIER) cc_final: 0.5554 (t) REVERT: C 913 MET cc_start: 0.7468 (pmm) cc_final: 0.5263 (mmp) REVERT: C 1059 ASP cc_start: 0.7379 (m-30) cc_final: 0.6987 (m-30) REVERT: C 1090 GLU cc_start: 0.8721 (mm-30) cc_final: 0.8463 (mm-30) REVERT: C 1149 VAL cc_start: 0.6470 (OUTLIER) cc_final: 0.6060 (t) REVERT: D 107 MET cc_start: 0.7298 (tmm) cc_final: 0.6972 (tmm) REVERT: E 543 LYS cc_start: 0.6351 (tptt) cc_final: 0.5261 (ttpp) REVERT: E 696 MET cc_start: 0.8865 (ttm) cc_final: 0.8630 (ttp) REVERT: E 819 GLN cc_start: 0.8381 (pt0) cc_final: 0.8154 (tm130) REVERT: E 912 CYS cc_start: 0.6457 (OUTLIER) cc_final: 0.5325 (t) REVERT: E 1149 VAL cc_start: 0.6678 (OUTLIER) cc_final: 0.6312 (t) REVERT: F 39 GLN cc_start: 0.5340 (tp40) cc_final: 0.5060 (tp40) outliers start: 52 outliers final: 24 residues processed: 246 average time/residue: 0.5150 time to fit residues: 154.0292 Evaluate side-chains 223 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 194 time to evaluate : 1.160 ------------------------------------------------------------------------------- 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 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 1149 VAL Chi-restraints excluded: chain B residue 1216 THR Chi-restraints excluded: chain C residue 19 VAL 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 736 CYS Chi-restraints excluded: chain C residue 784 THR Chi-restraints excluded: chain C residue 852 SER Chi-restraints excluded: chain C residue 912 CYS Chi-restraints excluded: chain C residue 1149 VAL Chi-restraints excluded: chain D residue 38 ARG 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 669 THR Chi-restraints excluded: chain E residue 677 VAL Chi-restraints excluded: chain E residue 736 CYS Chi-restraints excluded: chain E residue 852 SER Chi-restraints excluded: chain E residue 912 CYS Chi-restraints excluded: chain E residue 1149 VAL Chi-restraints excluded: chain F residue 83 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 136 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 208 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 388 optimal weight: 0.9980 chunk 197 optimal weight: 0.9990 chunk 336 optimal weight: 0.4980 chunk 191 optimal weight: 2.9990 chunk 91 optimal weight: 0.1980 chunk 95 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 GLN B 566 GLN ** B 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 566 GLN C1132 ASN ** D 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 102 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 = 0.3732 r_free = 0.3732 target = 0.135976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.099195 restraints weight = 44406.177| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.08 r_work: 0.3032 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 31212 Z= 0.108 Angle : 0.572 11.066 42495 Z= 0.300 Chirality : 0.042 0.246 4740 Planarity : 0.004 0.047 5490 Dihedral : 5.202 44.339 4497 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.07 % Favored : 94.86 % Rotamer: Outliers : 1.64 % Allowed : 13.48 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.71 (0.13), residues: 3888 helix: 1.09 (0.20), residues: 732 sheet: -0.04 (0.16), residues: 942 loop : -1.23 (0.12), residues: 2214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 181 TYR 0.035 0.001 TYR E 499 PHE 0.013 0.001 PHE E 183 TRP 0.008 0.001 TRP D 103 HIS 0.003 0.001 HIS C 681 Details of bonding type rmsd covalent geometry : bond 0.00244 (31140) covalent geometry : angle 0.56292 (42345) SS BOND : bond 0.00190 ( 57) SS BOND : angle 1.81447 ( 114) hydrogen bonds : bond 0.03823 ( 1088) hydrogen bonds : angle 4.74399 ( 3018) Misc. bond : bond 0.00005 ( 3) link_ALPHA1-3 : bond 0.01142 ( 3) link_ALPHA1-3 : angle 1.29647 ( 9) link_BETA1-4 : bond 0.00486 ( 6) link_BETA1-4 : angle 1.93379 ( 18) link_NAG-ASN : bond 0.00551 ( 3) link_NAG-ASN : angle 0.79517 ( 9) *********************** 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 266 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 211 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 467 PHE cc_start: 0.7876 (m-80) cc_final: 0.7573 (m-80) REVERT: B 826 GLN cc_start: 0.7743 (mm110) cc_final: 0.7087 (pm20) REVERT: B 906 MET cc_start: 0.8042 (tpt) cc_final: 0.7754 (tpt) REVERT: B 1059 ASP cc_start: 0.7192 (m-30) cc_final: 0.6951 (m-30) REVERT: B 1090 GLU cc_start: 0.8715 (mm-30) cc_final: 0.8508 (mm-30) REVERT: B 1149 VAL cc_start: 0.6526 (OUTLIER) cc_final: 0.5993 (t) REVERT: C 258 GLN cc_start: 0.9309 (OUTLIER) cc_final: 0.8172 (tt0) REVERT: C 361 TYR cc_start: 0.5678 (OUTLIER) cc_final: 0.5015 (m-10) REVERT: C 569 MET cc_start: 0.7639 (mtm) cc_final: 0.7331 (mmm) REVERT: C 826 GLN cc_start: 0.7929 (mm-40) cc_final: 0.7229 (pm20) REVERT: C 912 CYS cc_start: 0.6930 (OUTLIER) cc_final: 0.5435 (t) REVERT: C 913 MET cc_start: 0.7412 (pmm) cc_final: 0.5221 (mmp) REVERT: C 1059 ASP cc_start: 0.7183 (m-30) cc_final: 0.6763 (m-30) REVERT: C 1090 GLU cc_start: 0.8695 (mm-30) cc_final: 0.8440 (mm-30) REVERT: C 1149 VAL cc_start: 0.6489 (OUTLIER) cc_final: 0.6077 (t) REVERT: D 52 LYS cc_start: 0.5706 (ttmt) cc_final: 0.5434 (tttp) REVERT: D 102 ASN cc_start: 0.8542 (t160) cc_final: 0.7974 (t0) REVERT: E 452 MET cc_start: 0.7131 (mpp) cc_final: 0.6908 (mtt) REVERT: E 543 LYS cc_start: 0.6338 (tptt) cc_final: 0.5200 (ttpp) REVERT: E 696 MET cc_start: 0.8831 (ttm) cc_final: 0.8604 (ttp) REVERT: E 819 GLN cc_start: 0.8392 (pt0) cc_final: 0.8148 (tm130) REVERT: E 912 CYS cc_start: 0.6483 (OUTLIER) cc_final: 0.5382 (t) REVERT: E 1149 VAL cc_start: 0.6632 (OUTLIER) cc_final: 0.6256 (t) REVERT: F 39 GLN cc_start: 0.5274 (tp40) cc_final: 0.4984 (tp40) REVERT: F 102 ASN cc_start: 0.8348 (t0) cc_final: 0.7890 (t0) outliers start: 55 outliers final: 29 residues processed: 248 average time/residue: 0.5695 time to fit residues: 171.0420 Evaluate side-chains 230 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 194 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 155 ASN 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 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 A residue 28 THR Chi-restraints excluded: chain C residue 19 VAL 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 736 CYS Chi-restraints excluded: chain C residue 784 THR Chi-restraints excluded: chain C residue 852 SER Chi-restraints excluded: chain C residue 912 CYS Chi-restraints excluded: chain C residue 1149 VAL Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain E residue 361 TYR Chi-restraints excluded: chain E residue 450 LEU 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 736 CYS Chi-restraints excluded: chain E residue 852 SER Chi-restraints excluded: chain E residue 912 CYS Chi-restraints excluded: chain E residue 989 VAL Chi-restraints excluded: chain E residue 1149 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 372 optimal weight: 7.9990 chunk 326 optimal weight: 5.9990 chunk 41 optimal weight: 0.0170 chunk 384 optimal weight: 10.0000 chunk 317 optimal weight: 8.9990 chunk 117 optimal weight: 0.4980 chunk 62 optimal weight: 7.9990 chunk 301 optimal weight: 0.6980 chunk 159 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 97 optimal weight: 6.9990 overall best weight: 2.2422 ------------------------------------------------------------------------------- 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 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 836 HIS ** D 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 466 GLN ** E 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 102 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.133129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.095542 restraints weight = 44220.667| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 2.10 r_work: 0.2966 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 31212 Z= 0.188 Angle : 0.646 11.308 42495 Z= 0.338 Chirality : 0.045 0.268 4740 Planarity : 0.004 0.049 5490 Dihedral : 5.482 44.472 4497 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.63 % Favored : 94.29 % Rotamer: Outliers : 1.79 % Allowed : 13.60 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.82 (0.13), residues: 3888 helix: 0.87 (0.20), residues: 726 sheet: -0.14 (0.16), residues: 981 loop : -1.25 (0.12), residues: 2181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 46 TYR 0.032 0.002 TYR E 499 PHE 0.015 0.002 PHE E 183 TRP 0.006 0.001 TRP B1184 HIS 0.005 0.001 HIS E1138 Details of bonding type rmsd covalent geometry : bond 0.00453 (31140) covalent geometry : angle 0.63439 (42345) SS BOND : bond 0.00475 ( 57) SS BOND : angle 2.23918 ( 114) hydrogen bonds : bond 0.04823 ( 1088) hydrogen bonds : angle 4.95122 ( 3018) Misc. bond : bond 0.00050 ( 3) link_ALPHA1-3 : bond 0.00970 ( 3) link_ALPHA1-3 : angle 1.31751 ( 9) link_BETA1-4 : bond 0.00445 ( 6) link_BETA1-4 : angle 2.05793 ( 18) link_NAG-ASN : bond 0.00321 ( 3) link_NAG-ASN : angle 0.82888 ( 9) *********************** 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 260 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 200 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 467 PHE cc_start: 0.7907 (m-80) cc_final: 0.7636 (m-80) REVERT: B 826 GLN cc_start: 0.7962 (mm110) cc_final: 0.7251 (pm20) REVERT: B 906 MET cc_start: 0.8139 (OUTLIER) cc_final: 0.7753 (tpt) REVERT: B 913 MET cc_start: 0.7550 (pmm) cc_final: 0.5828 (mmp) REVERT: B 1059 ASP cc_start: 0.7154 (m-30) cc_final: 0.6951 (m-30) REVERT: A 46 GLU cc_start: 0.7350 (OUTLIER) cc_final: 0.6969 (pp20) REVERT: A 80 TYR cc_start: 0.6899 (m-80) cc_final: 0.6618 (m-10) REVERT: C 258 GLN cc_start: 0.9367 (OUTLIER) cc_final: 0.8220 (tt0) REVERT: C 826 GLN cc_start: 0.7893 (mm-40) cc_final: 0.7301 (pm20) REVERT: C 913 MET cc_start: 0.7404 (pmm) cc_final: 0.5191 (mmp) REVERT: C 1059 ASP cc_start: 0.7298 (m-30) cc_final: 0.6958 (m-30) REVERT: E 452 MET cc_start: 0.7137 (mpp) cc_final: 0.6924 (mtt) REVERT: E 543 LYS cc_start: 0.6343 (tptt) cc_final: 0.5271 (ttpp) REVERT: E 819 GLN cc_start: 0.8367 (pt0) cc_final: 0.8119 (tm130) REVERT: F 39 GLN cc_start: 0.5334 (tp40) cc_final: 0.4997 (tp40) outliers start: 60 outliers final: 35 residues processed: 237 average time/residue: 0.5291 time to fit residues: 151.5445 Evaluate side-chains 227 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 189 time to evaluate : 0.995 ------------------------------------------------------------------------------- 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 650 CYS 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 815 GLN Chi-restraints excluded: chain B residue 852 SER Chi-restraints excluded: chain B residue 906 MET Chi-restraints excluded: chain B residue 943 MET Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain C residue 19 VAL 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 650 CYS Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 784 THR Chi-restraints excluded: chain C residue 852 SER Chi-restraints excluded: chain C residue 912 CYS Chi-restraints excluded: chain C residue 989 VAL Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain E residue 361 TYR Chi-restraints excluded: chain E residue 388 LEU 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 736 CYS Chi-restraints excluded: chain E residue 852 SER Chi-restraints excluded: chain E residue 912 CYS 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 373 optimal weight: 3.9990 chunk 238 optimal weight: 0.7980 chunk 84 optimal weight: 0.7980 chunk 58 optimal weight: 4.9990 chunk 265 optimal weight: 1.9990 chunk 127 optimal weight: 9.9990 chunk 138 optimal weight: 9.9990 chunk 295 optimal weight: 4.9990 chunk 173 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 266 optimal weight: 0.9980 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** ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.134010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.096683 restraints weight = 44172.462| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 2.08 r_work: 0.2993 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 31212 Z= 0.155 Angle : 0.618 10.639 42495 Z= 0.325 Chirality : 0.044 0.279 4740 Planarity : 0.004 0.047 5490 Dihedral : 5.389 44.290 4497 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.27 % Favored : 94.65 % Rotamer: Outliers : 1.37 % Allowed : 13.92 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.79 (0.13), residues: 3888 helix: 0.90 (0.20), residues: 726 sheet: -0.16 (0.16), residues: 999 loop : -1.22 (0.12), residues: 2163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 46 TYR 0.029 0.001 TYR E 499 PHE 0.014 0.001 PHE E 183 TRP 0.010 0.001 TRP F 103 HIS 0.004 0.001 HIS C 681 Details of bonding type rmsd covalent geometry : bond 0.00367 (31140) covalent geometry : angle 0.60798 (42345) SS BOND : bond 0.00374 ( 57) SS BOND : angle 2.09979 ( 114) hydrogen bonds : bond 0.04478 ( 1088) hydrogen bonds : angle 4.88996 ( 3018) Misc. bond : bond 0.00033 ( 3) link_ALPHA1-3 : bond 0.01009 ( 3) link_ALPHA1-3 : angle 1.38418 ( 9) link_BETA1-4 : bond 0.00437 ( 6) link_BETA1-4 : angle 1.93177 ( 18) link_NAG-ASN : bond 0.00380 ( 3) link_NAG-ASN : angle 0.86416 ( 9) *********************** 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 237 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 191 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 467 PHE cc_start: 0.7896 (m-80) cc_final: 0.7629 (m-80) REVERT: B 826 GLN cc_start: 0.7888 (mm110) cc_final: 0.7175 (pm20) REVERT: B 906 MET cc_start: 0.8190 (tpt) cc_final: 0.7784 (tpt) REVERT: B 913 MET cc_start: 0.7611 (pmm) cc_final: 0.5818 (mmp) REVERT: B 1059 ASP cc_start: 0.7344 (m-30) cc_final: 0.7075 (m-30) REVERT: B 1149 VAL cc_start: 0.7179 (OUTLIER) cc_final: 0.6647 (t) REVERT: A 46 GLU cc_start: 0.7252 (OUTLIER) cc_final: 0.6859 (pp20) REVERT: A 80 TYR cc_start: 0.6930 (m-80) cc_final: 0.6634 (m-10) REVERT: C 258 GLN cc_start: 0.9355 (OUTLIER) cc_final: 0.8245 (tt0) REVERT: C 569 MET cc_start: 0.7832 (OUTLIER) cc_final: 0.7483 (mmm) REVERT: C 826 GLN cc_start: 0.7867 (mm-40) cc_final: 0.7272 (pm20) REVERT: C 912 CYS cc_start: 0.7055 (OUTLIER) cc_final: 0.5628 (t) REVERT: C 913 MET cc_start: 0.7408 (pmm) cc_final: 0.5228 (mmp) REVERT: C 1090 GLU cc_start: 0.8685 (mm-30) cc_final: 0.8429 (mm-30) REVERT: D 102 ASN cc_start: 0.8692 (t160) cc_final: 0.8263 (t0) REVERT: E 543 LYS cc_start: 0.6306 (tptt) cc_final: 0.5227 (ttpp) REVERT: E 819 GLN cc_start: 0.8367 (pt0) cc_final: 0.8134 (tm130) REVERT: E 873 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8502 (mt) REVERT: E 912 CYS cc_start: 0.6586 (OUTLIER) cc_final: 0.5464 (t) REVERT: F 39 GLN cc_start: 0.5338 (tp40) cc_final: 0.4992 (tp40) outliers start: 46 outliers final: 31 residues processed: 222 average time/residue: 0.6312 time to fit residues: 168.7748 Evaluate side-chains 228 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 190 time to evaluate : 1.359 ------------------------------------------------------------------------------- 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 650 CYS 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 815 GLN Chi-restraints excluded: chain B residue 852 SER Chi-restraints excluded: chain B residue 943 MET 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 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 569 MET Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 650 CYS Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 784 THR Chi-restraints excluded: chain C residue 852 SER Chi-restraints excluded: chain C residue 912 CYS Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 38 ARG 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 736 CYS Chi-restraints excluded: chain E residue 852 SER Chi-restraints excluded: chain E residue 873 LEU Chi-restraints excluded: chain E residue 912 CYS Chi-restraints excluded: chain F residue 28 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 263 optimal weight: 5.9990 chunk 282 optimal weight: 0.1980 chunk 87 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 78 optimal weight: 0.7980 chunk 346 optimal weight: 4.9990 chunk 259 optimal weight: 0.0570 chunk 338 optimal weight: 1.9990 chunk 295 optimal weight: 7.9990 overall best weight: 0.8100 ------------------------------------------------------------------------------- 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 681 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.136095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.098990 restraints weight = 44239.360| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.06 r_work: 0.3026 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 31212 Z= 0.110 Angle : 0.571 11.225 42495 Z= 0.300 Chirality : 0.043 0.224 4740 Planarity : 0.004 0.050 5490 Dihedral : 5.027 35.996 4497 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.04 % Favored : 94.88 % Rotamer: Outliers : 1.22 % Allowed : 14.19 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.67 (0.13), residues: 3888 helix: 1.00 (0.20), residues: 744 sheet: -0.04 (0.16), residues: 936 loop : -1.15 (0.12), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 45 TYR 0.028 0.001 TYR E 499 PHE 0.013 0.001 PHE E 183 TRP 0.011 0.001 TRP F 103 HIS 0.003 0.001 HIS C 681 Details of bonding type rmsd covalent geometry : bond 0.00248 (31140) covalent geometry : angle 0.56272 (42345) SS BOND : bond 0.00267 ( 57) SS BOND : angle 1.81145 ( 114) hydrogen bonds : bond 0.03799 ( 1088) hydrogen bonds : angle 4.72576 ( 3018) Misc. bond : bond 0.00006 ( 3) link_ALPHA1-3 : bond 0.01069 ( 3) link_ALPHA1-3 : angle 1.46099 ( 9) link_BETA1-4 : bond 0.00462 ( 6) link_BETA1-4 : angle 1.75132 ( 18) link_NAG-ASN : bond 0.00504 ( 3) link_NAG-ASN : angle 0.87059 ( 9) ********************** 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 246 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 205 time to evaluate : 1.229 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 467 PHE cc_start: 0.7914 (m-80) cc_final: 0.7640 (m-80) REVERT: B 826 GLN cc_start: 0.7819 (mm110) cc_final: 0.7117 (pm20) REVERT: B 906 MET cc_start: 0.8098 (tpt) cc_final: 0.7729 (tpt) REVERT: B 913 MET cc_start: 0.7487 (pmm) cc_final: 0.5841 (mmp) REVERT: B 1149 VAL cc_start: 0.6496 (OUTLIER) cc_final: 0.5999 (t) REVERT: C 258 GLN cc_start: 0.9275 (OUTLIER) cc_final: 0.8134 (tt0) REVERT: C 569 MET cc_start: 0.7816 (OUTLIER) cc_final: 0.7466 (mmm) REVERT: C 826 GLN cc_start: 0.7891 (mm-40) cc_final: 0.7206 (pm20) REVERT: C 912 CYS cc_start: 0.6723 (OUTLIER) cc_final: 0.5328 (t) REVERT: C 913 MET cc_start: 0.7312 (pmm) cc_final: 0.5265 (mmp) REVERT: C 1090 GLU cc_start: 0.8660 (mm-30) cc_final: 0.8432 (mm-30) REVERT: D 102 ASN cc_start: 0.8414 (t160) cc_final: 0.8087 (t0) REVERT: E 543 LYS cc_start: 0.6335 (tptt) cc_final: 0.5228 (ttpp) REVERT: E 819 GLN cc_start: 0.8382 (pt0) cc_final: 0.8140 (tm130) REVERT: E 912 CYS cc_start: 0.6515 (OUTLIER) cc_final: 0.5445 (t) REVERT: E 1059 ASP cc_start: 0.7213 (m-30) cc_final: 0.6849 (m-30) REVERT: E 1149 VAL cc_start: 0.6590 (OUTLIER) cc_final: 0.6154 (t) REVERT: F 39 GLN cc_start: 0.5219 (tp40) cc_final: 0.4932 (tp40) outliers start: 41 outliers final: 31 residues processed: 235 average time/residue: 0.6503 time to fit residues: 183.5151 Evaluate side-chains 225 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 188 time to evaluate : 1.218 ------------------------------------------------------------------------------- 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 650 CYS 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 943 MET Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1216 THR 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 569 MET Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 650 CYS Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 784 THR Chi-restraints excluded: chain C residue 852 SER Chi-restraints excluded: chain C residue 912 CYS Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 38 ARG 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 736 CYS Chi-restraints excluded: chain E residue 784 THR Chi-restraints excluded: chain E residue 852 SER Chi-restraints excluded: chain E residue 912 CYS Chi-restraints excluded: chain E residue 1121 THR Chi-restraints excluded: chain E residue 1149 VAL Chi-restraints excluded: chain F residue 28 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 251 optimal weight: 6.9990 chunk 305 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 154 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 206 optimal weight: 0.2980 chunk 168 optimal weight: 9.9990 chunk 256 optimal weight: 10.0000 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1097 GLN ** 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 = 0.3710 r_free = 0.3710 target = 0.134321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.097044 restraints weight = 44329.143| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 2.09 r_work: 0.2989 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 31212 Z= 0.151 Angle : 0.607 10.994 42495 Z= 0.318 Chirality : 0.044 0.233 4740 Planarity : 0.004 0.047 5490 Dihedral : 5.138 35.978 4497 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.43 % Favored : 94.50 % Rotamer: Outliers : 1.25 % Allowed : 14.22 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.68 (0.13), residues: 3888 helix: 0.99 (0.20), residues: 735 sheet: -0.14 (0.16), residues: 996 loop : -1.12 (0.12), residues: 2157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 46 TYR 0.024 0.001 TYR E 499 PHE 0.014 0.001 PHE E 183 TRP 0.005 0.001 TRP D 103 HIS 0.008 0.001 HIS C 194 Details of bonding type rmsd covalent geometry : bond 0.00359 (31140) covalent geometry : angle 0.59826 (42345) SS BOND : bond 0.00338 ( 57) SS BOND : angle 1.90356 ( 114) hydrogen bonds : bond 0.04335 ( 1088) hydrogen bonds : angle 4.80291 ( 3018) Misc. bond : bond 0.00028 ( 3) link_ALPHA1-3 : bond 0.00912 ( 3) link_ALPHA1-3 : angle 1.37781 ( 9) link_BETA1-4 : bond 0.00425 ( 6) link_BETA1-4 : angle 1.84988 ( 18) link_NAG-ASN : bond 0.00400 ( 3) link_NAG-ASN : angle 0.85649 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10114.91 seconds wall clock time: 173 minutes 6.09 seconds (10386.09 seconds total)