Starting phenix.real_space_refine on Mon May 26 23:15:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qyn_18759/05_2025/8qyn_18759.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qyn_18759/05_2025/8qyn_18759.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qyn_18759/05_2025/8qyn_18759.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qyn_18759/05_2025/8qyn_18759.map" model { file = "/net/cci-nas-00/data/ceres_data/8qyn_18759/05_2025/8qyn_18759.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qyn_18759/05_2025/8qyn_18759.cif" } resolution = 2.88 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= 0.018 sd= 0.125 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 184 5.16 5 C 18477 2.51 5 N 4971 2.21 5 O 5483 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 29115 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 1805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1805 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 221} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 1937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1937 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 241} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 1826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1826 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 226} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 1840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1840 Unusual residues: {'ACE': 1} Classifications: {'peptide': 241, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'ACE_C-N': 1, 'PTRANS': 8, 'TRANS': 232} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "E" Number of atoms: 1889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1889 Unusual residues: {'ACE': 1} Classifications: {'peptide': 240, 'undetermined': 1} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 10, 'TRANS': 229} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 1885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1885 Classifications: {'peptide': 242} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 236} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "G" Number of atoms: 1892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1892 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 8, 'TRANS': 234} Chain: "H" Number of atoms: 1008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1008 Unusual residues: {'ACE': 1} Classifications: {'peptide': 127, 'undetermined': 1} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 7, 'TRANS': 119} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "I" Number of atoms: 2180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2180 Classifications: {'peptide': 273} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 259} Chain breaks: 2 Chain: "J" Number of atoms: 1952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1952 Unusual residues: {'ACE': 1} Classifications: {'peptide': 249, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 15, 'TRANS': 233} Chain breaks: 2 Chain: "K" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1616 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 202} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "K" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 80 Classifications: {'peptide': 16} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'TRANS': 15} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'UNK:plan-1': 16} Unresolved non-hydrogen planarities: 16 Chain: "L" Number of atoms: 1412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1412 Classifications: {'peptide': 180} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 170} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "M" Number of atoms: 1581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1581 Unusual residues: {'ACE': 1} Classifications: {'peptide': 197, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 8, 'TRANS': 188} Chain: "N" Number of atoms: 1651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1651 Unusual residues: {'ACE': 1} Classifications: {'peptide': 216, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'ACE_C-N': 1, 'PTRANS': 6, 'TRANS': 209} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "O" Number of atoms: 1509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1509 Classifications: {'peptide': 197} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 190} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "P" Number of atoms: 1537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1537 Classifications: {'peptide': 198} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 190} Chain breaks: 1 Chain: "Q" Number of atoms: 1515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1515 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 194} Chain breaks: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Time building chain proxies: 16.07, per 1000 atoms: 0.55 Number of scatterers: 29115 At special positions: 0 Unit cell: (148.96, 143.853, 148.109, 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 184 16.00 O 5483 8.00 N 4971 7.00 C 18477 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.92 Conformation dependent library (CDL) restraints added in 3.6 seconds 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6936 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 36 sheets defined 40.3% alpha, 19.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.43 Creating SS restraints... Processing helix chain 'A' and resid 3 through 7 removed outlier: 3.794A pdb=" N TYR A 6 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER A 7 " --> pdb=" O ARG A 4 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3 through 7' Processing helix chain 'A' and resid 19 through 30 removed outlier: 3.923A pdb=" N GLU A 23 " --> pdb=" O LEU A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 102 removed outlier: 3.805A pdb=" N VAL A 85 " --> pdb=" O PRO A 81 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU A 86 " --> pdb=" O ASP A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 120 removed outlier: 3.757A pdb=" N GLU A 120 " --> pdb=" O SER A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 123 No H-bonds generated for 'chain 'A' and resid 121 through 123' Processing helix chain 'A' and resid 166 through 177 removed outlier: 3.861A pdb=" N GLY A 170 " --> pdb=" O ASN A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 199 removed outlier: 4.107A pdb=" N SER A 198 " --> pdb=" O THR A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 234 removed outlier: 3.542A pdb=" N ILE A 233 " --> pdb=" O TYR A 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 27 Processing helix chain 'B' and resid 28 through 31 Processing helix chain 'B' and resid 79 through 102 removed outlier: 3.624A pdb=" N VAL B 85 " --> pdb=" O SER B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 121 removed outlier: 3.635A pdb=" N ILE B 117 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N TYR B 121 " --> pdb=" O ILE B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 179 removed outlier: 3.754A pdb=" N ALA B 171 " --> pdb=" O ASN B 167 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN B 177 " --> pdb=" O SER B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 201 Processing helix chain 'B' and resid 229 through 248 removed outlier: 3.529A pdb=" N GLU B 248 " --> pdb=" O GLU B 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 25 removed outlier: 3.680A pdb=" N GLU C 20 " --> pdb=" O LEU C 16 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA C 25 " --> pdb=" O TYR C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 29 Processing helix chain 'C' and resid 55 through 60 removed outlier: 3.512A pdb=" N THR C 58 " --> pdb=" O ASP C 55 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ARG C 60 " --> pdb=" O ARG C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 98 removed outlier: 3.559A pdb=" N ARG C 81 " --> pdb=" O THR C 77 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ILE C 82 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL C 83 " --> pdb=" O ASP C 79 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ARG C 95 " --> pdb=" O CYS C 91 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU C 96 " --> pdb=" O GLN C 92 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR C 97 " --> pdb=" O SER C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 117 Processing helix chain 'C' and resid 118 through 120 No H-bonds generated for 'chain 'C' and resid 118 through 120' Processing helix chain 'C' and resid 164 through 176 removed outlier: 4.170A pdb=" N VAL C 168 " --> pdb=" O GLY C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 196 Processing helix chain 'C' and resid 221 through 234 Processing helix chain 'D' and resid 21 through 30 removed outlier: 3.621A pdb=" N GLU D 25 " --> pdb=" O LEU D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 34 Processing helix chain 'D' and resid 60 through 64 Processing helix chain 'D' and resid 81 through 104 removed outlier: 3.601A pdb=" N ALA D 85 " --> pdb=" O LEU D 81 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS D 86 " --> pdb=" O ILE D 82 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N THR D 87 " --> pdb=" O ALA D 83 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU D 88 " --> pdb=" O ASP D 84 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASP D 90 " --> pdb=" O LYS D 86 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LYS D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 121 removed outlier: 3.982A pdb=" N LEU D 119 " --> pdb=" O ALA D 115 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA D 120 " --> pdb=" O VAL D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 183 removed outlier: 3.654A pdb=" N GLU D 183 " --> pdb=" O SER D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 206 Processing helix chain 'D' and resid 230 through 239 Processing helix chain 'E' and resid 19 through 26 removed outlier: 3.714A pdb=" N GLU E 23 " --> pdb=" O ILE E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 32 removed outlier: 3.511A pdb=" N LYS E 30 " --> pdb=" O GLU E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 100 Processing helix chain 'E' and resid 104 through 118 removed outlier: 4.154A pdb=" N ILE E 118 " --> pdb=" O SER E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 121 No H-bonds generated for 'chain 'E' and resid 119 through 121' Processing helix chain 'E' and resid 165 through 175 Processing helix chain 'E' and resid 176 through 182 removed outlier: 3.661A pdb=" N PHE E 179 " --> pdb=" O MET E 176 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N MET E 180 " --> pdb=" O SER E 177 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLU E 181 " --> pdb=" O GLU E 178 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N CYS E 182 " --> pdb=" O PHE E 179 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 176 through 182' Processing helix chain 'E' and resid 183 through 196 removed outlier: 3.577A pdb=" N LEU E 187 " --> pdb=" O ASN E 183 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N LYS E 189 " --> pdb=" O ASN E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 199 No H-bonds generated for 'chain 'E' and resid 197 through 199' Processing helix chain 'E' and resid 225 through 228 Processing helix chain 'E' and resid 229 through 234 Processing helix chain 'F' and resid 21 through 31 removed outlier: 3.700A pdb=" N GLU F 25 " --> pdb=" O VAL F 21 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL F 31 " --> pdb=" O ALA F 27 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 34 No H-bonds generated for 'chain 'F' and resid 32 through 34' Processing helix chain 'F' and resid 81 through 104 Processing helix chain 'F' and resid 108 through 122 Processing helix chain 'F' and resid 123 through 125 No H-bonds generated for 'chain 'F' and resid 123 through 125' Processing helix chain 'F' and resid 169 through 178 Processing helix chain 'F' and resid 179 through 180 No H-bonds generated for 'chain 'F' and resid 179 through 180' Processing helix chain 'F' and resid 181 through 185 removed outlier: 3.830A pdb=" N MET F 185 " --> pdb=" O MET F 182 " (cutoff:3.500A) Processing helix chain 'F' and resid 186 through 202 removed outlier: 4.564A pdb=" N LYS F 192 " --> pdb=" O ARG F 188 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLU F 193 " --> pdb=" O ASP F 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 229 through 245 removed outlier: 3.645A pdb=" N LYS F 245 " --> pdb=" O LYS F 241 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 31 removed outlier: 4.021A pdb=" N GLU G 26 " --> pdb=" O LEU G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 35 removed outlier: 3.822A pdb=" N GLY G 35 " --> pdb=" O ILE G 32 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 32 through 35' Processing helix chain 'G' and resid 62 through 66 removed outlier: 3.527A pdb=" N VAL G 66 " --> pdb=" O SER G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 106 Processing helix chain 'G' and resid 110 through 125 removed outlier: 3.821A pdb=" N VAL G 124 " --> pdb=" O ASP G 120 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N TYR G 125 " --> pdb=" O ILE G 121 " (cutoff:3.500A) Processing helix chain 'G' and resid 126 through 128 No H-bonds generated for 'chain 'G' and resid 126 through 128' Processing helix chain 'G' and resid 171 through 186 Processing helix chain 'G' and resid 190 through 207 removed outlier: 3.664A pdb=" N LEU G 202 " --> pdb=" O ALA G 198 " (cutoff:3.500A) Processing helix chain 'G' and resid 231 through 244 Processing helix chain 'H' and resid 37 through 43 removed outlier: 4.311A pdb=" N LEU H 43 " --> pdb=" O LYS H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 54 Processing helix chain 'H' and resid 54 through 71 Processing helix chain 'H' and resid 73 through 87 Processing helix chain 'H' and resid 99 through 107 removed outlier: 3.537A pdb=" N ASP H 103 " --> pdb=" O ASN H 99 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 118 removed outlier: 3.960A pdb=" N ILE H 117 " --> pdb=" O GLY H 113 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU H 118 " --> pdb=" O PHE H 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 113 through 118' Processing helix chain 'H' and resid 120 through 124 removed outlier: 3.681A pdb=" N SER H 124 " --> pdb=" O PRO H 121 " (cutoff:3.500A) Processing helix chain 'H' and resid 129 through 139 Processing helix chain 'I' and resid 17 through 22 removed outlier: 4.525A pdb=" N GLU I 21 " --> pdb=" O GLY I 17 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU I 22 " --> pdb=" O THR I 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 17 through 22' Processing helix chain 'I' and resid 32 through 45 removed outlier: 3.595A pdb=" N ARG I 45 " --> pdb=" O LEU I 41 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 66 removed outlier: 3.603A pdb=" N TYR I 66 " --> pdb=" O LEU I 62 " (cutoff:3.500A) Processing helix chain 'I' and resid 76 through 87 Processing helix chain 'I' and resid 145 through 155 Processing helix chain 'I' and resid 173 through 175 No H-bonds generated for 'chain 'I' and resid 173 through 175' Processing helix chain 'I' and resid 180 through 184 Processing helix chain 'I' and resid 214 through 226 Processing helix chain 'I' and resid 243 through 249 Processing helix chain 'I' and resid 250 through 256 Processing helix chain 'I' and resid 265 through 278 removed outlier: 3.609A pdb=" N SER I 269 " --> pdb=" O ASN I 265 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR I 278 " --> pdb=" O LYS I 274 " (cutoff:3.500A) Processing helix chain 'J' and resid 23 through 25 No H-bonds generated for 'chain 'J' and resid 23 through 25' Processing helix chain 'J' and resid 26 through 40 Processing helix chain 'J' and resid 99 through 114 removed outlier: 3.575A pdb=" N GLY J 114 " --> pdb=" O VAL J 110 " (cutoff:3.500A) Processing helix chain 'J' and resid 127 through 129 No H-bonds generated for 'chain 'J' and resid 127 through 129' Processing helix chain 'J' and resid 131 through 135 Processing helix chain 'J' and resid 148 through 159 removed outlier: 3.633A pdb=" N GLN J 152 " --> pdb=" O GLN J 148 " (cutoff:3.500A) Processing helix chain 'J' and resid 186 through 198 Processing helix chain 'J' and resid 213 through 229 removed outlier: 3.552A pdb=" N ALA J 217 " --> pdb=" O ASN J 213 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N TRP J 227 " --> pdb=" O TYR J 223 " (cutoff:3.500A) Processing helix chain 'K' and resid 18 through 33 removed outlier: 3.634A pdb=" N ALA K 27 " --> pdb=" O ALA K 23 " (cutoff:3.500A) Processing helix chain 'K' and resid 92 through 114 Processing helix chain 'K' and resid 118 through 133 removed outlier: 3.711A pdb=" N ALA K 122 " --> pdb=" O ARG K 118 " (cutoff:3.500A) Processing helix chain 'K' and resid 173 through 184 removed outlier: 3.895A pdb=" N ALA K 177 " --> pdb=" O GLY K 173 " (cutoff:3.500A) Processing helix chain 'K' and resid 190 through 204 Processing helix chain 'K' and resid 224 through 226 No H-bonds generated for 'chain 'K' and resid 224 through 226' Processing helix chain 'L' and resid 56 through 79 Processing helix chain 'L' and resid 83 through 96 Processing helix chain 'L' and resid 97 through 99 No H-bonds generated for 'chain 'L' and resid 97 through 99' Processing helix chain 'L' and resid 142 through 154 removed outlier: 3.592A pdb=" N MET L 146 " --> pdb=" O CYS L 142 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N GLY L 148 " --> pdb=" O GLU L 144 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N MET L 149 " --> pdb=" O GLN L 145 " (cutoff:3.500A) Processing helix chain 'L' and resid 159 through 173 Processing helix chain 'M' and resid 52 through 72 Processing helix chain 'M' and resid 76 through 95 removed outlier: 3.727A pdb=" N ARG M 93 " --> pdb=" O ALA M 89 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N SER M 94 " --> pdb=" O ASP M 90 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG M 95 " --> pdb=" O CYS M 91 " (cutoff:3.500A) Processing helix chain 'M' and resid 135 through 147 Processing helix chain 'M' and resid 152 through 169 removed outlier: 3.761A pdb=" N VAL M 157 " --> pdb=" O ARG M 153 " (cutoff:3.500A) Processing helix chain 'N' and resid 1 through 7 removed outlier: 3.509A pdb=" N SER N 5 " --> pdb=" O MET N 1 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU N 7 " --> pdb=" O LEU N 3 " (cutoff:3.500A) Processing helix chain 'N' and resid 107 through 130 Processing helix chain 'N' and resid 134 through 148 removed outlier: 3.842A pdb=" N GLN N 148 " --> pdb=" O ASN N 144 " (cutoff:3.500A) Processing helix chain 'N' and resid 190 through 201 Processing helix chain 'N' and resid 207 through 223 removed outlier: 3.684A pdb=" N THR N 223 " --> pdb=" O ILE N 219 " (cutoff:3.500A) Processing helix chain 'O' and resid 85 through 108 Processing helix chain 'O' and resid 112 through 126 Processing helix chain 'O' and resid 167 through 171 removed outlier: 3.544A pdb=" N SER O 170 " --> pdb=" O GLY O 167 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ALA O 171 " --> pdb=" O SER O 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 167 through 171' Processing helix chain 'O' and resid 173 through 180 Processing helix chain 'O' and resid 195 through 212 removed outlier: 3.869A pdb=" N GLU O 212 " --> pdb=" O ILE O 208 " (cutoff:3.500A) Processing helix chain 'P' and resid 101 through 123 removed outlier: 3.507A pdb=" N PHE P 105 " --> pdb=" O ASP P 101 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU P 122 " --> pdb=" O ASP P 118 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLY P 123 " --> pdb=" O GLU P 119 " (cutoff:3.500A) Processing helix chain 'P' and resid 129 through 147 removed outlier: 3.728A pdb=" N LYS P 147 " --> pdb=" O SER P 143 " (cutoff:3.500A) Processing helix chain 'P' and resid 187 through 202 Proline residue: P 193 - end of helix Processing helix chain 'P' and resid 206 through 225 removed outlier: 3.548A pdb=" N ASP P 225 " --> pdb=" O LEU P 221 " (cutoff:3.500A) Processing helix chain 'Q' and resid 17 through 21 removed outlier: 3.515A pdb=" N ALA Q 21 " --> pdb=" O TRP Q 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 17 through 21' Processing helix chain 'Q' and resid 25 through 29 Processing helix chain 'Q' and resid 82 through 105 Processing helix chain 'Q' and resid 109 through 124 removed outlier: 3.839A pdb=" N MET Q 120 " --> pdb=" O LEU Q 116 " (cutoff:3.500A) Processing helix chain 'Q' and resid 169 through 177 Processing helix chain 'Q' and resid 182 through 199 Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 163 Processing sheet with id=AA2, first strand: chain 'A' and resid 66 through 67 Processing sheet with id=AA3, first strand: chain 'B' and resid 161 through 164 Processing sheet with id=AA4, first strand: chain 'B' and resid 65 through 67 Processing sheet with id=AA5, first strand: chain 'C' and resid 158 through 161 Processing sheet with id=AA6, first strand: chain 'C' and resid 62 through 64 removed outlier: 3.815A pdb=" N VAL C 134 " --> pdb=" O CYS C 70 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY C 135 " --> pdb=" O ARG C 143 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N HIS C 154 " --> pdb=" O GLN C 146 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 167 through 170 removed outlier: 4.774A pdb=" N GLN D 221 " --> pdb=" O ASN D 225 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ASN D 225 " --> pdb=" O GLN D 221 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 67 through 71 removed outlier: 6.890A pdb=" N ILE D 67 " --> pdb=" O MET D 78 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N MET D 78 " --> pdb=" O ILE D 67 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N GLU D 69 " --> pdb=" O CYS D 76 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N CYS D 76 " --> pdb=" O GLU D 69 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE D 74 " --> pdb=" O ASP D 71 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY D 144 " --> pdb=" O GLY D 75 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP D 147 " --> pdb=" O GLY D 150 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR D 161 " --> pdb=" O ASP D 157 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 158 through 161 Processing sheet with id=AB1, first strand: chain 'E' and resid 63 through 67 removed outlier: 3.617A pdb=" N ILE E 72 " --> pdb=" O LEU E 64 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ILE E 70 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU E 132 " --> pdb=" O THR E 147 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ILE E 144 " --> pdb=" O CYS E 156 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 163 through 166 removed outlier: 3.999A pdb=" N GLY F 45 " --> pdb=" O CYS F 42 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLY F 218 " --> pdb=" O ARG F 224 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ARG F 224 " --> pdb=" O GLY F 218 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 67 through 69 Processing sheet with id=AB4, first strand: chain 'G' and resid 5 through 6 removed outlier: 5.797A pdb=" N SER G 5 " --> pdb=" O VAL I 10 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'G' and resid 165 through 169 removed outlier: 6.650A pdb=" N THR G 38 " --> pdb=" O GLN G 53 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN G 53 " --> pdb=" O THR G 38 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 69 through 73 removed outlier: 3.522A pdb=" N PHE G 70 " --> pdb=" O CYS G 78 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N CYS G 78 " --> pdb=" O PHE G 70 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE G 76 " --> pdb=" O ILE G 72 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE G 141 " --> pdb=" O GLY G 77 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N VAL G 151 " --> pdb=" O PHE G 163 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 14 through 15 removed outlier: 3.515A pdb=" N ILE H 14 " --> pdb=" O LEU N 39 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 56 through 57 removed outlier: 3.545A pdb=" N THR I 56 " --> pdb=" O ARG I 51 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N PHE I 123 " --> pdb=" O VAL I 96 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N CYS I 98 " --> pdb=" O CYS I 121 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N CYS I 121 " --> pdb=" O CYS I 98 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL I 122 " --> pdb=" O GLN I 136 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LYS I 70 " --> pdb=" O PHE I 133 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N CYS I 135 " --> pdb=" O LYS I 70 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ILE I 72 " --> pdb=" O CYS I 135 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N CYS I 137 " --> pdb=" O ILE I 72 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N ALA I 74 " --> pdb=" O CYS I 137 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N CYS I 169 " --> pdb=" O ILE I 75 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 212 through 213 Processing sheet with id=AC1, first strand: chain 'J' and resid 1 through 4 removed outlier: 3.524A pdb=" N SER J 42 " --> pdb=" O SER J 79 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N VAL J 77 " --> pdb=" O ILE J 44 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N TYR J 46 " --> pdb=" O ALA J 75 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N ALA J 75 " --> pdb=" O TYR J 46 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N THR J 16 " --> pdb=" O VAL J 86 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N LEU J 88 " --> pdb=" O THR J 16 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU J 18 " --> pdb=" O LEU J 88 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N LEU J 90 " --> pdb=" O LEU J 18 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LEU J 17 " --> pdb=" O ILE J 119 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N LEU J 121 " --> pdb=" O LEU J 17 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N MET J 19 " --> pdb=" O LEU J 121 " (cutoff:3.500A) removed outlier: 9.434A pdb=" N SER J 123 " --> pdb=" O MET J 19 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N VAL J 118 " --> pdb=" O ALA J 202 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N LEU J 204 " --> pdb=" O VAL J 118 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N VAL J 120 " --> pdb=" O LEU J 204 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N LYS J 206 " --> pdb=" O VAL J 120 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N SER J 122 " --> pdb=" O LYS J 206 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N VAL J 208 " --> pdb=" O SER J 122 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N SER J 124 " --> pdb=" O VAL J 208 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'K' and resid 41 through 42 Processing sheet with id=AC3, first strand: chain 'K' and resid 41 through 42 removed outlier: 3.604A pdb=" N LEU K 143 " --> pdb=" O TYR K 154 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 167 through 170 removed outlier: 3.924A pdb=" N GLY K 54 " --> pdb=" O TYR K 51 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'K' and resid 256 through 259 removed outlier: 3.888A pdb=" N UNK K 256 " --> pdb=" O THR L 199 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR L 199 " --> pdb=" O UNK K 256 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE L 186 " --> pdb=" O ALA L 24 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASP L 25 " --> pdb=" O ALA L 10 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ALA L 10 " --> pdb=" O ASP L 25 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 42 through 44 Processing sheet with id=AC7, first strand: chain 'M' and resid 129 through 132 removed outlier: 3.578A pdb=" N ILE M 183 " --> pdb=" O VAL M 13 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE M 182 " --> pdb=" O HIS M 189 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'M' and resid 26 through 27 removed outlier: 3.512A pdb=" N SER N 186 " --> pdb=" O GLN M 27 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL N 187 " --> pdb=" O THR N 62 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY N 70 " --> pdb=" O PHE N 67 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL N 71 " --> pdb=" O VAL N 238 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL N 73 " --> pdb=" O TYR N 236 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLY N 242 " --> pdb=" O ARG N 239 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'M' and resid 35 through 39 removed outlier: 6.673A pdb=" N ILE M 42 " --> pdb=" O MET M 38 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N LEU M 102 " --> pdb=" O MET M 118 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N MET M 118 " --> pdb=" O LEU M 102 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'N' and resid 18 through 19 Processing sheet with id=AD2, first strand: chain 'N' and resid 93 through 94 removed outlier: 4.049A pdb=" N MET N 159 " --> pdb=" O THR N 103 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY N 162 " --> pdb=" O GLY N 169 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'O' and resid 163 through 165 Processing sheet with id=AD4, first strand: chain 'O' and resid 57 through 58 Processing sheet with id=AD5, first strand: chain 'O' and resid 71 through 75 removed outlier: 6.843A pdb=" N THR O 78 " --> pdb=" O LEU O 74 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N VAL O 149 " --> pdb=" O ASP O 161 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN O 159 " --> pdb=" O SER O 151 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'P' and resid 181 through 184 Processing sheet with id=AD7, first strand: chain 'P' and resid 87 through 91 removed outlier: 6.735A pdb=" N THR P 94 " --> pdb=" O VAL P 90 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'Q' and resid 159 through 163 removed outlier: 5.111A pdb=" N THR Q 36 " --> pdb=" O ASP Q 51 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'Q' and resid 69 through 70 removed outlier: 3.678A pdb=" N ASP Q 138 " --> pdb=" O GLY Q 142 " (cutoff:3.500A) 1458 hydrogen bonds defined for protein. 4164 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: 9.72 Time building geometry restraints manager: 8.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6914 1.33 - 1.45: 5744 1.45 - 1.57: 16693 1.57 - 1.69: 0 1.69 - 1.81: 292 Bond restraints: 29643 Sorted by residual: bond pdb=" N ILE M 151 " pdb=" CA ILE M 151 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.25e-02 6.40e+03 9.79e+00 bond pdb=" N THR M 150 " pdb=" CA THR M 150 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.16e-02 7.43e+03 6.78e+00 bond pdb=" N SER M 152 " pdb=" CA SER M 152 " ideal model delta sigma weight residual 1.455 1.486 -0.032 1.25e-02 6.40e+03 6.37e+00 bond pdb=" N GLU M 154 " pdb=" CA GLU M 154 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.18e-02 7.18e+03 6.11e+00 bond pdb=" N ARG M 153 " pdb=" CA ARG M 153 " ideal model delta sigma weight residual 1.459 1.489 -0.029 1.23e-02 6.61e+03 5.72e+00 ... (remaining 29638 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.23: 38871 1.23 - 2.47: 919 2.47 - 3.70: 214 3.70 - 4.94: 31 4.94 - 6.17: 9 Bond angle restraints: 40044 Sorted by residual: angle pdb=" N GLY M 133 " pdb=" CA GLY M 133 " pdb=" C GLY M 133 " ideal model delta sigma weight residual 111.21 115.28 -4.07 1.04e+00 9.25e-01 1.53e+01 angle pdb=" CA TYR M 12 " pdb=" C TYR M 12 " pdb=" O TYR M 12 " ideal model delta sigma weight residual 121.10 117.10 4.00 1.10e+00 8.26e-01 1.32e+01 angle pdb=" CA ASP M 11 " pdb=" C ASP M 11 " pdb=" O ASP M 11 " ideal model delta sigma weight residual 121.20 117.53 3.67 1.04e+00 9.25e-01 1.25e+01 angle pdb=" N GLU L 165 " pdb=" CA GLU L 165 " pdb=" CB GLU L 165 " ideal model delta sigma weight residual 110.12 114.70 -4.58 1.47e+00 4.63e-01 9.70e+00 angle pdb=" C SER F 63 " pdb=" N ASN F 64 " pdb=" CA ASN F 64 " ideal model delta sigma weight residual 121.54 127.00 -5.46 1.91e+00 2.74e-01 8.17e+00 ... (remaining 40039 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 16213 17.70 - 35.39: 1404 35.39 - 53.08: 231 53.08 - 70.78: 48 70.78 - 88.47: 14 Dihedral angle restraints: 17910 sinusoidal: 7099 harmonic: 10811 Sorted by residual: dihedral pdb=" CA PHE O 130 " pdb=" C PHE O 130 " pdb=" N PRO O 131 " pdb=" CA PRO O 131 " ideal model delta harmonic sigma weight residual 180.00 -160.62 -19.38 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA ASP K 60 " pdb=" CB ASP K 60 " pdb=" CG ASP K 60 " pdb=" OD1 ASP K 60 " ideal model delta sinusoidal sigma weight residual -30.00 -87.77 57.77 1 2.00e+01 2.50e-03 1.12e+01 dihedral pdb=" CA PRO O 131 " pdb=" C PRO O 131 " pdb=" N TYR O 132 " pdb=" CA TYR O 132 " ideal model delta harmonic sigma weight residual 180.00 163.47 16.53 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 17907 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 3057 0.036 - 0.072: 997 0.072 - 0.108: 347 0.108 - 0.144: 110 0.144 - 0.180: 4 Chirality restraints: 4515 Sorted by residual: chirality pdb=" CA VAL M 13 " pdb=" N VAL M 13 " pdb=" C VAL M 13 " pdb=" CB VAL M 13 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.09e-01 chirality pdb=" CA ASN F 64 " pdb=" N ASN F 64 " pdb=" C ASN F 64 " pdb=" CB ASN F 64 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.80e-01 chirality pdb=" CA PHE O 207 " pdb=" N PHE O 207 " pdb=" C PHE O 207 " pdb=" CB PHE O 207 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.72e-01 ... (remaining 4512 not shown) Planarity restraints: 5137 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP F 216 " -0.023 2.00e-02 2.50e+03 2.19e-02 1.20e+01 pdb=" CG TRP F 216 " 0.059 2.00e-02 2.50e+03 pdb=" CD1 TRP F 216 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP F 216 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP F 216 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP F 216 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP F 216 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 216 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 216 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP F 216 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU E 186 " 0.016 2.00e-02 2.50e+03 3.15e-02 9.91e+00 pdb=" C GLU E 186 " -0.054 2.00e-02 2.50e+03 pdb=" O GLU E 186 " 0.020 2.00e-02 2.50e+03 pdb=" N LEU E 187 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP D 157 " 0.039 5.00e-02 4.00e+02 5.81e-02 5.41e+00 pdb=" N PRO D 158 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO D 158 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO D 158 " 0.032 5.00e-02 4.00e+02 ... (remaining 5134 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 6767 2.79 - 3.32: 24699 3.32 - 3.85: 44025 3.85 - 4.37: 50506 4.37 - 4.90: 94888 Nonbonded interactions: 220885 Sorted by model distance: nonbonded pdb=" OH TYR I 175 " pdb=" OE1 GLU I 207 " model vdw 2.265 3.040 nonbonded pdb=" O GLY B 165 " pdb=" OG SER B 168 " model vdw 2.273 3.040 nonbonded pdb=" OD1 ASP C 39 " pdb=" NH1 ARG C 213 " model vdw 2.278 3.120 nonbonded pdb=" OG SER C 130 " pdb=" O THR C 147 " model vdw 2.282 3.040 nonbonded pdb=" NH1 ARG E 164 " pdb=" OD2 ASP I 243 " model vdw 2.288 3.120 ... (remaining 220880 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: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.580 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: 1.100 Check model and map are aligned: 0.190 Set scattering table: 0.220 Process input model: 60.650 Find NCS groups from input model: 1.250 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 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 : 0.004 0.039 29643 Z= 0.159 Angle : 0.497 6.172 40044 Z= 0.272 Chirality : 0.042 0.180 4515 Planarity : 0.004 0.058 5137 Dihedral : 13.482 88.475 10974 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % 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 (0.14), residues: 3663 helix: 2.72 (0.15), residues: 1296 sheet: 0.39 (0.18), residues: 847 loop : -0.98 (0.15), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.001 TRP F 216 HIS 0.005 0.001 HIS M 132 PHE 0.025 0.001 PHE L 69 TYR 0.028 0.001 TYR B 121 ARG 0.003 0.000 ARG F 41 Details of bonding type rmsd hydrogen bonds : bond 0.18447 ( 1456) hydrogen bonds : angle 6.20156 ( 4164) covalent geometry : bond 0.00368 (29643) covalent geometry : angle 0.49735 (40044) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 347 time to evaluate : 3.041 Fit side-chains REVERT: B 140 ASP cc_start: 0.8082 (t0) cc_final: 0.7794 (t0) REVERT: C 200 GLN cc_start: 0.7767 (pp30) cc_final: 0.7547 (pp30) REVERT: F 207 ASP cc_start: 0.8213 (m-30) cc_final: 0.7911 (m-30) REVERT: F 222 ASN cc_start: 0.8846 (t0) cc_final: 0.8169 (t0) REVERT: G 236 ASP cc_start: 0.8313 (t70) cc_final: 0.8068 (p0) REVERT: J 32 MET cc_start: 0.8534 (mmm) cc_final: 0.8298 (mmt) REVERT: L 116 THR cc_start: 0.8705 (t) cc_final: 0.8463 (p) REVERT: L 173 ASN cc_start: 0.8423 (m110) cc_final: 0.8004 (m110) REVERT: M 1 MET cc_start: 0.7629 (ptm) cc_final: 0.7163 (ptm) REVERT: M 158 GLU cc_start: 0.8570 (tp30) cc_final: 0.7980 (tp30) REVERT: M 162 LYS cc_start: 0.8122 (mtpt) cc_final: 0.7674 (mtpp) REVERT: N 165 LYS cc_start: 0.9048 (mtmm) cc_final: 0.8787 (mtpt) REVERT: N 221 GLN cc_start: 0.7876 (mm110) cc_final: 0.7485 (mp10) outliers start: 0 outliers final: 2 residues processed: 347 average time/residue: 1.7180 time to fit residues: 679.3460 Evaluate side-chains 273 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 271 time to evaluate : 3.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 216 TRP Chi-restraints excluded: chain J residue 55 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 310 optimal weight: 1.9990 chunk 278 optimal weight: 0.9990 chunk 154 optimal weight: 8.9990 chunk 95 optimal weight: 5.9990 chunk 188 optimal weight: 10.0000 chunk 149 optimal weight: 0.8980 chunk 288 optimal weight: 7.9990 chunk 111 optimal weight: 10.0000 chunk 175 optimal weight: 7.9990 chunk 214 optimal weight: 10.0000 chunk 334 optimal weight: 10.0000 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 ASN A 169 ASN G 224 ASN H 108 ASN J 148 GLN J 229 GLN P 83 ASN Q 41 GLN Q 188 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.091904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.065206 restraints weight = 56758.553| |-----------------------------------------------------------------------------| r_work (start): 0.2854 rms_B_bonded: 2.75 r_work: 0.2732 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2605 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.0877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 29643 Z= 0.179 Angle : 0.541 7.209 40044 Z= 0.289 Chirality : 0.044 0.175 4515 Planarity : 0.004 0.053 5137 Dihedral : 4.117 42.269 4093 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.74 % Allowed : 8.27 % Favored : 90.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % 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: 1.02 (0.14), residues: 3663 helix: 2.71 (0.15), residues: 1310 sheet: 0.52 (0.18), residues: 832 loop : -1.11 (0.15), residues: 1521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 13 HIS 0.006 0.001 HIS G 12 PHE 0.026 0.001 PHE A 173 TYR 0.027 0.001 TYR B 121 ARG 0.007 0.000 ARG F 41 Details of bonding type rmsd hydrogen bonds : bond 0.05675 ( 1456) hydrogen bonds : angle 4.60460 ( 4164) covalent geometry : bond 0.00443 (29643) covalent geometry : angle 0.54115 (40044) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 272 time to evaluate : 3.460 Fit side-chains REVERT: B 140 ASP cc_start: 0.8363 (t0) cc_final: 0.7887 (t0) REVERT: C 23 GLN cc_start: 0.8234 (tm-30) cc_final: 0.7824 (tm-30) REVERT: C 200 GLN cc_start: 0.8075 (pp30) cc_final: 0.7604 (pp30) REVERT: D 211 ASN cc_start: 0.9295 (p0) cc_final: 0.9059 (p0) REVERT: F 207 ASP cc_start: 0.8085 (m-30) cc_final: 0.7612 (m-30) REVERT: F 222 ASN cc_start: 0.8990 (t0) cc_final: 0.8297 (t0) REVERT: G 236 ASP cc_start: 0.8571 (t70) cc_final: 0.8075 (p0) REVERT: H 90 GLN cc_start: 0.8839 (mt0) cc_final: 0.8523 (mt0) REVERT: I 243 ASP cc_start: 0.8331 (OUTLIER) cc_final: 0.8055 (t0) REVERT: L 116 THR cc_start: 0.8650 (t) cc_final: 0.8383 (p) REVERT: L 173 ASN cc_start: 0.8541 (m110) cc_final: 0.7992 (m110) REVERT: N 221 GLN cc_start: 0.7681 (mm110) cc_final: 0.7277 (mp10) outliers start: 23 outliers final: 6 residues processed: 279 average time/residue: 1.5544 time to fit residues: 499.6680 Evaluate side-chains 269 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 262 time to evaluate : 3.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 133 MET Chi-restraints excluded: chain F residue 101 SER Chi-restraints excluded: chain I residue 243 ASP Chi-restraints excluded: chain M residue 148 THR Chi-restraints excluded: chain N residue 130 LYS Chi-restraints excluded: chain N residue 180 ILE Chi-restraints excluded: chain N residue 187 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 289 optimal weight: 8.9990 chunk 121 optimal weight: 9.9990 chunk 332 optimal weight: 6.9990 chunk 159 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 285 optimal weight: 1.9990 chunk 207 optimal weight: 0.9990 chunk 86 optimal weight: 7.9990 chunk 335 optimal weight: 6.9990 chunk 96 optimal weight: 3.9990 chunk 172 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 12 HIS G 224 ASN J 148 GLN P 83 ASN Q 41 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.093632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.066960 restraints weight = 57011.874| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 2.75 r_work: 0.2757 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2631 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.1034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 29643 Z= 0.125 Angle : 0.492 8.083 40044 Z= 0.263 Chirality : 0.042 0.170 4515 Planarity : 0.004 0.057 5137 Dihedral : 3.942 29.153 4088 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.83 % Allowed : 10.49 % Favored : 88.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % 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: 1.13 (0.14), residues: 3663 helix: 2.76 (0.15), residues: 1310 sheet: 0.67 (0.18), residues: 829 loop : -1.07 (0.15), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 13 HIS 0.004 0.001 HIS G 12 PHE 0.024 0.001 PHE A 173 TYR 0.022 0.001 TYR P 189 ARG 0.005 0.000 ARG N 9 Details of bonding type rmsd hydrogen bonds : bond 0.04624 ( 1456) hydrogen bonds : angle 4.29319 ( 4164) covalent geometry : bond 0.00301 (29643) covalent geometry : angle 0.49212 (40044) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 277 time to evaluate : 3.196 Fit side-chains REVERT: B 140 ASP cc_start: 0.8323 (t0) cc_final: 0.7816 (t0) REVERT: C 23 GLN cc_start: 0.8266 (tm-30) cc_final: 0.7793 (tm-30) REVERT: D 211 ASN cc_start: 0.9283 (p0) cc_final: 0.9040 (p0) REVERT: E 217 LYS cc_start: 0.8580 (ttpt) cc_final: 0.8089 (tptm) REVERT: F 207 ASP cc_start: 0.8070 (m-30) cc_final: 0.7575 (m-30) REVERT: F 222 ASN cc_start: 0.8948 (t0) cc_final: 0.8229 (t0) REVERT: G 236 ASP cc_start: 0.8557 (t70) cc_final: 0.8065 (p0) REVERT: I 33 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7923 (tm-30) REVERT: L 116 THR cc_start: 0.8714 (t) cc_final: 0.8463 (p) REVERT: L 173 ASN cc_start: 0.8565 (m110) cc_final: 0.8059 (m110) REVERT: N 9 ARG cc_start: 0.8679 (tpp80) cc_final: 0.8238 (ptp-110) REVERT: N 210 GLN cc_start: 0.8850 (mt0) cc_final: 0.8635 (pt0) REVERT: N 221 GLN cc_start: 0.7665 (mm110) cc_final: 0.7284 (mp10) REVERT: P 95 MET cc_start: 0.9087 (ptt) cc_final: 0.8851 (ptt) outliers start: 26 outliers final: 9 residues processed: 288 average time/residue: 1.5572 time to fit residues: 517.2349 Evaluate side-chains 274 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 264 time to evaluate : 3.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain F residue 101 SER Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain I residue 33 GLU Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain M residue 148 THR Chi-restraints excluded: chain N residue 73 VAL Chi-restraints excluded: chain N residue 130 LYS Chi-restraints excluded: chain N residue 187 VAL Chi-restraints excluded: chain N residue 199 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 15 optimal weight: 10.0000 chunk 142 optimal weight: 10.0000 chunk 357 optimal weight: 8.9990 chunk 301 optimal weight: 8.9990 chunk 42 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 224 optimal weight: 1.9990 chunk 298 optimal weight: 6.9990 chunk 238 optimal weight: 7.9990 chunk 359 optimal weight: 0.9990 chunk 241 optimal weight: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 224 ASN H 108 ASN J 229 GLN P 83 ASN Q 41 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.091347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.064570 restraints weight = 57334.106| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 2.76 r_work: 0.2720 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2593 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.1126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 29643 Z= 0.184 Angle : 0.529 7.099 40044 Z= 0.282 Chirality : 0.043 0.178 4515 Planarity : 0.004 0.057 5137 Dihedral : 4.078 30.657 4088 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.12 % Allowed : 11.93 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % 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 (0.14), residues: 3663 helix: 2.67 (0.15), residues: 1312 sheet: 0.67 (0.18), residues: 828 loop : -1.14 (0.15), residues: 1523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 13 HIS 0.006 0.001 HIS I 125 PHE 0.027 0.001 PHE L 69 TYR 0.025 0.001 TYR B 121 ARG 0.006 0.000 ARG K 186 Details of bonding type rmsd hydrogen bonds : bond 0.05515 ( 1456) hydrogen bonds : angle 4.28732 ( 4164) covalent geometry : bond 0.00460 (29643) covalent geometry : angle 0.52945 (40044) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 274 time to evaluate : 3.106 Fit side-chains REVERT: A 60 ARG cc_start: 0.8814 (OUTLIER) cc_final: 0.8406 (mtp85) REVERT: B 140 ASP cc_start: 0.8393 (t0) cc_final: 0.7939 (t0) REVERT: C 23 GLN cc_start: 0.8313 (tm-30) cc_final: 0.7824 (tm-30) REVERT: E 217 LYS cc_start: 0.8601 (ttpt) cc_final: 0.8091 (tptm) REVERT: F 207 ASP cc_start: 0.8153 (m-30) cc_final: 0.7601 (m-30) REVERT: F 222 ASN cc_start: 0.8963 (t0) cc_final: 0.8254 (t0) REVERT: G 236 ASP cc_start: 0.8574 (t70) cc_final: 0.8073 (p0) REVERT: H 90 GLN cc_start: 0.8898 (mt0) cc_final: 0.8576 (mt0) REVERT: I 33 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7915 (tm-30) REVERT: J 229 GLN cc_start: 0.8527 (OUTLIER) cc_final: 0.8320 (tp40) REVERT: L 116 THR cc_start: 0.8679 (t) cc_final: 0.8438 (p) REVERT: L 173 ASN cc_start: 0.8548 (m110) cc_final: 0.8056 (m110) REVERT: N 221 GLN cc_start: 0.7632 (mm110) cc_final: 0.7331 (mm110) REVERT: O 234 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7699 (pm20) outliers start: 35 outliers final: 16 residues processed: 290 average time/residue: 1.5273 time to fit residues: 510.8104 Evaluate side-chains 283 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 263 time to evaluate : 3.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ARG Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain F residue 101 SER Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain I residue 33 GLU Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 229 GLN Chi-restraints excluded: chain L residue 88 MET Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 148 THR Chi-restraints excluded: chain N residue 73 VAL Chi-restraints excluded: chain N residue 180 ILE Chi-restraints excluded: chain N residue 187 VAL Chi-restraints excluded: chain O residue 172 MET Chi-restraints excluded: chain O residue 234 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 113 optimal weight: 9.9990 chunk 317 optimal weight: 5.9990 chunk 212 optimal weight: 10.0000 chunk 162 optimal weight: 8.9990 chunk 121 optimal weight: 9.9990 chunk 265 optimal weight: 4.9990 chunk 326 optimal weight: 20.0000 chunk 184 optimal weight: 5.9990 chunk 81 optimal weight: 0.9990 chunk 282 optimal weight: 10.0000 chunk 99 optimal weight: 7.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 224 ASN H 108 ASN P 83 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.090125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.063417 restraints weight = 57038.139| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 2.74 r_work: 0.2736 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2610 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8864 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 29643 Z= 0.241 Angle : 0.574 7.547 40044 Z= 0.306 Chirality : 0.045 0.193 4515 Planarity : 0.005 0.059 5137 Dihedral : 4.282 32.350 4088 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.57 % Allowed : 12.32 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % 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: 0.91 (0.14), residues: 3663 helix: 2.58 (0.15), residues: 1307 sheet: 0.55 (0.18), residues: 833 loop : -1.21 (0.14), residues: 1523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 13 HIS 0.007 0.001 HIS I 125 PHE 0.031 0.002 PHE L 69 TYR 0.026 0.002 TYR B 121 ARG 0.007 0.000 ARG K 186 Details of bonding type rmsd hydrogen bonds : bond 0.06234 ( 1456) hydrogen bonds : angle 4.36060 ( 4164) covalent geometry : bond 0.00608 (29643) covalent geometry : angle 0.57426 (40044) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 265 time to evaluate : 3.472 Fit side-chains REVERT: A 166 ASN cc_start: 0.9243 (t0) cc_final: 0.8850 (t0) REVERT: B 140 ASP cc_start: 0.8401 (t0) cc_final: 0.8078 (t0) REVERT: C 23 GLN cc_start: 0.8542 (tm-30) cc_final: 0.8017 (tm-30) REVERT: E 217 LYS cc_start: 0.8685 (ttpt) cc_final: 0.8264 (tptm) REVERT: F 222 ASN cc_start: 0.9059 (t0) cc_final: 0.8328 (t0) REVERT: H 90 GLN cc_start: 0.8928 (mt0) cc_final: 0.8592 (mt0) REVERT: H 138 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8686 (mt) REVERT: I 33 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7949 (tm-30) REVERT: I 243 ASP cc_start: 0.8516 (OUTLIER) cc_final: 0.8294 (t0) REVERT: L 116 THR cc_start: 0.8739 (t) cc_final: 0.8529 (p) REVERT: L 173 ASN cc_start: 0.8603 (m110) cc_final: 0.8115 (m110) REVERT: M 49 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7974 (tt0) REVERT: N 210 GLN cc_start: 0.8954 (mt0) cc_final: 0.8748 (pt0) REVERT: N 221 GLN cc_start: 0.7788 (mm110) cc_final: 0.7499 (mm110) REVERT: P 172 MET cc_start: 0.9134 (OUTLIER) cc_final: 0.8895 (ptp) outliers start: 49 outliers final: 18 residues processed: 293 average time/residue: 1.6652 time to fit residues: 569.4152 Evaluate side-chains 284 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 261 time to evaluate : 3.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain F residue 101 SER Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain I residue 33 GLU Chi-restraints excluded: chain I residue 243 ASP Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain K residue 236 ASN Chi-restraints excluded: chain L residue 88 MET Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 49 GLU Chi-restraints excluded: chain M residue 148 THR Chi-restraints excluded: chain N residue 7 LEU Chi-restraints excluded: chain N residue 73 VAL Chi-restraints excluded: chain N residue 180 ILE Chi-restraints excluded: chain N residue 187 VAL Chi-restraints excluded: chain N residue 219 ILE Chi-restraints excluded: chain P residue 172 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 127 optimal weight: 0.9980 chunk 14 optimal weight: 8.9990 chunk 283 optimal weight: 20.0000 chunk 313 optimal weight: 7.9990 chunk 111 optimal weight: 7.9990 chunk 118 optimal weight: 0.8980 chunk 331 optimal weight: 9.9990 chunk 167 optimal weight: 5.9990 chunk 356 optimal weight: 9.9990 chunk 55 optimal weight: 0.7980 chunk 215 optimal weight: 7.9990 overall best weight: 3.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 224 ASN H 108 ASN J 229 GLN P 83 ASN P 230 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.091182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.064518 restraints weight = 57040.129| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 2.75 r_work: 0.2718 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2591 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 29643 Z= 0.166 Angle : 0.526 6.943 40044 Z= 0.281 Chirality : 0.043 0.177 4515 Planarity : 0.004 0.059 5137 Dihedral : 4.187 31.402 4088 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.41 % Allowed : 13.37 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % 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: 0.98 (0.14), residues: 3663 helix: 2.67 (0.15), residues: 1304 sheet: 0.60 (0.18), residues: 832 loop : -1.18 (0.15), residues: 1527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 13 HIS 0.005 0.001 HIS I 125 PHE 0.024 0.001 PHE L 69 TYR 0.015 0.001 TYR K 51 ARG 0.008 0.000 ARG K 186 Details of bonding type rmsd hydrogen bonds : bond 0.05297 ( 1456) hydrogen bonds : angle 4.23534 ( 4164) covalent geometry : bond 0.00410 (29643) covalent geometry : angle 0.52559 (40044) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 272 time to evaluate : 3.413 Fit side-chains REVERT: B 140 ASP cc_start: 0.8394 (t0) cc_final: 0.7928 (t0) REVERT: C 23 GLN cc_start: 0.8344 (tm-30) cc_final: 0.7792 (tm-30) REVERT: E 217 LYS cc_start: 0.8591 (ttpt) cc_final: 0.8151 (tptt) REVERT: F 207 ASP cc_start: 0.8203 (m-30) cc_final: 0.7864 (m-30) REVERT: F 222 ASN cc_start: 0.8965 (t0) cc_final: 0.8224 (t0) REVERT: H 90 GLN cc_start: 0.8908 (mt0) cc_final: 0.8563 (mt0) REVERT: I 33 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7920 (tt0) REVERT: L 116 THR cc_start: 0.8675 (t) cc_final: 0.8437 (p) REVERT: L 173 ASN cc_start: 0.8506 (m110) cc_final: 0.7990 (m110) REVERT: N 221 GLN cc_start: 0.7628 (mm110) cc_final: 0.7341 (mm110) REVERT: O 234 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7675 (pm20) outliers start: 44 outliers final: 27 residues processed: 294 average time/residue: 1.5297 time to fit residues: 519.1816 Evaluate side-chains 294 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 265 time to evaluate : 2.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 154 HIS Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain F residue 101 SER Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain I residue 33 GLU Chi-restraints excluded: chain I residue 243 ASP Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain L residue 26 ARG Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 88 MET Chi-restraints excluded: chain L residue 153 LEU Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 132 HIS Chi-restraints excluded: chain M residue 148 THR Chi-restraints excluded: chain M residue 150 THR Chi-restraints excluded: chain N residue 7 LEU Chi-restraints excluded: chain N residue 73 VAL Chi-restraints excluded: chain N residue 180 ILE Chi-restraints excluded: chain N residue 187 VAL Chi-restraints excluded: chain N residue 219 ILE Chi-restraints excluded: chain O residue 234 GLU Chi-restraints excluded: chain P residue 230 ASN Chi-restraints excluded: chain Q residue 222 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 259 optimal weight: 0.9990 chunk 310 optimal weight: 0.2980 chunk 357 optimal weight: 7.9990 chunk 171 optimal weight: 4.9990 chunk 69 optimal weight: 0.7980 chunk 158 optimal weight: 5.9990 chunk 164 optimal weight: 1.9990 chunk 12 optimal weight: 0.0770 chunk 203 optimal weight: 9.9990 chunk 102 optimal weight: 2.9990 chunk 307 optimal weight: 9.9990 overall best weight: 0.8342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 109 GLN G 224 ASN H 108 ASN ** M 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 83 ASN P 230 ASN Q 41 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.094928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.068496 restraints weight = 56613.102| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 2.74 r_work: 0.2853 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 29643 Z= 0.093 Angle : 0.470 7.123 40044 Z= 0.251 Chirality : 0.041 0.168 4515 Planarity : 0.004 0.058 5137 Dihedral : 3.868 31.430 4088 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.77 % Allowed : 14.56 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % 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: 1.20 (0.14), residues: 3663 helix: 2.80 (0.15), residues: 1310 sheet: 0.74 (0.18), residues: 831 loop : -1.04 (0.15), residues: 1522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 114 HIS 0.004 0.000 HIS F 121 PHE 0.022 0.001 PHE A 173 TYR 0.024 0.001 TYR L 147 ARG 0.010 0.000 ARG P 231 Details of bonding type rmsd hydrogen bonds : bond 0.03414 ( 1456) hydrogen bonds : angle 3.95583 ( 4164) covalent geometry : bond 0.00204 (29643) covalent geometry : angle 0.46956 (40044) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 284 time to evaluate : 3.189 Fit side-chains REVERT: C 23 GLN cc_start: 0.8467 (tm-30) cc_final: 0.8021 (tm-30) REVERT: E 217 LYS cc_start: 0.8619 (ttpt) cc_final: 0.8170 (tptm) REVERT: F 207 ASP cc_start: 0.8156 (m-30) cc_final: 0.7671 (m-30) REVERT: F 222 ASN cc_start: 0.8965 (t0) cc_final: 0.8193 (t0) REVERT: I 33 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7929 (tm-30) REVERT: L 116 THR cc_start: 0.8704 (t) cc_final: 0.8497 (p) REVERT: L 173 ASN cc_start: 0.8487 (m110) cc_final: 0.8021 (m110) REVERT: N 9 ARG cc_start: 0.8681 (tpp80) cc_final: 0.8108 (ttp80) REVERT: N 221 GLN cc_start: 0.7716 (mm110) cc_final: 0.7435 (mm110) REVERT: O 201 ARG cc_start: 0.8189 (tpp-160) cc_final: 0.7933 (tpp-160) REVERT: P 172 MET cc_start: 0.9016 (OUTLIER) cc_final: 0.8768 (ptp) outliers start: 24 outliers final: 11 residues processed: 295 average time/residue: 1.4574 time to fit residues: 499.0181 Evaluate side-chains 282 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 269 time to evaluate : 3.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 154 HIS Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain I residue 33 GLU Chi-restraints excluded: chain L residue 88 MET Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 148 THR Chi-restraints excluded: chain M residue 150 THR Chi-restraints excluded: chain N residue 187 VAL Chi-restraints excluded: chain P residue 172 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 317 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 98 optimal weight: 3.9990 chunk 300 optimal weight: 9.9990 chunk 50 optimal weight: 5.9990 chunk 99 optimal weight: 9.9990 chunk 259 optimal weight: 2.9990 chunk 366 optimal weight: 30.0000 chunk 216 optimal weight: 8.9990 chunk 65 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 69 ASN B 109 GLN G 224 ASN J 148 GLN N 210 GLN P 83 ASN Q 41 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.092309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.065685 restraints weight = 57110.421| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 2.73 r_work: 0.2792 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2664 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 29643 Z= 0.168 Angle : 0.528 9.762 40044 Z= 0.280 Chirality : 0.043 0.168 4515 Planarity : 0.004 0.058 5137 Dihedral : 4.031 30.595 4088 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.12 % Allowed : 14.53 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % 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: 1.13 (0.14), residues: 3663 helix: 2.76 (0.15), residues: 1310 sheet: 0.68 (0.18), residues: 832 loop : -1.09 (0.15), residues: 1521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 101 HIS 0.006 0.001 HIS M 132 PHE 0.026 0.001 PHE L 69 TYR 0.021 0.001 TYR P 189 ARG 0.012 0.000 ARG K 186 Details of bonding type rmsd hydrogen bonds : bond 0.05133 ( 1456) hydrogen bonds : angle 4.10393 ( 4164) covalent geometry : bond 0.00415 (29643) covalent geometry : angle 0.52848 (40044) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 270 time to evaluate : 3.143 Fit side-chains REVERT: A 140 ASN cc_start: 0.8615 (m110) cc_final: 0.8215 (m-40) REVERT: B 140 ASP cc_start: 0.8278 (t0) cc_final: 0.7981 (t0) REVERT: C 23 GLN cc_start: 0.8480 (tm-30) cc_final: 0.7988 (tm-30) REVERT: E 217 LYS cc_start: 0.8626 (ttpt) cc_final: 0.8257 (tptt) REVERT: F 207 ASP cc_start: 0.8239 (m-30) cc_final: 0.7690 (m-30) REVERT: F 222 ASN cc_start: 0.9021 (t0) cc_final: 0.8282 (t0) REVERT: H 90 GLN cc_start: 0.8918 (mt0) cc_final: 0.8592 (mt0) REVERT: I 33 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7932 (tm-30) REVERT: L 116 THR cc_start: 0.8727 (t) cc_final: 0.8523 (p) REVERT: L 173 ASN cc_start: 0.8487 (m110) cc_final: 0.7998 (m110) REVERT: N 221 GLN cc_start: 0.7759 (mm110) cc_final: 0.7457 (mm110) REVERT: O 201 ARG cc_start: 0.8188 (tpp-160) cc_final: 0.7978 (tpp-160) REVERT: P 172 MET cc_start: 0.9056 (OUTLIER) cc_final: 0.8796 (ptp) outliers start: 35 outliers final: 17 residues processed: 286 average time/residue: 1.5576 time to fit residues: 515.4305 Evaluate side-chains 286 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 267 time to evaluate : 3.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 154 HIS Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain I residue 33 GLU Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain L residue 14 MET Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 88 MET Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 148 THR Chi-restraints excluded: chain M residue 150 THR Chi-restraints excluded: chain N residue 187 VAL Chi-restraints excluded: chain P residue 101 ASP Chi-restraints excluded: chain P residue 172 MET Chi-restraints excluded: chain Q residue 222 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 251 optimal weight: 50.0000 chunk 342 optimal weight: 0.0970 chunk 266 optimal weight: 6.9990 chunk 227 optimal weight: 5.9990 chunk 258 optimal weight: 1.9990 chunk 116 optimal weight: 4.9990 chunk 153 optimal weight: 9.9990 chunk 7 optimal weight: 2.9990 chunk 175 optimal weight: 0.8980 chunk 244 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 69 ASN B 109 GLN G 224 ASN H 108 ASN N 210 GLN P 83 ASN Q 41 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.095114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.068810 restraints weight = 56639.505| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 2.73 r_work: 0.2860 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 29643 Z= 0.093 Angle : 0.476 9.840 40044 Z= 0.253 Chirality : 0.041 0.154 4515 Planarity : 0.004 0.058 5137 Dihedral : 3.800 31.492 4088 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.93 % Allowed : 14.88 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % 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: 1.24 (0.14), residues: 3663 helix: 2.84 (0.15), residues: 1309 sheet: 0.75 (0.18), residues: 818 loop : -0.99 (0.15), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 114 HIS 0.005 0.001 HIS M 132 PHE 0.021 0.001 PHE O 163 TYR 0.024 0.001 TYR L 147 ARG 0.013 0.000 ARG K 186 Details of bonding type rmsd hydrogen bonds : bond 0.03374 ( 1456) hydrogen bonds : angle 3.89100 ( 4164) covalent geometry : bond 0.00208 (29643) covalent geometry : angle 0.47597 (40044) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 279 time to evaluate : 3.102 Fit side-chains REVERT: A 140 ASN cc_start: 0.8536 (m110) cc_final: 0.8148 (m-40) REVERT: C 23 GLN cc_start: 0.8476 (tm-30) cc_final: 0.7985 (tm-30) REVERT: E 217 LYS cc_start: 0.8608 (ttpt) cc_final: 0.8257 (tptt) REVERT: F 207 ASP cc_start: 0.8095 (m-30) cc_final: 0.7642 (m-30) REVERT: F 222 ASN cc_start: 0.8972 (t0) cc_final: 0.8202 (t0) REVERT: I 33 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7925 (tm-30) REVERT: L 116 THR cc_start: 0.8707 (t) cc_final: 0.8498 (p) REVERT: L 173 ASN cc_start: 0.8442 (m110) cc_final: 0.7970 (m110) REVERT: N 9 ARG cc_start: 0.8651 (tpp80) cc_final: 0.8070 (ttp80) REVERT: N 92 LYS cc_start: 0.6830 (mmpt) cc_final: 0.6050 (mttt) REVERT: N 221 GLN cc_start: 0.7714 (mm110) cc_final: 0.7402 (mm110) REVERT: O 201 ARG cc_start: 0.8218 (tpp-160) cc_final: 0.7928 (tpp-160) REVERT: O 234 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7710 (pm20) REVERT: P 172 MET cc_start: 0.8981 (OUTLIER) cc_final: 0.8707 (ptp) REVERT: P 240 LYS cc_start: 0.8827 (mppt) cc_final: 0.8513 (mmpt) outliers start: 29 outliers final: 17 residues processed: 296 average time/residue: 1.5250 time to fit residues: 521.7174 Evaluate side-chains 293 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 273 time to evaluate : 3.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 154 HIS Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain I residue 33 GLU Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 88 MET Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 148 THR Chi-restraints excluded: chain M residue 150 THR Chi-restraints excluded: chain N residue 187 VAL Chi-restraints excluded: chain O residue 234 GLU Chi-restraints excluded: chain P residue 101 ASP Chi-restraints excluded: chain P residue 172 MET Chi-restraints excluded: chain Q residue 222 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 215 optimal weight: 0.9990 chunk 136 optimal weight: 6.9990 chunk 120 optimal weight: 3.9990 chunk 276 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 234 optimal weight: 9.9990 chunk 56 optimal weight: 5.9990 chunk 47 optimal weight: 0.0470 chunk 156 optimal weight: 0.9980 chunk 198 optimal weight: 0.4980 chunk 217 optimal weight: 10.0000 overall best weight: 1.3082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 ASN A 169 ASN G 224 ASN J 148 GLN N 210 GLN P 83 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.094878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.068455 restraints weight = 56637.898| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 2.73 r_work: 0.2855 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 29643 Z= 0.101 Angle : 0.481 10.945 40044 Z= 0.255 Chirality : 0.041 0.153 4515 Planarity : 0.004 0.058 5137 Dihedral : 3.748 30.943 4088 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.87 % Allowed : 15.17 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % 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: 1.31 (0.14), residues: 3663 helix: 2.87 (0.15), residues: 1310 sheet: 0.81 (0.18), residues: 821 loop : -0.95 (0.15), residues: 1532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 114 HIS 0.005 0.001 HIS M 132 PHE 0.018 0.001 PHE A 173 TYR 0.021 0.001 TYR P 189 ARG 0.013 0.000 ARG K 186 Details of bonding type rmsd hydrogen bonds : bond 0.03652 ( 1456) hydrogen bonds : angle 3.87357 ( 4164) covalent geometry : bond 0.00233 (29643) covalent geometry : angle 0.48119 (40044) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 276 time to evaluate : 3.267 Fit side-chains REVERT: A 140 ASN cc_start: 0.8546 (m110) cc_final: 0.8129 (m-40) REVERT: C 23 GLN cc_start: 0.8484 (tm-30) cc_final: 0.7990 (tm-30) REVERT: E 217 LYS cc_start: 0.8612 (ttpt) cc_final: 0.8256 (tptt) REVERT: F 207 ASP cc_start: 0.8101 (m-30) cc_final: 0.7643 (m-30) REVERT: F 222 ASN cc_start: 0.8985 (t0) cc_final: 0.8222 (t0) REVERT: I 33 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7922 (tm-30) REVERT: L 116 THR cc_start: 0.8709 (t) cc_final: 0.8505 (p) REVERT: L 158 MET cc_start: 0.9043 (mpp) cc_final: 0.8615 (mpt) REVERT: L 173 ASN cc_start: 0.8408 (m110) cc_final: 0.7937 (m110) REVERT: M 174 ASN cc_start: 0.6955 (p0) cc_final: 0.6688 (p0) REVERT: N 9 ARG cc_start: 0.8654 (tpp80) cc_final: 0.8097 (ttp80) REVERT: N 221 GLN cc_start: 0.7745 (mm110) cc_final: 0.7432 (mm110) REVERT: O 201 ARG cc_start: 0.8246 (tpp-160) cc_final: 0.7967 (tpp-160) REVERT: P 172 MET cc_start: 0.8958 (OUTLIER) cc_final: 0.8670 (ptp) REVERT: P 230 ASN cc_start: 0.7150 (t0) cc_final: 0.6641 (m-40) REVERT: P 240 LYS cc_start: 0.8791 (mppt) cc_final: 0.8483 (mmpt) outliers start: 27 outliers final: 17 residues processed: 290 average time/residue: 1.6357 time to fit residues: 551.1286 Evaluate side-chains 291 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 272 time to evaluate : 3.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 154 HIS Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain I residue 33 GLU Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 88 MET Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 148 THR Chi-restraints excluded: chain M residue 150 THR Chi-restraints excluded: chain N residue 187 VAL Chi-restraints excluded: chain P residue 101 ASP Chi-restraints excluded: chain P residue 172 MET Chi-restraints excluded: chain Q residue 222 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 106 optimal weight: 5.9990 chunk 242 optimal weight: 10.0000 chunk 133 optimal weight: 4.9990 chunk 315 optimal weight: 9.9990 chunk 356 optimal weight: 0.0670 chunk 31 optimal weight: 3.9990 chunk 277 optimal weight: 5.9990 chunk 238 optimal weight: 0.9980 chunk 134 optimal weight: 7.9990 chunk 205 optimal weight: 0.0010 chunk 342 optimal weight: 5.9990 overall best weight: 2.0128 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 224 ASN J 148 GLN P 83 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.094006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.067592 restraints weight = 56712.852| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 2.72 r_work: 0.2834 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2707 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29643 Z= 0.120 Angle : 0.498 10.891 40044 Z= 0.264 Chirality : 0.042 0.157 4515 Planarity : 0.004 0.059 5137 Dihedral : 3.798 30.191 4088 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.77 % Allowed : 15.59 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % 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: 1.30 (0.14), residues: 3663 helix: 2.85 (0.15), residues: 1313 sheet: 0.79 (0.18), residues: 833 loop : -0.94 (0.15), residues: 1517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 102 HIS 0.005 0.001 HIS M 132 PHE 0.023 0.001 PHE O 163 TYR 0.025 0.001 TYR L 147 ARG 0.013 0.000 ARG K 186 Details of bonding type rmsd hydrogen bonds : bond 0.04135 ( 1456) hydrogen bonds : angle 3.91924 ( 4164) covalent geometry : bond 0.00287 (29643) covalent geometry : angle 0.49826 (40044) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18207.20 seconds wall clock time: 314 minutes 2.81 seconds (18842.81 seconds total)