Starting phenix.real_space_refine on Wed Nov 15 16:21:42 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tz6_26203/11_2023/7tz6_26203_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tz6_26203/11_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_26203/11_2023/7tz6_26203.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tz6_26203/11_2023/7tz6_26203.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tz6_26203/11_2023/7tz6_26203_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tz6_26203/11_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-1.21rc1-5144/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: 20.49, 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: 37.12 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: 7.16 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: 20.27 Time building geometry restraints manager: 39.27 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: 24601 17.83 - 35.67: 1503 35.67 - 53.50: 178 53.50 - 71.33: 56 71.33 - 89.16: 38 Dihedral angle restraints: 26376 sinusoidal: 12076 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 26373 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: 5.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.710 Extract box with map and model: 28.860 Check model and map are aligned: 0.760 Set scattering table: 0.440 Process input model: 163.180 Find NCS groups from input model: 2.080 Set up NCS constraints: 0.460 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:10.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 213.410 ------------------------------------------------------------------------------- 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 : 12.100 89.163 12134 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 *********************** 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 : 3.835 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: 2.5576 time to fit residues: 2351.6752 Evaluate side-chains 455 residues out of total 3468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 451 time to evaluate : 3.794 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 1 average time/residue: 0.5789 time to fit residues: 5.7244 ------------------------------------------------------------------------------- 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: 4.9990 chunk 306 optimal weight: 2.9990 chunk 169 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 206 optimal weight: 4.9990 chunk 163 optimal weight: 10.0000 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: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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: 0.8332 moved from start: 0.1905 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= 0.293 Angle : 0.598 17.124 45694 Z= 0.290 Chirality : 0.040 0.150 4992 Planarity : 0.005 0.068 5834 Dihedral : 6.559 89.865 4560 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.73 % Allowed : 12.77 % 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: 1.77 (0.11), residues: 1986 sheet: -0.13 (0.24), residues: 414 loop : -0.03 (0.15), residues: 1682 *********************** 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 508 residues out of total 3468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 448 time to evaluate : 3.860 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: 60 outliers final: 37 residues processed: 491 average time/residue: 2.0956 time to fit residues: 1273.6782 Evaluate side-chains 452 residues out of total 3468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 415 time to evaluate : 3.944 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 30 residues processed: 10 average time/residue: 0.8197 time to fit residues: 17.7238 ------------------------------------------------------------------------------- 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: 0.3980 chunk 113 optimal weight: 3.9990 chunk 305 optimal weight: 2.9990 chunk 249 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 367 optimal weight: 0.8980 chunk 397 optimal weight: 4.9990 chunk 327 optimal weight: 3.9990 chunk 364 optimal weight: 4.9990 chunk 125 optimal weight: 4.9990 chunk 294 optimal weight: 2.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** G 3 GLN N 136 GLN O 349 GLN ** P 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 255 ASN T 36 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 33586 Z= 0.275 Angle : 0.567 19.071 45694 Z= 0.275 Chirality : 0.039 0.150 4992 Planarity : 0.004 0.073 5834 Dihedral : 6.351 89.505 4560 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.13 % Allowed : 12.63 % Favored : 85.24 % 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: 1.37 (0.13), residues: 4082 helix: 1.93 (0.11), residues: 1988 sheet: 0.02 (0.24), residues: 414 loop : -0.02 (0.15), residues: 1680 *********************** 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 513 residues out of total 3468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 439 time to evaluate : 3.898 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: 74 outliers final: 44 residues processed: 487 average time/residue: 2.1401 time to fit residues: 1301.1369 Evaluate side-chains 452 residues out of total 3468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 408 time to evaluate : 3.972 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 36 residues processed: 10 average time/residue: 0.8586 time to fit residues: 18.6289 ------------------------------------------------------------------------------- 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: 6.9990 chunk 276 optimal weight: 3.9990 chunk 190 optimal weight: 0.0030 chunk 40 optimal weight: 2.9990 chunk 175 optimal weight: 3.9990 chunk 246 optimal weight: 0.0670 chunk 368 optimal weight: 0.9990 chunk 390 optimal weight: 4.9990 chunk 192 optimal weight: 4.9990 chunk 349 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 overall best weight: 1.4134 ------------------------------------------------------------------------------- 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 C 148 ASN G 3 GLN N 136 GLN N 274 ASN O 349 GLN ** P 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 36 ASN X 16 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 33586 Z= 0.200 Angle : 0.523 13.115 45694 Z= 0.256 Chirality : 0.038 0.150 4992 Planarity : 0.004 0.075 5834 Dihedral : 6.241 89.704 4560 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.85 % Allowed : 13.75 % Favored : 84.40 % 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: 1.57 (0.13), residues: 4082 helix: 2.11 (0.11), residues: 1982 sheet: 0.11 (0.24), residues: 414 loop : 0.06 (0.16), residues: 1686 *********************** 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 503 residues out of total 3468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 439 time to evaluate : 3.929 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: 64 outliers final: 43 residues processed: 482 average time/residue: 2.0642 time to fit residues: 1236.5815 Evaluate side-chains 453 residues out of total 3468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 410 time to evaluate : 3.872 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 37 residues processed: 7 average time/residue: 0.9466 time to fit residues: 14.7881 ------------------------------------------------------------------------------- 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: 2.9990 chunk 221 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 290 optimal weight: 3.9990 chunk 161 optimal weight: 5.9990 chunk 333 optimal weight: 0.9990 chunk 269 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 199 optimal weight: 6.9990 chunk 350 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 G 3 GLN N 136 GLN N 173 ASN N 274 ASN O 349 GLN P 255 ASN T 36 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 33586 Z= 0.367 Angle : 0.611 18.569 45694 Z= 0.299 Chirality : 0.041 0.159 4992 Planarity : 0.005 0.091 5834 Dihedral : 6.449 89.859 4560 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.60 % Allowed : 13.47 % Favored : 83.94 % 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: 1.17 (0.13), residues: 4082 helix: 1.80 (0.11), residues: 1984 sheet: 0.05 (0.24), residues: 414 loop : -0.21 (0.15), residues: 1684 *********************** 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 511 residues out of total 3468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 421 time to evaluate : 3.927 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: 90 outliers final: 46 residues processed: 476 average time/residue: 2.0139 time to fit residues: 1203.7154 Evaluate side-chains 442 residues out of total 3468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 396 time to evaluate : 3.898 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 36 residues processed: 11 average time/residue: 0.6286 time to fit residues: 17.4774 ------------------------------------------------------------------------------- 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: 6.9990 chunk 77 optimal weight: 0.3980 chunk 229 optimal weight: 0.7980 chunk 96 optimal weight: 2.9990 chunk 390 optimal weight: 3.9990 chunk 324 optimal weight: 2.9990 chunk 180 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 chunk 205 optimal weight: 0.1980 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 148 ASN G 3 GLN G 6 HIS N 136 GLN O 349 GLN P 341 GLN ** T 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 16 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 33586 Z= 0.201 Angle : 0.532 14.844 45694 Z= 0.261 Chirality : 0.038 0.152 4992 Planarity : 0.004 0.088 5834 Dihedral : 6.243 89.688 4560 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.73 % Allowed : 15.05 % Favored : 83.22 % 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: 2.01 (0.11), residues: 2000 sheet: 0.16 (0.24), residues: 414 loop : -0.06 (0.16), residues: 1668 *********************** 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 475 residues out of total 3468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 415 time to evaluate : 3.918 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: 60 outliers final: 42 residues processed: 463 average time/residue: 2.0654 time to fit residues: 1197.3129 Evaluate side-chains 438 residues out of total 3468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 396 time to evaluate : 3.854 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 39 residues processed: 4 average time/residue: 1.1897 time to fit residues: 11.5166 ------------------------------------------------------------------------------- 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: 0.0980 chunk 44 optimal weight: 4.9990 chunk 222 optimal weight: 4.9990 chunk 285 optimal weight: 2.9990 chunk 221 optimal weight: 0.9990 chunk 329 optimal weight: 4.9990 chunk 218 optimal weight: 3.9990 chunk 389 optimal weight: 4.9990 chunk 243 optimal weight: 3.9990 chunk 237 optimal weight: 2.9990 chunk 179 optimal weight: 5.9990 overall best weight: 2.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 GLN C 148 ASN G 3 GLN G 6 HIS N 136 GLN N 173 ASN O 349 GLN P 255 ASN ** 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: 0.8371 moved from start: 0.2780 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= 0.276 Angle : 0.557 17.061 45694 Z= 0.273 Chirality : 0.039 0.148 4992 Planarity : 0.004 0.099 5834 Dihedral : 6.251 88.839 4560 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.99 % Allowed : 15.05 % Favored : 82.96 % 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: 1.42 (0.13), residues: 4082 helix: 2.00 (0.11), residues: 2002 sheet: 0.18 (0.24), residues: 414 loop : -0.11 (0.16), residues: 1666 *********************** 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 479 residues out of total 3468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 410 time to evaluate : 3.809 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: 69 outliers final: 52 residues processed: 460 average time/residue: 1.9877 time to fit residues: 1144.8832 Evaluate side-chains 445 residues out of total 3468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 393 time to evaluate : 3.950 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 43 residues processed: 10 average time/residue: 1.3790 time to fit residues: 23.6862 ------------------------------------------------------------------------------- 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: 3.9990 chunk 155 optimal weight: 6.9990 chunk 232 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 247 optimal weight: 3.9990 chunk 265 optimal weight: 2.9990 chunk 192 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 306 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 O 349 GLN ** 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: 0.8390 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 33586 Z= 0.350 Angle : 0.590 19.925 45694 Z= 0.291 Chirality : 0.040 0.162 4992 Planarity : 0.005 0.105 5834 Dihedral : 6.370 89.227 4560 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.10 % Allowed : 15.22 % Favored : 82.67 % 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: 1.24 (0.13), residues: 4082 helix: 1.87 (0.11), residues: 1998 sheet: 0.16 (0.24), residues: 414 loop : -0.24 (0.16), residues: 1670 *********************** 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 476 residues out of total 3468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 403 time to evaluate : 3.904 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: 73 outliers final: 50 residues processed: 458 average time/residue: 2.0439 time to fit residues: 1172.7960 Evaluate side-chains 441 residues out of total 3468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 391 time to evaluate : 3.827 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 43 residues processed: 8 average time/residue: 0.9234 time to fit residues: 16.0919 ------------------------------------------------------------------------------- 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: 3.9990 chunk 373 optimal weight: 1.9990 chunk 340 optimal weight: 1.9990 chunk 362 optimal weight: 3.9990 chunk 372 optimal weight: 0.5980 chunk 218 optimal weight: 4.9990 chunk 158 optimal weight: 7.9990 chunk 284 optimal weight: 4.9990 chunk 111 optimal weight: 0.8980 chunk 327 optimal weight: 3.9990 chunk 343 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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: 0.8359 moved from start: 0.2911 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= 0.191 Angle : 0.533 14.748 45694 Z= 0.262 Chirality : 0.038 0.159 4992 Planarity : 0.004 0.054 5834 Dihedral : 6.163 88.604 4560 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.44 % Allowed : 15.89 % Favored : 82.67 % 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: 1.53 (0.13), residues: 4082 helix: 2.09 (0.12), residues: 2002 sheet: 0.26 (0.24), residues: 414 loop : -0.05 (0.16), residues: 1666 *********************** 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 458 residues out of total 3468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 408 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 outliers start: 50 outliers final: 44 residues processed: 452 average time/residue: 2.0316 time to fit residues: 1161.5210 Evaluate side-chains 447 residues out of total 3468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 403 time to evaluate : 3.832 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 41 residues processed: 3 average time/residue: 0.9912 time to fit residues: 9.1879 ------------------------------------------------------------------------------- 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: 3.9990 chunk 238 optimal weight: 2.9990 chunk 383 optimal weight: 1.9990 chunk 234 optimal weight: 4.9990 chunk 182 optimal weight: 4.9990 chunk 266 optimal weight: 3.9990 chunk 402 optimal weight: 4.9990 chunk 370 optimal weight: 3.9990 chunk 320 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 247 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 P 255 ASN ** T 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 33586 Z= 0.295 Angle : 0.569 19.150 45694 Z= 0.278 Chirality : 0.039 0.160 4992 Planarity : 0.004 0.152 5834 Dihedral : 6.226 89.646 4560 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.47 % Allowed : 16.06 % Favored : 82.47 % 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: 1.41 (0.13), residues: 4082 helix: 2.00 (0.11), residues: 2004 sheet: 0.21 (0.24), residues: 414 loop : -0.14 (0.16), residues: 1664 ********************** 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 444 residues out of total 3468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 393 time to evaluate : 4.023 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: 51 outliers final: 42 residues processed: 437 average time/residue: 2.0645 time to fit residues: 1149.9356 Evaluate side-chains 429 residues out of total 3468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 387 time to evaluate : 3.850 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 40 residues processed: 3 average time/residue: 1.0433 time to fit residues: 9.5619 ------------------------------------------------------------------------------- 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: 0.4980 chunk 254 optimal weight: 5.9990 chunk 341 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 295 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 321 optimal weight: 3.9990 chunk 134 optimal weight: 0.8980 chunk 329 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- 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 ** T 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.147564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.128911 restraints weight = 141192.428| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 2.01 r_work: 0.3532 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3422 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 33586 Z= 0.240 Angle : 0.551 17.299 45694 Z= 0.270 Chirality : 0.039 0.157 4992 Planarity : 0.004 0.054 5834 Dihedral : 6.150 89.683 4560 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.44 % Allowed : 16.12 % Favored : 82.44 % 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: 2.06 (0.11), residues: 2004 sheet: 0.22 (0.24), residues: 414 loop : -0.09 (0.16), residues: 1664 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19656.49 seconds wall clock time: 338 minutes 14.08 seconds (20294.08 seconds total)