Starting phenix.real_space_refine on Mon May 19 01:50:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uav_42072/05_2025/8uav_42072.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uav_42072/05_2025/8uav_42072.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8uav_42072/05_2025/8uav_42072.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uav_42072/05_2025/8uav_42072.map" model { file = "/net/cci-nas-00/data/ceres_data/8uav_42072/05_2025/8uav_42072.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uav_42072/05_2025/8uav_42072.cif" } resolution = 2.37 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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 60 5.16 5 C 11270 2.51 5 N 3110 2.21 5 O 3300 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 17740 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1774 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 5, 'TRANS': 225} Chain: "B" Number of atoms: 1774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1774 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 5, 'TRANS': 225} Chain: "C" Number of atoms: 1774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1774 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 5, 'TRANS': 225} Chain: "D" Number of atoms: 1774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1774 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 5, 'TRANS': 225} Chain: "E" Number of atoms: 1774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1774 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 5, 'TRANS': 225} Chain: "F" Number of atoms: 1774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1774 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 5, 'TRANS': 225} Chain: "G" Number of atoms: 1774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1774 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 5, 'TRANS': 225} Chain: "H" Number of atoms: 1774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1774 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 5, 'TRANS': 225} Chain: "I" Number of atoms: 1774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1774 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 5, 'TRANS': 225} Chain: "J" Number of atoms: 1774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1774 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 5, 'TRANS': 225} Time building chain proxies: 12.05, per 1000 atoms: 0.68 Number of scatterers: 17740 At special positions: 0 Unit cell: (93.06, 89.1, 163.02, 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 60 16.00 O 3300 8.00 N 3110 7.00 C 11270 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 6 " - pdb=" SG CYS A 59 " distance=2.03 Simple disulfide: pdb=" SG CYS B 6 " - pdb=" SG CYS B 59 " distance=2.03 Simple disulfide: pdb=" SG CYS C 6 " - pdb=" SG CYS C 59 " distance=2.03 Simple disulfide: pdb=" SG CYS D 6 " - pdb=" SG CYS D 59 " distance=2.03 Simple disulfide: pdb=" SG CYS E 6 " - pdb=" SG CYS E 59 " distance=2.03 Simple disulfide: pdb=" SG CYS F 6 " - pdb=" SG CYS F 59 " distance=2.03 Simple disulfide: pdb=" SG CYS G 6 " - pdb=" SG CYS G 59 " distance=2.03 Simple disulfide: pdb=" SG CYS H 6 " - pdb=" SG CYS H 59 " distance=2.03 Simple disulfide: pdb=" SG CYS I 6 " - pdb=" SG CYS I 59 " distance=2.03 Simple disulfide: pdb=" SG CYS J 6 " - pdb=" SG CYS J 59 " 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 Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.38 Conformation dependent library (CDL) restraints added in 2.4 seconds 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4220 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 30 sheets defined 45.0% alpha, 18.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.10 Creating SS restraints... Processing helix chain 'A' and resid 35 through 49 removed outlier: 3.568A pdb=" N SER A 40 " --> pdb=" O TRP A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 116 removed outlier: 4.135A pdb=" N GLU A 102 " --> pdb=" O ASP A 98 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA A 103 " --> pdb=" O ILE A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 130 No H-bonds generated for 'chain 'A' and resid 128 through 130' Processing helix chain 'A' and resid 131 through 141 removed outlier: 3.537A pdb=" N HIS A 135 " --> pdb=" O GLU A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 181 Processing helix chain 'A' and resid 197 through 230 removed outlier: 4.416A pdb=" N LYS A 209 " --> pdb=" O HIS A 205 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N VAL A 210 " --> pdb=" O ALA A 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 49 removed outlier: 3.568A pdb=" N SER B 40 " --> pdb=" O TRP B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 116 removed outlier: 4.139A pdb=" N GLU B 102 " --> pdb=" O ASP B 98 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA B 103 " --> pdb=" O ILE B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 130 No H-bonds generated for 'chain 'B' and resid 128 through 130' Processing helix chain 'B' and resid 131 through 141 removed outlier: 3.548A pdb=" N HIS B 135 " --> pdb=" O GLU B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 181 Processing helix chain 'B' and resid 197 through 230 removed outlier: 4.412A pdb=" N LYS B 209 " --> pdb=" O HIS B 205 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N VAL B 210 " --> pdb=" O ALA B 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 49 removed outlier: 3.563A pdb=" N SER C 40 " --> pdb=" O TRP C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 116 removed outlier: 4.146A pdb=" N GLU C 102 " --> pdb=" O ASP C 98 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA C 103 " --> pdb=" O ILE C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 130 No H-bonds generated for 'chain 'C' and resid 128 through 130' Processing helix chain 'C' and resid 131 through 141 removed outlier: 3.508A pdb=" N HIS C 135 " --> pdb=" O GLU C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 181 Processing helix chain 'C' and resid 197 through 230 removed outlier: 4.419A pdb=" N LYS C 209 " --> pdb=" O HIS C 205 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N VAL C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 49 removed outlier: 3.561A pdb=" N SER D 40 " --> pdb=" O TRP D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 116 removed outlier: 4.136A pdb=" N GLU D 102 " --> pdb=" O ASP D 98 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA D 103 " --> pdb=" O ILE D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 130 No H-bonds generated for 'chain 'D' and resid 128 through 130' Processing helix chain 'D' and resid 131 through 141 removed outlier: 3.511A pdb=" N HIS D 135 " --> pdb=" O GLU D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 181 Processing helix chain 'D' and resid 197 through 230 removed outlier: 4.420A pdb=" N LYS D 209 " --> pdb=" O HIS D 205 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N VAL D 210 " --> pdb=" O ALA D 206 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 49 removed outlier: 3.566A pdb=" N SER E 40 " --> pdb=" O TRP E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 116 removed outlier: 4.154A pdb=" N GLU E 102 " --> pdb=" O ASP E 98 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA E 103 " --> pdb=" O ILE E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 130 No H-bonds generated for 'chain 'E' and resid 128 through 130' Processing helix chain 'E' and resid 131 through 141 removed outlier: 3.541A pdb=" N HIS E 135 " --> pdb=" O GLU E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 162 through 181 Processing helix chain 'E' and resid 197 through 230 removed outlier: 4.417A pdb=" N LYS E 209 " --> pdb=" O HIS E 205 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N VAL E 210 " --> pdb=" O ALA E 206 " (cutoff:3.500A) Processing helix chain 'F' and resid 35 through 49 removed outlier: 3.570A pdb=" N SER F 40 " --> pdb=" O TRP F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 116 removed outlier: 4.139A pdb=" N GLU F 102 " --> pdb=" O ASP F 98 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA F 103 " --> pdb=" O ILE F 99 " (cutoff:3.500A) Processing helix chain 'F' and resid 128 through 130 No H-bonds generated for 'chain 'F' and resid 128 through 130' Processing helix chain 'F' and resid 131 through 141 removed outlier: 3.546A pdb=" N HIS F 135 " --> pdb=" O GLU F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 181 Processing helix chain 'F' and resid 197 through 230 removed outlier: 4.412A pdb=" N LYS F 209 " --> pdb=" O HIS F 205 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL F 210 " --> pdb=" O ALA F 206 " (cutoff:3.500A) Processing helix chain 'G' and resid 35 through 49 removed outlier: 3.563A pdb=" N SER G 40 " --> pdb=" O TRP G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 116 removed outlier: 4.146A pdb=" N GLU G 102 " --> pdb=" O ASP G 98 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA G 103 " --> pdb=" O ILE G 99 " (cutoff:3.500A) Processing helix chain 'G' and resid 128 through 130 No H-bonds generated for 'chain 'G' and resid 128 through 130' Processing helix chain 'G' and resid 131 through 141 removed outlier: 3.508A pdb=" N HIS G 135 " --> pdb=" O GLU G 131 " (cutoff:3.500A) Processing helix chain 'G' and resid 162 through 181 Processing helix chain 'G' and resid 197 through 230 removed outlier: 4.419A pdb=" N LYS G 209 " --> pdb=" O HIS G 205 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N VAL G 210 " --> pdb=" O ALA G 206 " (cutoff:3.500A) Processing helix chain 'H' and resid 35 through 49 removed outlier: 3.557A pdb=" N SER H 40 " --> pdb=" O TRP H 36 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 116 removed outlier: 4.136A pdb=" N GLU H 102 " --> pdb=" O ASP H 98 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA H 103 " --> pdb=" O ILE H 99 " (cutoff:3.500A) Processing helix chain 'H' and resid 128 through 130 No H-bonds generated for 'chain 'H' and resid 128 through 130' Processing helix chain 'H' and resid 131 through 141 removed outlier: 3.511A pdb=" N HIS H 135 " --> pdb=" O GLU H 131 " (cutoff:3.500A) Processing helix chain 'H' and resid 162 through 181 Processing helix chain 'H' and resid 197 through 230 removed outlier: 4.420A pdb=" N LYS H 209 " --> pdb=" O HIS H 205 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N VAL H 210 " --> pdb=" O ALA H 206 " (cutoff:3.500A) Processing helix chain 'I' and resid 35 through 49 removed outlier: 3.564A pdb=" N SER I 40 " --> pdb=" O TRP I 36 " (cutoff:3.500A) Processing helix chain 'I' and resid 96 through 116 removed outlier: 4.151A pdb=" N GLU I 102 " --> pdb=" O ASP I 98 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA I 103 " --> pdb=" O ILE I 99 " (cutoff:3.500A) Processing helix chain 'I' and resid 128 through 130 No H-bonds generated for 'chain 'I' and resid 128 through 130' Processing helix chain 'I' and resid 131 through 141 removed outlier: 3.540A pdb=" N HIS I 135 " --> pdb=" O GLU I 131 " (cutoff:3.500A) Processing helix chain 'I' and resid 162 through 181 Processing helix chain 'I' and resid 197 through 230 removed outlier: 4.416A pdb=" N LYS I 209 " --> pdb=" O HIS I 205 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N VAL I 210 " --> pdb=" O ALA I 206 " (cutoff:3.500A) Processing helix chain 'J' and resid 35 through 49 removed outlier: 3.557A pdb=" N SER J 40 " --> pdb=" O TRP J 36 " (cutoff:3.500A) Processing helix chain 'J' and resid 96 through 116 removed outlier: 4.135A pdb=" N GLU J 102 " --> pdb=" O ASP J 98 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA J 103 " --> pdb=" O ILE J 99 " (cutoff:3.500A) Processing helix chain 'J' and resid 128 through 130 No H-bonds generated for 'chain 'J' and resid 128 through 130' Processing helix chain 'J' and resid 131 through 141 removed outlier: 3.537A pdb=" N HIS J 135 " --> pdb=" O GLU J 131 " (cutoff:3.500A) Processing helix chain 'J' and resid 162 through 181 Processing helix chain 'J' and resid 197 through 230 removed outlier: 4.415A pdb=" N LYS J 209 " --> pdb=" O HIS J 205 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N VAL J 210 " --> pdb=" O ALA J 206 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 9 removed outlier: 3.841A pdb=" N GLY A 9 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N VAL A 52 " --> pdb=" O GLY A 9 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 16 removed outlier: 4.122A pdb=" N TYR A 13 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS A 29 " --> pdb=" O VAL A 26 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY A 63 " --> pdb=" O GLU A 30 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 120 through 126 removed outlier: 3.929A pdb=" N ALA A 147 " --> pdb=" O LYS A 87 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N PHE A 153 " --> pdb=" O ALA A 93 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE A 148 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N VAL A 187 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N GLY A 150 " --> pdb=" O VAL A 187 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LEU A 189 " --> pdb=" O GLY A 150 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ALA A 152 " --> pdb=" O LEU A 189 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 5 through 9 removed outlier: 3.822A pdb=" N GLY B 9 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL B 52 " --> pdb=" O GLY B 9 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 11 through 16 removed outlier: 4.134A pdb=" N TYR B 13 " --> pdb=" O LYS B 25 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS B 29 " --> pdb=" O VAL B 26 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY B 63 " --> pdb=" O GLU B 30 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 120 through 126 removed outlier: 3.933A pdb=" N ALA B 147 " --> pdb=" O LYS B 87 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N PHE B 153 " --> pdb=" O ALA B 93 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE B 148 " --> pdb=" O LEU B 185 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N VAL B 187 " --> pdb=" O ILE B 148 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N GLY B 150 " --> pdb=" O VAL B 187 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU B 189 " --> pdb=" O GLY B 150 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ALA B 152 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 7 through 9 removed outlier: 3.808A pdb=" N GLY C 9 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL C 52 " --> pdb=" O GLY C 9 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 11 through 16 removed outlier: 4.154A pdb=" N TYR C 13 " --> pdb=" O LYS C 25 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLY C 63 " --> pdb=" O GLU C 30 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 120 through 126 removed outlier: 3.940A pdb=" N ALA C 147 " --> pdb=" O LYS C 87 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N PHE C 153 " --> pdb=" O ALA C 93 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ILE C 148 " --> pdb=" O LEU C 185 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N VAL C 187 " --> pdb=" O ILE C 148 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N GLY C 150 " --> pdb=" O VAL C 187 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LEU C 189 " --> pdb=" O GLY C 150 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ALA C 152 " --> pdb=" O LEU C 189 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 7 through 9 removed outlier: 3.797A pdb=" N GLY D 9 " --> pdb=" O VAL D 52 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL D 52 " --> pdb=" O GLY D 9 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 11 through 16 removed outlier: 4.146A pdb=" N TYR D 13 " --> pdb=" O LYS D 25 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY D 63 " --> pdb=" O GLU D 30 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 120 through 126 removed outlier: 3.930A pdb=" N ALA D 147 " --> pdb=" O LYS D 87 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N PHE D 153 " --> pdb=" O ALA D 93 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ILE D 148 " --> pdb=" O LEU D 185 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N VAL D 187 " --> pdb=" O ILE D 148 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N GLY D 150 " --> pdb=" O VAL D 187 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LEU D 189 " --> pdb=" O GLY D 150 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ALA D 152 " --> pdb=" O LEU D 189 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 7 through 9 removed outlier: 3.815A pdb=" N GLY E 9 " --> pdb=" O VAL E 52 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL E 52 " --> pdb=" O GLY E 9 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 11 through 16 removed outlier: 4.149A pdb=" N TYR E 13 " --> pdb=" O LYS E 25 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY E 63 " --> pdb=" O GLU E 30 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 120 through 126 removed outlier: 3.912A pdb=" N ALA E 147 " --> pdb=" O LYS E 87 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N PHE E 153 " --> pdb=" O ALA E 93 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE E 148 " --> pdb=" O LEU E 185 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N VAL E 187 " --> pdb=" O ILE E 148 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N GLY E 150 " --> pdb=" O VAL E 187 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LEU E 189 " --> pdb=" O GLY E 150 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ALA E 152 " --> pdb=" O LEU E 189 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 5 through 9 removed outlier: 3.812A pdb=" N GLY F 9 " --> pdb=" O VAL F 52 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL F 52 " --> pdb=" O GLY F 9 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 11 through 16 removed outlier: 4.134A pdb=" N TYR F 13 " --> pdb=" O LYS F 25 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS F 29 " --> pdb=" O VAL F 26 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY F 63 " --> pdb=" O GLU F 30 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 120 through 126 removed outlier: 3.933A pdb=" N ALA F 147 " --> pdb=" O LYS F 87 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N PHE F 153 " --> pdb=" O ALA F 93 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ILE F 148 " --> pdb=" O LEU F 185 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N VAL F 187 " --> pdb=" O ILE F 148 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N GLY F 150 " --> pdb=" O VAL F 187 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LEU F 189 " --> pdb=" O GLY F 150 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ALA F 152 " --> pdb=" O LEU F 189 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 7 through 9 removed outlier: 3.818A pdb=" N GLY G 9 " --> pdb=" O VAL G 52 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL G 52 " --> pdb=" O GLY G 9 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 11 through 16 removed outlier: 4.158A pdb=" N TYR G 13 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY G 63 " --> pdb=" O GLU G 30 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 120 through 126 removed outlier: 3.939A pdb=" N ALA G 147 " --> pdb=" O LYS G 87 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N PHE G 153 " --> pdb=" O ALA G 93 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ILE G 148 " --> pdb=" O LEU G 185 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N VAL G 187 " --> pdb=" O ILE G 148 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N GLY G 150 " --> pdb=" O VAL G 187 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LEU G 189 " --> pdb=" O GLY G 150 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ALA G 152 " --> pdb=" O LEU G 189 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 7 through 9 removed outlier: 3.802A pdb=" N GLY H 9 " --> pdb=" O VAL H 52 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL H 52 " --> pdb=" O GLY H 9 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 11 through 16 removed outlier: 4.142A pdb=" N TYR H 13 " --> pdb=" O LYS H 25 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY H 63 " --> pdb=" O GLU H 30 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 120 through 126 removed outlier: 3.930A pdb=" N ALA H 147 " --> pdb=" O LYS H 87 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N PHE H 153 " --> pdb=" O ALA H 93 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE H 148 " --> pdb=" O LEU H 185 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N VAL H 187 " --> pdb=" O ILE H 148 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N GLY H 150 " --> pdb=" O VAL H 187 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU H 189 " --> pdb=" O GLY H 150 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ALA H 152 " --> pdb=" O LEU H 189 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 7 through 9 removed outlier: 3.815A pdb=" N GLY I 9 " --> pdb=" O VAL I 52 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL I 52 " --> pdb=" O GLY I 9 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 11 through 16 removed outlier: 4.151A pdb=" N TYR I 13 " --> pdb=" O LYS I 25 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY I 63 " --> pdb=" O GLU I 30 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 120 through 126 removed outlier: 3.912A pdb=" N ALA I 147 " --> pdb=" O LYS I 87 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N PHE I 153 " --> pdb=" O ALA I 93 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE I 148 " --> pdb=" O LEU I 185 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N VAL I 187 " --> pdb=" O ILE I 148 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N GLY I 150 " --> pdb=" O VAL I 187 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LEU I 189 " --> pdb=" O GLY I 150 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ALA I 152 " --> pdb=" O LEU I 189 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 7 through 9 removed outlier: 3.791A pdb=" N GLY J 9 " --> pdb=" O VAL J 52 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL J 52 " --> pdb=" O GLY J 9 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 11 through 16 removed outlier: 4.130A pdb=" N TYR J 13 " --> pdb=" O LYS J 25 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS J 29 " --> pdb=" O VAL J 26 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLY J 63 " --> pdb=" O GLU J 30 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 120 through 126 removed outlier: 3.925A pdb=" N ALA J 147 " --> pdb=" O LYS J 87 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N PHE J 153 " --> pdb=" O ALA J 93 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE J 148 " --> pdb=" O LEU J 185 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N VAL J 187 " --> pdb=" O ILE J 148 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N GLY J 150 " --> pdb=" O VAL J 187 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LEU J 189 " --> pdb=" O GLY J 150 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ALA J 152 " --> pdb=" O LEU J 189 " (cutoff:3.500A) 996 hydrogen bonds defined for protein. 2919 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: 5.89 Time building geometry restraints manager: 5.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 5880 1.35 - 1.46: 4338 1.46 - 1.58: 7822 1.58 - 1.70: 0 1.70 - 1.81: 100 Bond restraints: 18140 Sorted by residual: bond pdb=" C VAL J 182 " pdb=" O VAL J 182 " ideal model delta sigma weight residual 1.232 1.239 -0.007 8.90e-03 1.26e+04 5.83e-01 bond pdb=" C VAL A 182 " pdb=" O VAL A 182 " ideal model delta sigma weight residual 1.232 1.239 -0.006 8.90e-03 1.26e+04 5.10e-01 bond pdb=" CB MET I 1 " pdb=" CG MET I 1 " ideal model delta sigma weight residual 1.520 1.540 -0.020 3.00e-02 1.11e+03 4.40e-01 bond pdb=" C VAL H 182 " pdb=" O VAL H 182 " ideal model delta sigma weight residual 1.240 1.232 0.008 1.26e-02 6.30e+03 4.11e-01 bond pdb=" C VAL B 182 " pdb=" O VAL B 182 " ideal model delta sigma weight residual 1.240 1.232 0.008 1.26e-02 6.30e+03 3.99e-01 ... (remaining 18135 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.19: 24096 1.19 - 2.39: 344 2.39 - 3.58: 85 3.58 - 4.77: 12 4.77 - 5.97: 23 Bond angle restraints: 24560 Sorted by residual: angle pdb=" C GLU E 30 " pdb=" CA GLU E 30 " pdb=" CB GLU E 30 " ideal model delta sigma weight residual 109.75 114.62 -4.87 1.65e+00 3.67e-01 8.72e+00 angle pdb=" C GLU A 30 " pdb=" CA GLU A 30 " pdb=" CB GLU A 30 " ideal model delta sigma weight residual 109.75 114.61 -4.86 1.65e+00 3.67e-01 8.69e+00 angle pdb=" C GLU D 30 " pdb=" CA GLU D 30 " pdb=" CB GLU D 30 " ideal model delta sigma weight residual 109.75 114.60 -4.85 1.65e+00 3.67e-01 8.65e+00 angle pdb=" C GLU C 30 " pdb=" CA GLU C 30 " pdb=" CB GLU C 30 " ideal model delta sigma weight residual 109.75 114.60 -4.85 1.65e+00 3.67e-01 8.63e+00 angle pdb=" C GLU J 30 " pdb=" CA GLU J 30 " pdb=" CB GLU J 30 " ideal model delta sigma weight residual 109.75 114.59 -4.84 1.65e+00 3.67e-01 8.60e+00 ... (remaining 24555 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.26: 9336 17.26 - 34.53: 888 34.53 - 51.79: 223 51.79 - 69.05: 83 69.05 - 86.32: 40 Dihedral angle restraints: 10570 sinusoidal: 4000 harmonic: 6570 Sorted by residual: dihedral pdb=" CB GLU H 181 " pdb=" CG GLU H 181 " pdb=" CD GLU H 181 " pdb=" OE1 GLU H 181 " ideal model delta sinusoidal sigma weight residual 0.00 86.32 -86.32 1 3.00e+01 1.11e-03 9.98e+00 dihedral pdb=" CB GLU D 181 " pdb=" CG GLU D 181 " pdb=" CD GLU D 181 " pdb=" OE1 GLU D 181 " ideal model delta sinusoidal sigma weight residual 0.00 86.22 -86.22 1 3.00e+01 1.11e-03 9.96e+00 dihedral pdb=" CB GLU C 181 " pdb=" CG GLU C 181 " pdb=" CD GLU C 181 " pdb=" OE1 GLU C 181 " ideal model delta sinusoidal sigma weight residual 0.00 86.17 -86.17 1 3.00e+01 1.11e-03 9.95e+00 ... (remaining 10567 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 1668 0.024 - 0.048: 581 0.048 - 0.073: 238 0.073 - 0.097: 128 0.097 - 0.121: 165 Chirality restraints: 2780 Sorted by residual: chirality pdb=" CA ILE H 88 " pdb=" N ILE H 88 " pdb=" C ILE H 88 " pdb=" CB ILE H 88 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.67e-01 chirality pdb=" CA VAL I 188 " pdb=" N VAL I 188 " pdb=" C VAL I 188 " pdb=" CB VAL I 188 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.66e-01 chirality pdb=" CA ILE I 88 " pdb=" N ILE I 88 " pdb=" C ILE I 88 " pdb=" CB ILE I 88 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.64e-01 ... (remaining 2777 not shown) Planarity restraints: 3150 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL I 126 " 0.021 5.00e-02 4.00e+02 3.13e-02 1.57e+00 pdb=" N PRO I 127 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO I 127 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO I 127 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL E 126 " -0.020 5.00e-02 4.00e+02 3.10e-02 1.54e+00 pdb=" N PRO E 127 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO E 127 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO E 127 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 126 " 0.020 5.00e-02 4.00e+02 3.04e-02 1.48e+00 pdb=" N PRO C 127 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO C 127 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO C 127 " 0.017 5.00e-02 4.00e+02 ... (remaining 3147 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 5104 2.82 - 3.34: 15369 3.34 - 3.86: 29987 3.86 - 4.38: 32970 4.38 - 4.90: 59790 Nonbonded interactions: 143220 Sorted by model distance: nonbonded pdb=" OD1 ASP A 19 " pdb=" OG1 THR A 21 " model vdw 2.303 3.040 nonbonded pdb=" OD1 ASP D 19 " pdb=" OG1 THR D 21 " model vdw 2.306 3.040 nonbonded pdb=" OD1 ASP J 19 " pdb=" OG1 THR J 21 " model vdw 2.307 3.040 nonbonded pdb=" OD1 ASP H 19 " pdb=" OG1 THR H 21 " model vdw 2.307 3.040 nonbonded pdb=" OD1 ASP B 19 " pdb=" OG1 THR B 21 " model vdw 2.316 3.040 ... (remaining 143215 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: 0.16 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'J' } 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: 4.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.640 Check model and map are aligned: 0.110 Set scattering table: 0.180 Process input model: 42.350 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 18150 Z= 0.106 Angle : 0.414 5.968 24580 Z= 0.231 Chirality : 0.041 0.121 2780 Planarity : 0.003 0.031 3150 Dihedral : 16.273 86.317 6320 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.05 % Allowed : 15.48 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.18), residues: 2290 helix: 2.83 (0.17), residues: 910 sheet: 1.01 (0.23), residues: 460 loop : -0.57 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 95 HIS 0.002 0.000 HIS C 135 PHE 0.011 0.001 PHE F 107 TYR 0.003 0.001 TYR A 130 ARG 0.007 0.000 ARG H 141 Details of bonding type rmsd hydrogen bonds : bond 0.20044 ( 996) hydrogen bonds : angle 6.08087 ( 2919) SS BOND : bond 0.00047 ( 10) SS BOND : angle 0.15454 ( 20) covalent geometry : bond 0.00227 (18140) covalent geometry : angle 0.41448 (24560) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 130 time to evaluate : 1.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 ASP cc_start: 0.9199 (m-30) cc_final: 0.8994 (m-30) REVERT: B 101 ASP cc_start: 0.9169 (m-30) cc_final: 0.8930 (m-30) REVERT: D 101 ASP cc_start: 0.9157 (m-30) cc_final: 0.8951 (m-30) REVERT: E 101 ASP cc_start: 0.9166 (m-30) cc_final: 0.8959 (m-30) REVERT: F 101 ASP cc_start: 0.9173 (m-30) cc_final: 0.8934 (m-30) REVERT: H 101 ASP cc_start: 0.9164 (m-30) cc_final: 0.8954 (m-30) REVERT: I 101 ASP cc_start: 0.9169 (m-30) cc_final: 0.8959 (m-30) REVERT: J 101 ASP cc_start: 0.9200 (m-30) cc_final: 0.8998 (m-30) outliers start: 1 outliers final: 1 residues processed: 130 average time/residue: 1.4305 time to fit residues: 207.4117 Evaluate side-chains 81 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 80 time to evaluate : 1.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 50 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 194 optimal weight: 3.9990 chunk 174 optimal weight: 2.9990 chunk 96 optimal weight: 9.9990 chunk 59 optimal weight: 2.9990 chunk 117 optimal weight: 50.0000 chunk 93 optimal weight: 0.0370 chunk 180 optimal weight: 2.9990 chunk 69 optimal weight: 50.0000 chunk 109 optimal weight: 1.9990 chunk 134 optimal weight: 0.8980 chunk 208 optimal weight: 0.8980 overall best weight: 1.3662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 GLN B 221 GLN C 221 GLN D 221 GLN E 221 GLN F 221 GLN G 221 GLN H 221 GLN I 221 GLN J 221 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.159969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.068700 restraints weight = 27674.438| |-----------------------------------------------------------------------------| r_work (start): 0.2643 rms_B_bonded: 3.00 r_work: 0.2442 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.0935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 18150 Z= 0.153 Angle : 0.457 5.267 24580 Z= 0.259 Chirality : 0.044 0.138 2780 Planarity : 0.003 0.028 3150 Dihedral : 3.443 13.399 2443 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 1.34 % Allowed : 15.48 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.17), residues: 2290 helix: 2.36 (0.17), residues: 980 sheet: 0.62 (0.22), residues: 460 loop : -0.70 (0.20), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 95 HIS 0.004 0.001 HIS A 205 PHE 0.012 0.001 PHE H 107 TYR 0.004 0.001 TYR I 160 ARG 0.004 0.000 ARG H 141 Details of bonding type rmsd hydrogen bonds : bond 0.06271 ( 996) hydrogen bonds : angle 4.60934 ( 2919) SS BOND : bond 0.00106 ( 10) SS BOND : angle 0.11392 ( 20) covalent geometry : bond 0.00352 (18140) covalent geometry : angle 0.45735 (24560) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 89 time to evaluate : 1.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 0 residues processed: 111 average time/residue: 1.7057 time to fit residues: 207.4600 Evaluate side-chains 80 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 1.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 89 optimal weight: 2.9990 chunk 49 optimal weight: 8.9990 chunk 139 optimal weight: 30.0000 chunk 58 optimal weight: 0.4980 chunk 197 optimal weight: 1.9990 chunk 209 optimal weight: 50.0000 chunk 4 optimal weight: 40.0000 chunk 33 optimal weight: 3.9990 chunk 30 optimal weight: 50.0000 chunk 26 optimal weight: 40.0000 chunk 18 optimal weight: 0.0070 overall best weight: 1.9004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 GLN B 221 GLN C 221 GLN D 221 GLN E 221 GLN F 221 GLN G 221 GLN H 221 GLN I 221 GLN J 221 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.158520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.067289 restraints weight = 27617.360| |-----------------------------------------------------------------------------| r_work (start): 0.2612 rms_B_bonded: 2.97 r_work: 0.2448 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.1162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 18150 Z= 0.188 Angle : 0.466 6.137 24580 Z= 0.261 Chirality : 0.044 0.135 2780 Planarity : 0.003 0.030 3150 Dihedral : 3.563 14.807 2440 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.54 % Allowed : 15.11 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.17), residues: 2290 helix: 2.24 (0.17), residues: 980 sheet: 0.23 (0.22), residues: 470 loop : -0.78 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 95 HIS 0.004 0.001 HIS F 205 PHE 0.014 0.001 PHE F 107 TYR 0.004 0.001 TYR G 130 ARG 0.005 0.000 ARG H 141 Details of bonding type rmsd hydrogen bonds : bond 0.06675 ( 996) hydrogen bonds : angle 4.48431 ( 2919) SS BOND : bond 0.00047 ( 10) SS BOND : angle 0.11510 ( 20) covalent geometry : bond 0.00451 (18140) covalent geometry : angle 0.46642 (24560) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 1.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 0 residues processed: 87 average time/residue: 1.9000 time to fit residues: 180.8076 Evaluate side-chains 80 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 1.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 6 optimal weight: 50.0000 chunk 137 optimal weight: 2.9990 chunk 3 optimal weight: 10.0000 chunk 81 optimal weight: 3.9990 chunk 107 optimal weight: 0.7980 chunk 213 optimal weight: 50.0000 chunk 185 optimal weight: 50.0000 chunk 94 optimal weight: 7.9990 chunk 198 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 117 optimal weight: 50.0000 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 GLN B 221 GLN C 221 GLN D 221 GLN E 221 GLN F 221 GLN G 221 GLN H 221 GLN I 221 GLN J 221 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.157994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.066550 restraints weight = 27784.772| |-----------------------------------------------------------------------------| r_work (start): 0.2599 rms_B_bonded: 2.98 r_work: 0.2397 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 18150 Z= 0.225 Angle : 0.487 6.217 24580 Z= 0.271 Chirality : 0.045 0.134 2780 Planarity : 0.003 0.032 3150 Dihedral : 3.678 15.823 2440 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 0.81 % Allowed : 15.05 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.17), residues: 2290 helix: 2.16 (0.17), residues: 980 sheet: 0.17 (0.22), residues: 460 loop : -0.86 (0.19), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 95 HIS 0.004 0.001 HIS J 205 PHE 0.014 0.001 PHE B 107 TYR 0.005 0.001 TYR F 145 ARG 0.004 0.000 ARG A 141 Details of bonding type rmsd hydrogen bonds : bond 0.07054 ( 996) hydrogen bonds : angle 4.46993 ( 2919) SS BOND : bond 0.00025 ( 10) SS BOND : angle 0.12180 ( 20) covalent geometry : bond 0.00548 (18140) covalent geometry : angle 0.48761 (24560) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 1.933 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 0 residues processed: 93 average time/residue: 2.0050 time to fit residues: 203.6973 Evaluate side-chains 80 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 1.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 107 optimal weight: 0.5980 chunk 75 optimal weight: 50.0000 chunk 87 optimal weight: 1.9990 chunk 171 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 197 optimal weight: 0.5980 chunk 175 optimal weight: 0.7980 chunk 154 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 GLN B 221 GLN C 221 GLN D 221 GLN E 221 GLN F 221 GLN G 221 GLN H 221 GLN I 221 GLN J 221 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.160940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.070716 restraints weight = 28010.531| |-----------------------------------------------------------------------------| r_work (start): 0.2692 rms_B_bonded: 2.99 r_work: 0.2513 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 18150 Z= 0.106 Angle : 0.429 6.653 24580 Z= 0.234 Chirality : 0.043 0.131 2780 Planarity : 0.003 0.029 3150 Dihedral : 3.317 12.992 2440 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 0.54 % Allowed : 16.18 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.17), residues: 2290 helix: 2.25 (0.17), residues: 980 sheet: 0.01 (0.22), residues: 470 loop : -0.74 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.000 TRP I 95 HIS 0.003 0.001 HIS D 2 PHE 0.012 0.001 PHE F 107 TYR 0.005 0.001 TYR C 16 ARG 0.006 0.000 ARG H 141 Details of bonding type rmsd hydrogen bonds : bond 0.04856 ( 996) hydrogen bonds : angle 4.16961 ( 2919) SS BOND : bond 0.00038 ( 10) SS BOND : angle 0.15422 ( 20) covalent geometry : bond 0.00225 (18140) covalent geometry : angle 0.42944 (24560) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 1.737 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 141 ARG cc_start: 0.9023 (mtp85) cc_final: 0.8751 (mmm-85) REVERT: F 141 ARG cc_start: 0.9012 (mtp85) cc_final: 0.8750 (mmm-85) outliers start: 10 outliers final: 0 residues processed: 92 average time/residue: 1.9468 time to fit residues: 195.2840 Evaluate side-chains 80 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 1.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 165 optimal weight: 5.9990 chunk 175 optimal weight: 0.0980 chunk 169 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 185 optimal weight: 50.0000 chunk 187 optimal weight: 20.0000 chunk 159 optimal weight: 0.7980 chunk 186 optimal weight: 10.0000 chunk 104 optimal weight: 3.9990 chunk 123 optimal weight: 0.0470 chunk 62 optimal weight: 2.9990 overall best weight: 0.7480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 GLN B 221 GLN C 221 GLN D 221 GLN E 221 GLN F 221 GLN G 221 GLN H 221 GLN I 221 GLN J 221 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.160868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.070513 restraints weight = 27917.197| |-----------------------------------------------------------------------------| r_work (start): 0.2717 rms_B_bonded: 2.99 r_work: 0.2524 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 18150 Z= 0.106 Angle : 0.426 7.412 24580 Z= 0.231 Chirality : 0.043 0.133 2780 Planarity : 0.003 0.037 3150 Dihedral : 3.210 12.657 2440 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 0.70 % Allowed : 15.86 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.18), residues: 2290 helix: 2.33 (0.17), residues: 980 sheet: -0.01 (0.22), residues: 470 loop : -0.75 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 95 HIS 0.003 0.000 HIS H 205 PHE 0.011 0.001 PHE F 107 TYR 0.003 0.001 TYR E 13 ARG 0.009 0.000 ARG C 141 Details of bonding type rmsd hydrogen bonds : bond 0.04821 ( 996) hydrogen bonds : angle 4.10059 ( 2919) SS BOND : bond 0.00030 ( 10) SS BOND : angle 0.15088 ( 20) covalent geometry : bond 0.00228 (18140) covalent geometry : angle 0.42591 (24560) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 1.954 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 141 ARG cc_start: 0.8959 (mtp85) cc_final: 0.8692 (mmm-85) REVERT: F 141 ARG cc_start: 0.8951 (mtp85) cc_final: 0.8686 (mmm-85) outliers start: 13 outliers final: 1 residues processed: 90 average time/residue: 1.8351 time to fit residues: 181.0364 Evaluate side-chains 81 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 80 time to evaluate : 1.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 173 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 91 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 163 optimal weight: 10.0000 chunk 183 optimal weight: 0.9980 chunk 165 optimal weight: 9.9990 chunk 162 optimal weight: 6.9990 chunk 105 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 24 optimal weight: 50.0000 chunk 57 optimal weight: 0.7980 chunk 97 optimal weight: 20.0000 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 GLN B 221 GLN C 221 GLN D 221 GLN E 221 GLN F 221 GLN G 221 GLN H 221 GLN I 221 GLN J 221 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.160526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.069875 restraints weight = 27707.199| |-----------------------------------------------------------------------------| r_work (start): 0.2676 rms_B_bonded: 2.98 r_work: 0.2519 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 18150 Z= 0.117 Angle : 0.433 7.930 24580 Z= 0.235 Chirality : 0.042 0.131 2780 Planarity : 0.003 0.038 3150 Dihedral : 3.235 12.501 2440 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 0.81 % Allowed : 15.54 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.17), residues: 2290 helix: 2.33 (0.17), residues: 980 sheet: -0.04 (0.22), residues: 470 loop : -0.79 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 95 HIS 0.003 0.001 HIS B 205 PHE 0.011 0.001 PHE F 107 TYR 0.003 0.001 TYR C 13 ARG 0.009 0.000 ARG H 141 Details of bonding type rmsd hydrogen bonds : bond 0.05096 ( 996) hydrogen bonds : angle 4.10934 ( 2919) SS BOND : bond 0.00023 ( 10) SS BOND : angle 0.12889 ( 20) covalent geometry : bond 0.00263 (18140) covalent geometry : angle 0.43359 (24560) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 1.871 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 141 ARG cc_start: 0.9030 (mtp85) cc_final: 0.8782 (mmm-85) REVERT: F 141 ARG cc_start: 0.9031 (mtp85) cc_final: 0.8783 (mmm-85) outliers start: 15 outliers final: 0 residues processed: 92 average time/residue: 1.7704 time to fit residues: 178.8197 Evaluate side-chains 80 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 1.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 181 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 168 optimal weight: 30.0000 chunk 35 optimal weight: 4.9990 chunk 159 optimal weight: 5.9990 chunk 140 optimal weight: 50.0000 chunk 155 optimal weight: 1.9990 chunk 87 optimal weight: 0.1980 chunk 106 optimal weight: 1.9990 chunk 149 optimal weight: 0.9980 chunk 119 optimal weight: 50.0000 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 GLN B 221 GLN C 221 GLN D 221 GLN E 221 GLN F 221 GLN G 221 GLN H 221 GLN I 221 GLN J 221 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.159727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.068826 restraints weight = 27756.903| |-----------------------------------------------------------------------------| r_work (start): 0.2652 rms_B_bonded: 2.99 r_work: 0.2464 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 18150 Z= 0.136 Angle : 0.450 8.485 24580 Z= 0.243 Chirality : 0.043 0.131 2780 Planarity : 0.003 0.035 3150 Dihedral : 3.317 12.961 2440 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 0.27 % Allowed : 16.34 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.17), residues: 2290 helix: 2.31 (0.17), residues: 980 sheet: -0.08 (0.22), residues: 470 loop : -0.85 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 95 HIS 0.003 0.001 HIS A 205 PHE 0.012 0.001 PHE F 107 TYR 0.003 0.001 TYR C 13 ARG 0.009 0.000 ARG G 141 Details of bonding type rmsd hydrogen bonds : bond 0.05557 ( 996) hydrogen bonds : angle 4.15968 ( 2919) SS BOND : bond 0.00014 ( 10) SS BOND : angle 0.10379 ( 20) covalent geometry : bond 0.00316 (18140) covalent geometry : angle 0.44976 (24560) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 80 time to evaluate : 2.080 Fit side-chains revert: symmetry clash REVERT: B 141 ARG cc_start: 0.9012 (mtp85) cc_final: 0.8746 (mmm-85) REVERT: F 141 ARG cc_start: 0.9009 (mtp85) cc_final: 0.8743 (mmm-85) outliers start: 5 outliers final: 0 residues processed: 84 average time/residue: 1.9481 time to fit residues: 178.9195 Evaluate side-chains 80 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 1.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 5 optimal weight: 40.0000 chunk 27 optimal weight: 0.5980 chunk 142 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 148 optimal weight: 0.8980 chunk 169 optimal weight: 0.7980 chunk 222 optimal weight: 0.0010 chunk 71 optimal weight: 50.0000 chunk 192 optimal weight: 0.7980 chunk 170 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 GLN B 221 GLN C 221 GLN D 221 GLN E 221 GLN F 221 GLN G 221 GLN H 221 GLN I 221 GLN J 221 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.161780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.071563 restraints weight = 28054.330| |-----------------------------------------------------------------------------| r_work (start): 0.2688 rms_B_bonded: 2.93 r_work: 0.2511 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 18150 Z= 0.099 Angle : 0.431 9.007 24580 Z= 0.230 Chirality : 0.042 0.131 2780 Planarity : 0.003 0.038 3150 Dihedral : 3.148 12.224 2440 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 0.00 % Allowed : 17.04 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.17), residues: 2290 helix: 2.31 (0.17), residues: 980 sheet: -0.07 (0.22), residues: 470 loop : -0.80 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 95 HIS 0.003 0.000 HIS G 205 PHE 0.010 0.001 PHE F 107 TYR 0.003 0.001 TYR G 13 ARG 0.009 0.000 ARG H 141 Details of bonding type rmsd hydrogen bonds : bond 0.04507 ( 996) hydrogen bonds : angle 4.01743 ( 2919) SS BOND : bond 0.00022 ( 10) SS BOND : angle 0.16320 ( 20) covalent geometry : bond 0.00210 (18140) covalent geometry : angle 0.43148 (24560) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 1.712 Fit side-chains REVERT: B 141 ARG cc_start: 0.8922 (mtp85) cc_final: 0.8685 (mmm-85) REVERT: F 141 ARG cc_start: 0.8922 (mtp85) cc_final: 0.8685 (mmm-85) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 1.9023 time to fit residues: 180.7070 Evaluate side-chains 87 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 1.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 170 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 chunk 148 optimal weight: 0.7980 chunk 37 optimal weight: 0.0980 chunk 32 optimal weight: 0.8980 chunk 0 optimal weight: 50.0000 chunk 1 optimal weight: 7.9990 chunk 127 optimal weight: 0.5980 chunk 140 optimal weight: 50.0000 chunk 141 optimal weight: 30.0000 chunk 101 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 GLN B 221 GLN C 221 GLN D 221 GLN E 221 GLN F 221 GLN G 221 GLN H 221 GLN I 221 GLN J 221 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.160236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.069558 restraints weight = 27820.729| |-----------------------------------------------------------------------------| r_work (start): 0.2643 rms_B_bonded: 2.94 r_work: 0.2484 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 18150 Z= 0.125 Angle : 0.451 9.264 24580 Z= 0.241 Chirality : 0.043 0.132 2780 Planarity : 0.003 0.037 3150 Dihedral : 3.246 12.806 2440 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 0.00 % Allowed : 16.99 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.18), residues: 2290 helix: 2.36 (0.17), residues: 980 sheet: -0.04 (0.23), residues: 470 loop : -0.89 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 95 HIS 0.003 0.001 HIS A 205 PHE 0.012 0.001 PHE B 107 TYR 0.004 0.001 TYR G 16 ARG 0.009 0.000 ARG D 141 Details of bonding type rmsd hydrogen bonds : bond 0.05260 ( 996) hydrogen bonds : angle 4.09197 ( 2919) SS BOND : bond 0.00009 ( 10) SS BOND : angle 0.12398 ( 20) covalent geometry : bond 0.00287 (18140) covalent geometry : angle 0.45161 (24560) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 1.773 Fit side-chains REVERT: B 141 ARG cc_start: 0.8965 (mtp85) cc_final: 0.8725 (mmm-85) REVERT: F 141 ARG cc_start: 0.8956 (mtp85) cc_final: 0.8714 (mmm-85) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 2.0018 time to fit residues: 174.6233 Evaluate side-chains 80 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 1.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 108 optimal weight: 3.9990 chunk 119 optimal weight: 50.0000 chunk 128 optimal weight: 0.6980 chunk 179 optimal weight: 1.9990 chunk 208 optimal weight: 50.0000 chunk 144 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 125 optimal weight: 0.7980 chunk 181 optimal weight: 3.9990 chunk 159 optimal weight: 1.9990 chunk 70 optimal weight: 8.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 GLN B 221 GLN C 221 GLN D 221 GLN E 221 GLN F 221 GLN G 221 GLN H 221 GLN I 221 GLN J 221 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.158900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.068195 restraints weight = 27748.066| |-----------------------------------------------------------------------------| r_work (start): 0.2632 rms_B_bonded: 2.93 r_work: 0.2432 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 18150 Z= 0.155 Angle : 0.468 8.953 24580 Z= 0.251 Chirality : 0.043 0.131 2780 Planarity : 0.003 0.036 3150 Dihedral : 3.390 13.434 2440 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 0.11 % Allowed : 16.99 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.18), residues: 2290 helix: 2.31 (0.17), residues: 980 sheet: -0.07 (0.23), residues: 470 loop : -0.95 (0.19), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 95 HIS 0.003 0.001 HIS F 205 PHE 0.013 0.001 PHE B 107 TYR 0.004 0.001 TYR F 145 ARG 0.009 0.001 ARG G 141 Details of bonding type rmsd hydrogen bonds : bond 0.05936 ( 996) hydrogen bonds : angle 4.17414 ( 2919) SS BOND : bond 0.00008 ( 10) SS BOND : angle 0.08402 ( 20) covalent geometry : bond 0.00369 (18140) covalent geometry : angle 0.46773 (24560) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17264.47 seconds wall clock time: 297 minutes 3.75 seconds (17823.75 seconds total)