Starting phenix.real_space_refine on Sat Dec 9 18:52:36 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tz6_26203/12_2023/7tz6_26203_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tz6_26203/12_2023/7tz6_26203.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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tz6_26203/12_2023/7tz6_26203.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tz6_26203/12_2023/7tz6_26203.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tz6_26203/12_2023/7tz6_26203_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tz6_26203/12_2023/7tz6_26203_trim_updated.pdb" } 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= -0.015 sd= 0.691 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: 8 Type Number sf(0) Gaussians Fe 10 7.16 5 S 158 5.16 5 Cl 2 4.86 5 C 20972 2.51 5 N 5636 2.21 5 O 5958 1.98 5 F 6 1.80 5 H 32164 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 416": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 442": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 64906 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 6812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 6812 Classifications: {'peptide': 446} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 18, 'TRANS': 427} Chain: "B" Number of atoms: 6323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 6323 Classifications: {'peptide': 423} Link IDs: {'PTRANS': 17, 'TRANS': 405} Chain: "C" Number of atoms: 6067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 6067 Classifications: {'peptide': 378} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 355} Chain: "D" Number of atoms: 3786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 3786 Classifications: {'peptide': 241} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 218} Chain: "E" Number of atoms: 3021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 3021 Classifications: {'peptide': 196} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 184} Chain: "F" Number of atoms: 1816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 1816 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 3, 'TRANS': 101} Chain: "G" Number of atoms: 1264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1264 Classifications: {'peptide': 75} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 68} Chain: "H" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1077 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 1, 'TRANS': 65} Chain: "I" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 272 Classifications: {'peptide': 20} Link IDs: {'PTRANS': 2, 'TRANS': 17} Chain: "J" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 988 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 1, 'TRANS': 58} Chain: "K" Number of atoms: 863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 863 Classifications: {'peptide': 52} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 48} Chain: "N" Number of atoms: 6812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 6812 Classifications: {'peptide': 446} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 18, 'TRANS': 427} Chain: "O" Number of atoms: 6323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 6323 Classifications: {'peptide': 423} Link IDs: {'PTRANS': 17, 'TRANS': 405} Chain: "P" Number of atoms: 6067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 6067 Classifications: {'peptide': 378} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 355} Chain: "Q" Number of atoms: 3786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 3786 Classifications: {'peptide': 241} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 218} Chain: "R" Number of atoms: 3021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 3021 Classifications: {'peptide': 196} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 184} Chain: "S" Number of atoms: 1816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 1816 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 3, 'TRANS': 101} Chain: "T" Number of atoms: 1264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1264 Classifications: {'peptide': 75} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 68} Chain: "U" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1077 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 1, 'TRANS': 65} Chain: "V" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 272 Classifications: {'peptide': 20} Link IDs: {'PTRANS': 2, 'TRANS': 17} Chain: "W" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 988 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 1, 'TRANS': 58} Chain: "X" Number of atoms: 863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 863 Classifications: {'peptide': 52} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 48} Chain: "C" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 117 Unusual residues: {'HEM': 2, 'JHB': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 117 Unusual residues: {'HEM': 2, 'JHB': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Q" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 25191 SG CYS E 139 122.361 121.952 52.002 1.00 56.81 S ATOM 25446 SG CYS E 158 124.544 119.437 53.483 1.00 57.46 S ATOM 57480 SG CYS R 139 102.287 117.546 113.686 1.00 56.45 S ATOM 57735 SG CYS R 158 100.694 120.531 112.346 1.00 33.75 S Time building chain proxies: 20.58, per 1000 atoms: 0.32 Number of scatterers: 64906 At special positions: 0 Unit cell: (176.748, 181.896, 145.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Fe 10 26.01 Cl 2 17.00 S 158 16.00 F 6 9.00 O 5958 8.00 N 5636 7.00 C 20972 6.00 H 32164 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS E 144 " - pdb=" SG CYS E 160 " distance=2.03 Simple disulfide: pdb=" SG CYS H 24 " - pdb=" SG CYS H 68 " distance=2.03 Simple disulfide: pdb=" SG CYS H 40 " - pdb=" SG CYS H 54 " distance=2.03 Simple disulfide: pdb=" SG CYS R 144 " - pdb=" SG CYS R 160 " distance=2.03 Simple disulfide: pdb=" SG CYS U 24 " - pdb=" SG CYS U 68 " distance=2.02 Simple disulfide: pdb=" SG CYS U 40 " - pdb=" SG CYS U 54 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=10, symmetry=0 Number of additional bonds: simple=10, symmetry=0 Coordination: Other bonds: Time building additional restraints: 38.04 Conformation dependent library (CDL) restraints added in 4.8 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E1001 " pdb="FE2 FES E1001 " - pdb=" ND1 HIS E 161 " pdb="FE2 FES E1001 " - pdb=" ND1 HIS E 141 " pdb="FE1 FES E1001 " - pdb=" SG CYS E 158 " pdb="FE1 FES E1001 " - pdb=" SG CYS E 139 " pdb=" FES R1001 " pdb="FE2 FES R1001 " - pdb=" ND1 HIS R 161 " pdb="FE2 FES R1001 " - pdb=" ND1 HIS R 141 " pdb="FE1 FES R1001 " - pdb=" SG CYS R 158 " pdb="FE1 FES R1001 " - pdb=" SG CYS R 139 " Number of angles added : 6 8164 Ramachandran restraints generated. 4082 Oldfield, 0 Emsley, 4082 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7700 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 178 helices and 17 sheets defined 50.8% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.80 Creating SS restraints... Processing helix chain 'A' and resid 4 through 10 Processing helix chain 'A' and resid 45 through 47 No H-bonds generated for 'chain 'A' and resid 45 through 47' Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 74 through 81 Processing helix chain 'A' and resid 104 through 116 Proline residue: A 107 - end of helix removed outlier: 3.745A pdb=" N VAL A 110 " --> pdb=" O PRO A 107 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ALA A 114 " --> pdb=" O GLU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 143 removed outlier: 4.361A pdb=" N ASP A 142 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N THR A 143 " --> pdb=" O GLN A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 157 Processing helix chain 'A' and resid 162 through 164 No H-bonds generated for 'chain 'A' and resid 162 through 164' Processing helix chain 'A' and resid 171 through 174 No H-bonds generated for 'chain 'A' and resid 171 through 174' Processing helix chain 'A' and resid 179 through 189 Processing helix chain 'A' and resid 192 through 194 No H-bonds generated for 'chain 'A' and resid 192 through 194' Processing helix chain 'A' and resid 205 through 215 Processing helix chain 'A' and resid 265 through 277 removed outlier: 3.772A pdb=" N VAL A 268 " --> pdb=" O PRO A 265 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ASN A 274 " --> pdb=" O GLN A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 289 No H-bonds generated for 'chain 'A' and resid 287 through 289' Processing helix chain 'A' and resid 293 through 301 Processing helix chain 'A' and resid 331 through 347 Processing helix chain 'A' and resid 351 through 368 Processing helix chain 'A' and resid 373 through 385 removed outlier: 3.610A pdb=" N LEU A 384 " --> pdb=" O GLY A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 401 removed outlier: 3.614A pdb=" N GLU A 401 " --> pdb=" O SER A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 414 Processing helix chain 'A' and resid 434 through 441 removed outlier: 3.724A pdb=" N MET A 441 " --> pdb=" O ILE A 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 57 No H-bonds generated for 'chain 'B' and resid 55 through 57' Processing helix chain 'B' and resid 65 through 71 Processing helix chain 'B' and resid 82 through 91 Processing helix chain 'B' and resid 113 through 128 removed outlier: 3.875A pdb=" N VAL B 116 " --> pdb=" O ARG B 113 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N ASP B 117 " --> pdb=" O ASP B 114 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE B 118 " --> pdb=" O ASP B 115 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N MET B 120 " --> pdb=" O ASP B 117 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU B 123 " --> pdb=" O MET B 120 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU B 124 " --> pdb=" O GLU B 121 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N THR B 128 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 139 Processing helix chain 'B' and resid 141 through 153 removed outlier: 4.151A pdb=" N ASP B 147 " --> pdb=" O LEU B 144 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LYS B 148 " --> pdb=" O ARG B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 167 Processing helix chain 'B' and resid 180 through 182 No H-bonds generated for 'chain 'B' and resid 180 through 182' Processing helix chain 'B' and resid 188 through 198 Processing helix chain 'B' and resid 201 through 203 No H-bonds generated for 'chain 'B' and resid 201 through 203' Processing helix chain 'B' and resid 213 through 222 Processing helix chain 'B' and resid 267 through 279 removed outlier: 3.700A pdb=" N ALA B 271 " --> pdb=" O ALA B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 300 Processing helix chain 'B' and resid 330 through 349 removed outlier: 3.702A pdb=" N ALA B 333 " --> pdb=" O ALA B 330 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N GLY B 334 " --> pdb=" O ALA B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 372 removed outlier: 3.769A pdb=" N VAL B 372 " --> pdb=" O TYR B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 388 Processing helix chain 'B' and resid 395 through 403 Processing helix chain 'B' and resid 407 through 418 removed outlier: 3.713A pdb=" N ILE B 411 " --> pdb=" O ASP B 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 6 No H-bonds generated for 'chain 'C' and resid 4 through 6' Processing helix chain 'C' and resid 11 through 18 Processing helix chain 'C' and resid 29 through 51 removed outlier: 3.634A pdb=" N PHE C 33 " --> pdb=" O TRP C 30 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLY C 34 " --> pdb=" O TRP C 31 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU C 37 " --> pdb=" O GLY C 34 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N CYS C 40 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU C 41 " --> pdb=" O GLY C 38 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N THR C 47 " --> pdb=" O GLN C 44 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLY C 48 " --> pdb=" O ILE C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 71 Processing helix chain 'C' and resid 76 through 103 removed outlier: 3.922A pdb=" N ALA C 87 " --> pdb=" O HIS C 83 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N SER C 88 " --> pdb=" O ALA C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 108 No H-bonds generated for 'chain 'C' and resid 106 through 108' Processing helix chain 'C' and resid 110 through 132 removed outlier: 3.801A pdb=" N VAL C 132 " --> pdb=" O PHE C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 152 removed outlier: 3.914A pdb=" N VAL C 145 " --> pdb=" O TRP C 141 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU C 150 " --> pdb=" O ILE C 146 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N SER C 151 " --> pdb=" O THR C 147 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ALA C 152 " --> pdb=" O ASN C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 165 Processing helix chain 'C' and resid 172 through 201 Proline residue: C 186 - end of helix removed outlier: 3.609A pdb=" N VAL C 195 " --> pdb=" O ALA C 191 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU C 200 " --> pdb=" O HIS C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 245 removed outlier: 3.863A pdb=" N LYS C 227 " --> pdb=" O TYR C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 256 Processing helix chain 'C' and resid 275 through 281 Processing helix chain 'C' and resid 287 through 303 removed outlier: 3.627A pdb=" N ILE C 298 " --> pdb=" O LEU C 294 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N LEU C 301 " --> pdb=" O SER C 297 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N ALA C 302 " --> pdb=" O ILE C 298 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU C 303 " --> pdb=" O LEU C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 307 No H-bonds generated for 'chain 'C' and resid 305 through 307' Processing helix chain 'C' and resid 315 through 317 No H-bonds generated for 'chain 'C' and resid 315 through 317' Processing helix chain 'C' and resid 319 through 340 removed outlier: 3.924A pdb=" N GLY C 340 " --> pdb=" O THR C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 363 Processing helix chain 'C' and resid 365 through 376 Processing helix chain 'D' and resid 23 through 35 Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 48 through 50 No H-bonds generated for 'chain 'D' and resid 48 through 50' Processing helix chain 'D' and resid 58 through 67 removed outlier: 3.744A pdb=" N GLU D 67 " --> pdb=" O ALA D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 103 Processing helix chain 'D' and resid 124 through 131 Processing helix chain 'D' and resid 179 through 194 Processing helix chain 'D' and resid 198 through 231 removed outlier: 3.531A pdb=" N LYS D 207 " --> pdb=" O ARG D 203 " (cutoff:3.500A) Proline residue: D 217 - end of helix removed outlier: 4.695A pdb=" N VAL D 229 " --> pdb=" O HIS D 225 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N LEU D 230 " --> pdb=" O LYS D 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 18 No H-bonds generated for 'chain 'E' and resid 16 through 18' Processing helix chain 'E' and resid 29 through 62 removed outlier: 3.884A pdb=" N MET E 62 " --> pdb=" O PHE E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 68 No H-bonds generated for 'chain 'E' and resid 66 through 68' Processing helix chain 'E' and resid 103 through 109 Processing helix chain 'E' and resid 123 through 125 No H-bonds generated for 'chain 'E' and resid 123 through 125' Processing helix chain 'F' and resid 8 through 24 Processing helix chain 'F' and resid 26 through 29 Processing helix chain 'F' and resid 34 through 36 No H-bonds generated for 'chain 'F' and resid 34 through 36' Processing helix chain 'F' and resid 41 through 48 Processing helix chain 'F' and resid 52 through 71 Processing helix chain 'F' and resid 91 through 109 Processing helix chain 'G' and resid 33 through 70 removed outlier: 4.630A pdb=" N LEU G 46 " --> pdb=" O ARG G 42 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ARG G 47 " --> pdb=" O ALA G 43 " (cutoff:3.500A) Proline residue: G 50 - end of helix Processing helix chain 'H' and resid 16 through 26 removed outlier: 3.768A pdb=" N GLN H 26 " --> pdb=" O GLU H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 46 removed outlier: 4.001A pdb=" N LYS H 32 " --> pdb=" O GLU H 28 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ALA H 33 " --> pdb=" O LYS H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 72 removed outlier: 3.643A pdb=" N ALA H 64 " --> pdb=" O ASP H 60 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N CYS H 68 " --> pdb=" O ALA H 64 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL H 69 " --> pdb=" O ARG H 65 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA H 70 " --> pdb=" O ASP H 66 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N HIS H 71 " --> pdb=" O HIS H 67 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS H 72 " --> pdb=" O CYS H 68 " (cutoff:3.500A) Processing helix chain 'J' and resid 5 through 12 Processing helix chain 'J' and resid 17 through 46 removed outlier: 3.953A pdb=" N ARG J 33 " --> pdb=" O LEU J 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 8 through 36 Proline residue: K 19 - end of helix Processing helix chain 'K' and resid 39 through 44 removed outlier: 4.949A pdb=" N TRP K 44 " --> pdb=" O LEU K 40 " (cutoff:3.500A) Processing helix chain 'K' and resid 48 through 51 Processing helix chain 'N' and resid 4 through 9 Processing helix chain 'N' and resid 45 through 47 No H-bonds generated for 'chain 'N' and resid 45 through 47' Processing helix chain 'N' and resid 55 through 60 Processing helix chain 'N' and resid 74 through 81 Processing helix chain 'N' and resid 103 through 118 Proline residue: N 107 - end of helix removed outlier: 3.801A pdb=" N VAL N 110 " --> pdb=" O PRO N 107 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL N 117 " --> pdb=" O ALA N 114 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLN N 118 " --> pdb=" O ASP N 115 " (cutoff:3.500A) Processing helix chain 'N' and resid 124 through 143 removed outlier: 3.922A pdb=" N ASP N 132 " --> pdb=" O GLU N 128 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL N 133 " --> pdb=" O LYS N 129 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N THR N 143 " --> pdb=" O GLN N 139 " (cutoff:3.500A) Processing helix chain 'N' and resid 145 through 157 Processing helix chain 'N' and resid 162 through 164 No H-bonds generated for 'chain 'N' and resid 162 through 164' Processing helix chain 'N' and resid 171 through 174 No H-bonds generated for 'chain 'N' and resid 171 through 174' Processing helix chain 'N' and resid 179 through 189 Processing helix chain 'N' and resid 192 through 194 No H-bonds generated for 'chain 'N' and resid 192 through 194' Processing helix chain 'N' and resid 205 through 215 Processing helix chain 'N' and resid 265 through 277 removed outlier: 3.623A pdb=" N ASN N 274 " --> pdb=" O GLN N 271 " (cutoff:3.500A) Processing helix chain 'N' and resid 287 through 289 No H-bonds generated for 'chain 'N' and resid 287 through 289' Processing helix chain 'N' and resid 293 through 301 Processing helix chain 'N' and resid 331 through 348 Processing helix chain 'N' and resid 351 through 368 Processing helix chain 'N' and resid 372 through 385 Processing helix chain 'N' and resid 392 through 400 Processing helix chain 'N' and resid 404 through 414 Processing helix chain 'N' and resid 434 through 441 removed outlier: 3.654A pdb=" N MET N 441 " --> pdb=" O ILE N 437 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 57 No H-bonds generated for 'chain 'O' and resid 55 through 57' Processing helix chain 'O' and resid 65 through 70 Processing helix chain 'O' and resid 82 through 91 Processing helix chain 'O' and resid 113 through 128 removed outlier: 5.257A pdb=" N ASP O 117 " --> pdb=" O ASP O 114 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N MET O 120 " --> pdb=" O ASP O 117 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU O 124 " --> pdb=" O GLU O 121 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N THR O 128 " --> pdb=" O ASN O 125 " (cutoff:3.500A) Processing helix chain 'O' and resid 134 through 153 Proline residue: O 142 - end of helix removed outlier: 4.060A pdb=" N ARG O 145 " --> pdb=" O GLN O 141 " (cutoff:3.500A) Processing helix chain 'O' and resid 155 through 167 Processing helix chain 'O' and resid 171 through 173 No H-bonds generated for 'chain 'O' and resid 171 through 173' Processing helix chain 'O' and resid 180 through 182 No H-bonds generated for 'chain 'O' and resid 180 through 182' Processing helix chain 'O' and resid 188 through 198 Processing helix chain 'O' and resid 201 through 203 No H-bonds generated for 'chain 'O' and resid 201 through 203' Processing helix chain 'O' and resid 213 through 223 Processing helix chain 'O' and resid 267 through 279 removed outlier: 3.568A pdb=" N ALA O 271 " --> pdb=" O ALA O 267 " (cutoff:3.500A) Processing helix chain 'O' and resid 294 through 301 Processing helix chain 'O' and resid 333 through 348 Processing helix chain 'O' and resid 354 through 372 removed outlier: 3.655A pdb=" N VAL O 372 " --> pdb=" O TYR O 368 " (cutoff:3.500A) Processing helix chain 'O' and resid 375 through 388 Processing helix chain 'O' and resid 395 through 403 Processing helix chain 'O' and resid 407 through 419 Processing helix chain 'O' and resid 436 through 438 No H-bonds generated for 'chain 'O' and resid 436 through 438' Processing helix chain 'P' and resid 4 through 7 No H-bonds generated for 'chain 'P' and resid 4 through 7' Processing helix chain 'P' and resid 11 through 18 Processing helix chain 'P' and resid 29 through 31 No H-bonds generated for 'chain 'P' and resid 29 through 31' Processing helix chain 'P' and resid 33 through 54 removed outlier: 3.528A pdb=" N GLY P 38 " --> pdb=" O GLY P 34 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N MET P 53 " --> pdb=" O LEU P 49 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N HIS P 54 " --> pdb=" O PHE P 50 " (cutoff:3.500A) Processing helix chain 'P' and resid 62 through 71 removed outlier: 3.663A pdb=" N VAL P 66 " --> pdb=" O ALA P 62 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR P 67 " --> pdb=" O PHE P 63 " (cutoff:3.500A) Processing helix chain 'P' and resid 76 through 103 removed outlier: 3.634A pdb=" N SER P 88 " --> pdb=" O ALA P 84 " (cutoff:3.500A) Processing helix chain 'P' and resid 106 through 108 No H-bonds generated for 'chain 'P' and resid 106 through 108' Processing helix chain 'P' and resid 110 through 132 removed outlier: 3.750A pdb=" N VAL P 132 " --> pdb=" O PHE P 128 " (cutoff:3.500A) Processing helix chain 'P' and resid 137 through 152 removed outlier: 4.396A pdb=" N LEU P 150 " --> pdb=" O ILE P 146 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N SER P 151 " --> pdb=" O THR P 147 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ALA P 152 " --> pdb=" O ASN P 148 " (cutoff:3.500A) Processing helix chain 'P' and resid 157 through 165 Processing helix chain 'P' and resid 172 through 201 Proline residue: P 186 - end of helix Processing helix chain 'P' and resid 223 through 245 removed outlier: 3.561A pdb=" N LEU P 242 " --> pdb=" O ALA P 238 " (cutoff:3.500A) Processing helix chain 'P' and resid 253 through 256 Processing helix chain 'P' and resid 272 through 282 removed outlier: 5.571A pdb=" N PHE P 276 " --> pdb=" O TYR P 273 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG P 282 " --> pdb=" O ALA P 279 " (cutoff:3.500A) Processing helix chain 'P' and resid 287 through 307 removed outlier: 3.852A pdb=" N ILE P 298 " --> pdb=" O LEU P 294 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N LEU P 301 " --> pdb=" O SER P 297 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ALA P 302 " --> pdb=" O ILE P 298 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU P 303 " --> pdb=" O LEU P 299 " (cutoff:3.500A) Proline residue: P 305 - end of helix Processing helix chain 'P' and resid 315 through 317 No H-bonds generated for 'chain 'P' and resid 315 through 317' Processing helix chain 'P' and resid 319 through 340 Processing helix chain 'P' and resid 347 through 363 removed outlier: 3.605A pdb=" N PHE P 359 " --> pdb=" O SER P 355 " (cutoff:3.500A) Processing helix chain 'P' and resid 365 through 376 Processing helix chain 'Q' and resid 23 through 35 Processing helix chain 'Q' and resid 48 through 51 Processing helix chain 'Q' and resid 58 through 67 Processing helix chain 'Q' and resid 98 through 103 Processing helix chain 'Q' and resid 123 through 131 Processing helix chain 'Q' and resid 179 through 194 Processing helix chain 'Q' and resid 198 through 231 Proline residue: Q 217 - end of helix removed outlier: 4.469A pdb=" N VAL Q 229 " --> pdb=" O HIS Q 225 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N LEU Q 230 " --> pdb=" O LYS Q 226 " (cutoff:3.500A) Processing helix chain 'R' and resid 16 through 18 No H-bonds generated for 'chain 'R' and resid 16 through 18' Processing helix chain 'R' and resid 29 through 62 removed outlier: 3.950A pdb=" N MET R 62 " --> pdb=" O PHE R 58 " (cutoff:3.500A) Processing helix chain 'R' and resid 78 through 80 No H-bonds generated for 'chain 'R' and resid 78 through 80' Processing helix chain 'R' and resid 103 through 110 Processing helix chain 'R' and resid 114 through 116 No H-bonds generated for 'chain 'R' and resid 114 through 116' Processing helix chain 'R' and resid 123 through 125 No H-bonds generated for 'chain 'R' and resid 123 through 125' Processing helix chain 'S' and resid 8 through 24 removed outlier: 3.692A pdb=" N TRP S 12 " --> pdb=" O ALA S 8 " (cutoff:3.500A) Processing helix chain 'S' and resid 26 through 29 Processing helix chain 'S' and resid 34 through 36 No H-bonds generated for 'chain 'S' and resid 34 through 36' Processing helix chain 'S' and resid 41 through 48 Processing helix chain 'S' and resid 52 through 71 Processing helix chain 'S' and resid 77 through 79 No H-bonds generated for 'chain 'S' and resid 77 through 79' Processing helix chain 'S' and resid 83 through 85 No H-bonds generated for 'chain 'S' and resid 83 through 85' Processing helix chain 'S' and resid 91 through 107 Processing helix chain 'T' and resid 20 through 22 No H-bonds generated for 'chain 'T' and resid 20 through 22' Processing helix chain 'T' and resid 29 through 70 removed outlier: 3.633A pdb=" N ILE T 34 " --> pdb=" O PHE T 30 " (cutoff:3.500A) Proline residue: T 35 - end of helix removed outlier: 4.755A pdb=" N LEU T 46 " --> pdb=" O ARG T 42 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N ARG T 47 " --> pdb=" O ALA T 43 " (cutoff:3.500A) Proline residue: T 50 - end of helix Processing helix chain 'U' and resid 16 through 25 removed outlier: 3.792A pdb=" N GLN U 23 " --> pdb=" O THR U 19 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N CYS U 24 " --> pdb=" O VAL U 20 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU U 25 " --> pdb=" O ARG U 21 " (cutoff:3.500A) Processing helix chain 'U' and resid 28 through 46 removed outlier: 4.027A pdb=" N LYS U 32 " --> pdb=" O GLU U 28 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ALA U 33 " --> pdb=" O LYS U 29 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER U 46 " --> pdb=" O GLU U 42 " (cutoff:3.500A) Processing helix chain 'U' and resid 55 through 75 removed outlier: 3.569A pdb=" N PHE U 61 " --> pdb=" O GLU U 57 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA U 64 " --> pdb=" O ASP U 60 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N HIS U 67 " --> pdb=" O HIS U 63 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N HIS U 71 " --> pdb=" O HIS U 67 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LYS U 72 " --> pdb=" O CYS U 68 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N PHE U 74 " --> pdb=" O ALA U 70 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N ASN U 75 " --> pdb=" O HIS U 71 " (cutoff:3.500A) Processing helix chain 'W' and resid 5 through 13 Processing helix chain 'W' and resid 17 through 46 Processing helix chain 'W' and resid 52 through 54 No H-bonds generated for 'chain 'W' and resid 52 through 54' Processing helix chain 'X' and resid 3 through 5 No H-bonds generated for 'chain 'X' and resid 3 through 5' Processing helix chain 'X' and resid 8 through 36 Proline residue: X 19 - end of helix Processing helix chain 'X' and resid 39 through 42 No H-bonds generated for 'chain 'X' and resid 39 through 42' Processing helix chain 'X' and resid 48 through 51 Processing sheet with id= A, first strand: chain 'A' and resid 15 through 18 removed outlier: 3.849A pdb=" N ARG A 24 " --> pdb=" O MET A 195 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 239 through 244 removed outlier: 3.754A pdb=" N THR A 317 " --> pdb=" O TYR A 314 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 25 through 28 removed outlier: 3.587A pdb=" N VAL B 34 " --> pdb=" O MET B 204 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 243 through 247 removed outlier: 6.784A pdb=" N MET B 424 " --> pdb=" O ILE B 244 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N GLU B 246 " --> pdb=" O MET B 424 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ALA B 426 " --> pdb=" O GLU B 246 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 69 through 72 Processing sheet with id= F, first strand: chain 'E' and resid 74 through 77 Processing sheet with id= G, first strand: chain 'E' and resid 86 through 88 Processing sheet with id= H, first strand: chain 'E' and resid 156 through 158 Processing sheet with id= I, first strand: chain 'N' and resid 15 through 18 removed outlier: 3.783A pdb=" N ARG N 24 " --> pdb=" O MET N 195 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'N' and resid 239 through 244 removed outlier: 3.610A pdb=" N SER N 306 " --> pdb=" O VAL N 325 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'O' and resid 25 through 28 removed outlier: 3.767A pdb=" N VAL O 34 " --> pdb=" O MET O 204 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'O' and resid 242 through 247 Processing sheet with id= M, first strand: chain 'P' and resid 22 through 24 Processing sheet with id= N, first strand: chain 'Q' and resid 69 through 72 Processing sheet with id= O, first strand: chain 'R' and resid 74 through 77 Processing sheet with id= P, first strand: chain 'R' and resid 86 through 91 Processing sheet with id= Q, first strand: chain 'R' and resid 156 through 158 1548 hydrogen bonds defined for protein. 4266 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: 19.49 Time building geometry restraints manager: 40.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.11: 32118 1.11 - 1.38: 13249 1.38 - 1.65: 20107 1.65 - 1.93: 244 1.93 - 2.20: 32 Bond restraints: 65750 Sorted by residual: bond pdb=" C TYR C 256 " pdb=" N THR C 257 " ideal model delta sigma weight residual 1.331 1.384 -0.053 2.07e-02 2.33e+03 6.56e+00 bond pdb=" C2 JHB C1003 " pdb="CL JHB C1003 " ideal model delta sigma weight residual 1.729 1.779 -0.050 2.00e-02 2.50e+03 6.14e+00 bond pdb=" C2 JHB P1003 " pdb="CL JHB P1003 " ideal model delta sigma weight residual 1.729 1.778 -0.049 2.00e-02 2.50e+03 6.08e+00 bond pdb=" C7 JHB P1003 " pdb=" C8 JHB P1003 " ideal model delta sigma weight residual 1.367 1.406 -0.039 2.00e-02 2.50e+03 3.75e+00 bond pdb=" CB ILE C 146 " pdb=" CG2 ILE C 146 " ideal model delta sigma weight residual 1.521 1.585 -0.064 3.30e-02 9.18e+02 3.71e+00 ... (remaining 65745 not shown) Histogram of bond angle deviations from ideal: 75.32 - 96.16: 28 96.16 - 117.01: 84817 117.01 - 137.85: 33837 137.85 - 158.70: 0 158.70 - 179.55: 12 Bond angle restraints: 118694 Sorted by residual: angle pdb=" N ALA O 171 " pdb=" CA ALA O 171 " pdb=" C ALA O 171 " ideal model delta sigma weight residual 110.80 120.05 -9.25 2.13e+00 2.20e-01 1.89e+01 angle pdb=" N PRO X 46 " pdb=" CA PRO X 46 " pdb=" C PRO X 46 " ideal model delta sigma weight residual 112.47 120.35 -7.88 2.06e+00 2.36e-01 1.46e+01 angle pdb=" N ALA G 49 " pdb=" CA ALA G 49 " pdb=" C ALA G 49 " ideal model delta sigma weight residual 109.81 117.58 -7.77 2.21e+00 2.05e-01 1.24e+01 angle pdb=" C ASN O 170 " pdb=" N ALA O 171 " pdb=" CA ALA O 171 " ideal model delta sigma weight residual 121.54 128.17 -6.63 1.91e+00 2.74e-01 1.20e+01 angle pdb=" CA CYS U 68 " pdb=" CB CYS U 68 " pdb=" SG CYS U 68 " ideal model delta sigma weight residual 114.40 106.60 7.80 2.30e+00 1.89e-01 1.15e+01 ... (remaining 118689 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 28141 17.83 - 35.67: 1685 35.67 - 53.50: 292 53.50 - 71.33: 61 71.33 - 89.16: 39 Dihedral angle restraints: 30218 sinusoidal: 15918 harmonic: 14300 Sorted by residual: dihedral pdb=" CB CYS H 24 " pdb=" SG CYS H 24 " pdb=" SG CYS H 68 " pdb=" CB CYS H 68 " ideal model delta sinusoidal sigma weight residual 93.00 150.23 -57.23 1 1.00e+01 1.00e-02 4.40e+01 dihedral pdb=" CA LEU R 69 " pdb=" C LEU R 69 " pdb=" N ALA R 70 " pdb=" CA ALA R 70 " ideal model delta harmonic sigma weight residual 180.00 157.41 22.59 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA GLN O 153 " pdb=" C GLN O 153 " pdb=" N ASN O 154 " pdb=" CA ASN O 154 " ideal model delta harmonic sigma weight residual 180.00 158.88 21.12 0 5.00e+00 4.00e-02 1.78e+01 ... (remaining 30215 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 3728 0.047 - 0.095: 1002 0.095 - 0.142: 239 0.142 - 0.190: 22 0.190 - 0.237: 1 Chirality restraints: 4992 Sorted by residual: chirality pdb=" CA PRO X 46 " pdb=" N PRO X 46 " pdb=" C PRO X 46 " pdb=" CB PRO X 46 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA PRO N 260 " pdb=" N PRO N 260 " pdb=" C PRO N 260 " pdb=" CB PRO N 260 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.43e-01 chirality pdb=" CA VAL V 72 " pdb=" N VAL V 72 " pdb=" C VAL V 72 " pdb=" CB VAL V 72 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.31e-01 ... (remaining 4989 not shown) Planarity restraints: 9726 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1C HEC Q1001 " -0.013 2.00e-02 2.50e+03 3.40e-02 2.60e+01 pdb=" C2C HEC Q1001 " 0.091 2.00e-02 2.50e+03 pdb=" C3C HEC Q1001 " 0.003 2.00e-02 2.50e+03 pdb=" C4C HEC Q1001 " -0.002 2.00e-02 2.50e+03 pdb=" CAC HEC Q1001 " -0.025 2.00e-02 2.50e+03 pdb=" CHC HEC Q1001 " -0.020 2.00e-02 2.50e+03 pdb=" CHD HEC Q1001 " -0.003 2.00e-02 2.50e+03 pdb=" CMC HEC Q1001 " -0.029 2.00e-02 2.50e+03 pdb=" NC HEC Q1001 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP P 272 " 0.019 2.00e-02 2.50e+03 3.76e-02 1.42e+01 pdb=" C TRP P 272 " -0.065 2.00e-02 2.50e+03 pdb=" O TRP P 272 " 0.024 2.00e-02 2.50e+03 pdb=" N TYR P 273 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE W 20 " -0.018 2.00e-02 2.50e+03 3.55e-02 1.26e+01 pdb=" C PHE W 20 " 0.061 2.00e-02 2.50e+03 pdb=" O PHE W 20 " -0.023 2.00e-02 2.50e+03 pdb=" N ALA W 21 " -0.021 2.00e-02 2.50e+03 ... (remaining 9723 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.28: 8756 2.28 - 2.86: 142677 2.86 - 3.44: 161649 3.44 - 4.02: 222531 4.02 - 4.60: 347120 Nonbonded interactions: 882733 Sorted by model distance: nonbonded pdb=" O ASN O 170 " pdb=" H ALA O 173 " model vdw 1.696 1.850 nonbonded pdb="HE21 GLN N 32 " pdb=" OE2 GLU O 373 " model vdw 1.704 1.850 nonbonded pdb=" OE1 GLU N 429 " pdb=" H GLY T 5 " model vdw 1.707 1.850 nonbonded pdb=" HE ARG Q 28 " pdb=" OD2 ASP Q 185 " model vdw 1.712 1.850 nonbonded pdb=" OD2 ASP A 246 " pdb=" H VAL G 10 " model vdw 1.715 1.850 ... (remaining 882728 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'N' } ncs_group { reference = chain 'B' selection = chain 'O' } ncs_group { reference = chain 'C' selection = chain 'P' } ncs_group { reference = chain 'D' selection = chain 'Q' } ncs_group { reference = chain 'E' selection = chain 'R' } ncs_group { reference = chain 'F' selection = chain 'S' } ncs_group { reference = chain 'G' selection = chain 'T' } ncs_group { reference = chain 'H' selection = chain 'U' } ncs_group { reference = chain 'I' selection = chain 'V' } ncs_group { reference = chain 'J' selection = chain 'W' } ncs_group { reference = chain 'K' selection = chain 'X' } 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: 6.110 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: 0.690 Extract box with map and model: 28.690 Check model and map are aligned: 0.710 Set scattering table: 0.450 Process input model: 163.020 Find NCS groups from input model: 2.260 Set up NCS constraints: 0.500 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:13.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 215.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 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 : 0.005 0.077 33586 Z= 0.349 Angle : 0.766 9.249 45694 Z= 0.412 Chirality : 0.045 0.237 4992 Planarity : 0.006 0.067 5834 Dihedral : 12.160 89.163 12172 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 1.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.65 % Favored : 97.31 % Rotamer: Outliers : 0.26 % Allowed : 3.86 % Favored : 95.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % 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: 0.43 (0.13), residues: 4082 helix: 0.83 (0.11), residues: 1996 sheet: -0.38 (0.24), residues: 414 loop : -0.05 (0.16), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP P 77 HIS 0.011 0.002 HIS P 97 PHE 0.021 0.002 PHE B 199 TYR 0.019 0.002 TYR N 223 ARG 0.007 0.001 ARG W 33 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8164 Ramachandran restraints generated. 4082 Oldfield, 0 Emsley, 4082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8164 Ramachandran restraints generated. 4082 Oldfield, 0 Emsley, 4082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 776 residues out of total 3468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 767 time to evaluate : 3.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 773 average time/residue: 2.5541 time to fit residues: 2345.4547 Evaluate side-chains 455 residues out of total 3468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 451 time to evaluate : 3.825 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 1 average time/residue: 0.5845 time to fit residues: 5.7195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 341 optimal weight: 5.9990 chunk 306 optimal weight: 2.9990 chunk 169 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 206 optimal weight: 4.9990 chunk 163 optimal weight: 9.9990 chunk 316 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 192 optimal weight: 4.9990 chunk 235 optimal weight: 2.9990 chunk 366 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN A 240 GLN ** A 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 GLN C 8 HIS G 3 GLN G 28 HIS N 136 GLN N 252 HIS N 430 GLN N 435 ASN O 349 GLN O 412 ASN ** P 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 159 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 33586 Z= 0.295 Angle : 0.591 15.918 45694 Z= 0.289 Chirality : 0.040 0.148 4992 Planarity : 0.005 0.069 5834 Dihedral : 6.833 89.936 4598 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.79 % Allowed : 12.72 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % 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: 1.22 (0.13), residues: 4082 helix: 1.78 (0.11), residues: 1986 sheet: -0.13 (0.24), residues: 414 loop : -0.02 (0.15), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP P 141 HIS 0.011 0.001 HIS P 201 PHE 0.014 0.002 PHE W 20 TYR 0.020 0.002 TYR N 4 ARG 0.008 0.000 ARG B 227 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8164 Ramachandran restraints generated. 4082 Oldfield, 0 Emsley, 4082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8164 Ramachandran restraints generated. 4082 Oldfield, 0 Emsley, 4082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 3468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 447 time to evaluate : 3.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 62 outliers final: 38 residues processed: 493 average time/residue: 2.1101 time to fit residues: 1284.9918 Evaluate side-chains 453 residues out of total 3468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 415 time to evaluate : 3.792 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 30 residues processed: 11 average time/residue: 0.7902 time to fit residues: 18.5834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 203 optimal weight: 0.9990 chunk 113 optimal weight: 3.9990 chunk 305 optimal weight: 2.9990 chunk 249 optimal weight: 3.9990 chunk 101 optimal weight: 0.0470 chunk 367 optimal weight: 0.7980 chunk 397 optimal weight: 4.9990 chunk 327 optimal weight: 3.9990 chunk 364 optimal weight: 5.9990 chunk 125 optimal weight: 4.9990 chunk 294 optimal weight: 2.9990 overall best weight: 1.5684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN A 240 GLN ** A 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 3 GLN N 136 GLN O 349 GLN ** P 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 36 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 33586 Z= 0.209 Angle : 0.539 17.599 45694 Z= 0.261 Chirality : 0.038 0.152 4992 Planarity : 0.004 0.076 5834 Dihedral : 6.570 89.709 4598 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.70 % Allowed : 12.98 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % 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: 1.51 (0.13), residues: 4082 helix: 2.05 (0.11), residues: 1984 sheet: 0.03 (0.24), residues: 414 loop : 0.06 (0.16), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 91 HIS 0.009 0.001 HIS P 201 PHE 0.011 0.001 PHE P 91 TYR 0.020 0.001 TYR N 4 ARG 0.010 0.000 ARG B 227 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8164 Ramachandran restraints generated. 4082 Oldfield, 0 Emsley, 4082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8164 Ramachandran restraints generated. 4082 Oldfield, 0 Emsley, 4082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 3468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 442 time to evaluate : 3.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 59 outliers final: 39 residues processed: 482 average time/residue: 2.1132 time to fit residues: 1259.2628 Evaluate side-chains 449 residues out of total 3468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 410 time to evaluate : 3.845 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 33 residues processed: 9 average time/residue: 0.9066 time to fit residues: 17.9090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 363 optimal weight: 0.9980 chunk 276 optimal weight: 3.9990 chunk 190 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 chunk 175 optimal weight: 4.9990 chunk 246 optimal weight: 5.9990 chunk 368 optimal weight: 1.9990 chunk 390 optimal weight: 3.9990 chunk 192 optimal weight: 4.9990 chunk 349 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN A 18 GLN A 240 GLN A 252 HIS C 148 ASN G 3 GLN N 136 GLN O 349 GLN ** P 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 255 ASN T 36 ASN X 16 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 33586 Z= 0.333 Angle : 0.580 14.103 45694 Z= 0.287 Chirality : 0.040 0.155 4992 Planarity : 0.005 0.076 5834 Dihedral : 6.694 89.611 4598 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.42 % Allowed : 13.24 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % 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: 1.28 (0.13), residues: 4082 helix: 1.89 (0.11), residues: 1984 sheet: 0.03 (0.24), residues: 414 loop : -0.12 (0.15), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 91 HIS 0.009 0.001 HIS P 201 PHE 0.013 0.002 PHE F 26 TYR 0.021 0.002 TYR N 4 ARG 0.012 0.000 ARG B 227 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8164 Ramachandran restraints generated. 4082 Oldfield, 0 Emsley, 4082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8164 Ramachandran restraints generated. 4082 Oldfield, 0 Emsley, 4082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 3468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 435 time to evaluate : 3.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 84 outliers final: 48 residues processed: 491 average time/residue: 2.0739 time to fit residues: 1277.8631 Evaluate side-chains 460 residues out of total 3468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 412 time to evaluate : 3.878 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 38 residues processed: 12 average time/residue: 1.0882 time to fit residues: 23.8501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 325 optimal weight: 3.9990 chunk 221 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 290 optimal weight: 0.7980 chunk 161 optimal weight: 5.9990 chunk 333 optimal weight: 0.6980 chunk 269 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 199 optimal weight: 6.9990 chunk 350 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN A 240 GLN G 3 GLN N 136 GLN N 173 ASN N 274 ASN O 349 GLN T 36 ASN X 16 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 33586 Z= 0.223 Angle : 0.530 13.083 45694 Z= 0.260 Chirality : 0.038 0.151 4992 Planarity : 0.004 0.086 5834 Dihedral : 6.590 89.360 4598 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.87 % Allowed : 14.36 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % 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: 1.48 (0.13), residues: 4082 helix: 2.03 (0.11), residues: 1986 sheet: 0.12 (0.24), residues: 414 loop : -0.01 (0.16), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP P 141 HIS 0.008 0.001 HIS P 201 PHE 0.017 0.001 PHE G 55 TYR 0.020 0.001 TYR N 4 ARG 0.018 0.000 ARG B 227 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8164 Ramachandran restraints generated. 4082 Oldfield, 0 Emsley, 4082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8164 Ramachandran restraints generated. 4082 Oldfield, 0 Emsley, 4082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 3468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 423 time to evaluate : 3.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 65 outliers final: 42 residues processed: 470 average time/residue: 2.0292 time to fit residues: 1188.8769 Evaluate side-chains 438 residues out of total 3468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 396 time to evaluate : 3.807 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 38 residues processed: 6 average time/residue: 0.7830 time to fit residues: 12.2330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 131 optimal weight: 4.9990 chunk 351 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 229 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 390 optimal weight: 3.9990 chunk 324 optimal weight: 2.9990 chunk 180 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 129 optimal weight: 3.9990 chunk 205 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN A 240 GLN B 225 ASN C 148 ASN G 3 GLN N 9 GLN N 136 GLN O 349 GLN ** T 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 33586 Z= 0.393 Angle : 0.613 18.451 45694 Z= 0.302 Chirality : 0.041 0.161 4992 Planarity : 0.005 0.087 5834 Dihedral : 6.771 89.581 4598 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.51 % Allowed : 14.30 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % 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: 1.12 (0.13), residues: 4082 helix: 1.79 (0.11), residues: 1986 sheet: 0.04 (0.24), residues: 414 loop : -0.28 (0.15), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 91 HIS 0.010 0.001 HIS P 97 PHE 0.014 0.002 PHE P 183 TYR 0.021 0.002 TYR P 81 ARG 0.012 0.001 ARG B 227 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8164 Ramachandran restraints generated. 4082 Oldfield, 0 Emsley, 4082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8164 Ramachandran restraints generated. 4082 Oldfield, 0 Emsley, 4082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 3468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 412 time to evaluate : 4.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 87 outliers final: 54 residues processed: 474 average time/residue: 2.0862 time to fit residues: 1238.5965 Evaluate side-chains 451 residues out of total 3468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 397 time to evaluate : 3.831 Switching outliers to nearest non-outliers outliers start: 54 outliers final: 44 residues processed: 11 average time/residue: 0.6182 time to fit residues: 17.1369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 376 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 222 optimal weight: 3.9990 chunk 285 optimal weight: 2.9990 chunk 221 optimal weight: 3.9990 chunk 329 optimal weight: 0.8980 chunk 218 optimal weight: 3.9990 chunk 389 optimal weight: 6.9990 chunk 243 optimal weight: 2.9990 chunk 237 optimal weight: 2.9990 chunk 179 optimal weight: 4.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN A 240 GLN G 3 GLN N 136 GLN O 349 GLN ** T 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 16 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 33586 Z= 0.311 Angle : 0.578 19.286 45694 Z= 0.285 Chirality : 0.040 0.172 4992 Planarity : 0.005 0.096 5834 Dihedral : 6.732 89.714 4598 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.93 % Allowed : 15.31 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % 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: 1.18 (0.13), residues: 4082 helix: 1.83 (0.11), residues: 1988 sheet: 0.07 (0.24), residues: 414 loop : -0.24 (0.15), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 91 HIS 0.008 0.001 HIS P 201 PHE 0.011 0.002 PHE N 307 TYR 0.019 0.002 TYR P 81 ARG 0.014 0.000 ARG B 227 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8164 Ramachandran restraints generated. 4082 Oldfield, 0 Emsley, 4082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8164 Ramachandran restraints generated. 4082 Oldfield, 0 Emsley, 4082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 3468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 406 time to evaluate : 3.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 67 outliers final: 50 residues processed: 458 average time/residue: 2.0509 time to fit residues: 1179.7915 Evaluate side-chains 448 residues out of total 3468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 398 time to evaluate : 3.822 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 45 residues processed: 6 average time/residue: 1.0269 time to fit residues: 13.8503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 240 optimal weight: 0.9990 chunk 155 optimal weight: 0.8980 chunk 232 optimal weight: 5.9990 chunk 117 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 247 optimal weight: 0.2980 chunk 265 optimal weight: 1.9990 chunk 192 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 306 optimal weight: 1.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 GLN G 3 GLN G 6 HIS N 136 GLN N 173 ASN N 189 HIS ** T 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 16 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 33586 Z= 0.190 Angle : 0.521 13.847 45694 Z= 0.257 Chirality : 0.038 0.156 4992 Planarity : 0.004 0.110 5834 Dihedral : 6.557 89.030 4598 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.64 % Allowed : 15.80 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % 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: 1.51 (0.13), residues: 4082 helix: 2.07 (0.12), residues: 2006 sheet: 0.23 (0.24), residues: 414 loop : -0.06 (0.16), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 91 HIS 0.007 0.001 HIS P 201 PHE 0.011 0.001 PHE U 61 TYR 0.019 0.001 TYR N 4 ARG 0.017 0.000 ARG B 227 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8164 Ramachandran restraints generated. 4082 Oldfield, 0 Emsley, 4082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8164 Ramachandran restraints generated. 4082 Oldfield, 0 Emsley, 4082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 3468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 417 time to evaluate : 3.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 57 outliers final: 48 residues processed: 465 average time/residue: 2.0011 time to fit residues: 1161.4894 Evaluate side-chains 448 residues out of total 3468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 400 time to evaluate : 3.819 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 44 residues processed: 4 average time/residue: 0.8391 time to fit residues: 9.9656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 354 optimal weight: 2.9990 chunk 373 optimal weight: 2.9990 chunk 340 optimal weight: 2.9990 chunk 362 optimal weight: 2.9990 chunk 372 optimal weight: 0.9980 chunk 218 optimal weight: 3.9990 chunk 158 optimal weight: 9.9990 chunk 284 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 327 optimal weight: 3.9990 chunk 343 optimal weight: 0.7980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 GLN G 3 GLN G 6 HIS N 9 GLN N 136 GLN N 173 ASN ** T 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 33586 Z= 0.275 Angle : 0.554 16.956 45694 Z= 0.273 Chirality : 0.039 0.159 4992 Planarity : 0.004 0.054 5834 Dihedral : 6.580 89.769 4598 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.70 % Allowed : 16.09 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % 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: 1.44 (0.13), residues: 4082 helix: 2.02 (0.11), residues: 2006 sheet: 0.20 (0.24), residues: 414 loop : -0.12 (0.16), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 91 HIS 0.007 0.001 HIS P 196 PHE 0.012 0.001 PHE N 307 TYR 0.017 0.001 TYR N 4 ARG 0.008 0.000 ARG U 36 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8164 Ramachandran restraints generated. 4082 Oldfield, 0 Emsley, 4082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8164 Ramachandran restraints generated. 4082 Oldfield, 0 Emsley, 4082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 3468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 396 time to evaluate : 3.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 59 outliers final: 48 residues processed: 447 average time/residue: 2.0518 time to fit residues: 1149.8540 Evaluate side-chains 440 residues out of total 3468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 392 time to evaluate : 3.818 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 44 residues processed: 5 average time/residue: 1.0979 time to fit residues: 12.8683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 361 optimal weight: 7.9990 chunk 238 optimal weight: 2.9990 chunk 383 optimal weight: 1.9990 chunk 234 optimal weight: 4.9990 chunk 182 optimal weight: 3.9990 chunk 266 optimal weight: 3.9990 chunk 402 optimal weight: 0.3980 chunk 370 optimal weight: 3.9990 chunk 320 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 247 optimal weight: 0.5980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 GLN G 3 GLN G 6 HIS N 136 GLN ** T 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 33586 Z= 0.234 Angle : 0.545 16.815 45694 Z= 0.266 Chirality : 0.038 0.159 4992 Planarity : 0.005 0.152 5834 Dihedral : 6.512 89.384 4598 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.44 % Allowed : 16.32 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % 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: 1.51 (0.13), residues: 4082 helix: 2.08 (0.11), residues: 2006 sheet: 0.24 (0.24), residues: 414 loop : -0.08 (0.16), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP R 91 HIS 0.007 0.001 HIS P 201 PHE 0.017 0.001 PHE G 55 TYR 0.016 0.001 TYR P 81 ARG 0.019 0.000 ARG B 227 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8164 Ramachandran restraints generated. 4082 Oldfield, 0 Emsley, 4082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8164 Ramachandran restraints generated. 4082 Oldfield, 0 Emsley, 4082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 3468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 404 time to evaluate : 3.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 45 residues processed: 449 average time/residue: 2.0343 time to fit residues: 1143.1797 Evaluate side-chains 445 residues out of total 3468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 400 time to evaluate : 3.805 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 44 residues processed: 2 average time/residue: 1.2095 time to fit residues: 8.1733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 196 optimal weight: 0.8980 chunk 254 optimal weight: 5.9990 chunk 341 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 295 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 321 optimal weight: 3.9990 chunk 134 optimal weight: 0.8980 chunk 329 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 GLN G 3 GLN G 6 HIS N 136 GLN ** T 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.148140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.129568 restraints weight = 140776.877| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 2.00 r_work: 0.3543 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3437 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 33586 Z= 0.215 Angle : 0.532 15.830 45694 Z= 0.261 Chirality : 0.038 0.162 4992 Planarity : 0.004 0.053 5834 Dihedral : 6.431 89.009 4598 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.50 % Allowed : 16.32 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % 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: 1.60 (0.13), residues: 4082 helix: 2.15 (0.12), residues: 2006 sheet: 0.27 (0.24), residues: 414 loop : -0.03 (0.16), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP R 91 HIS 0.007 0.001 HIS P 201 PHE 0.011 0.001 PHE N 307 TYR 0.015 0.001 TYR P 81 ARG 0.008 0.000 ARG G 71 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19670.91 seconds wall clock time: 338 minutes 46.92 seconds (20326.92 seconds total)