Starting phenix.real_space_refine on Sat Dec 16 10:46:54 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mgz_23831/12_2023/7mgz_23831_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mgz_23831/12_2023/7mgz_23831.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mgz_23831/12_2023/7mgz_23831_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mgz_23831/12_2023/7mgz_23831_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mgz_23831/12_2023/7mgz_23831_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mgz_23831/12_2023/7mgz_23831.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mgz_23831/12_2023/7mgz_23831.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mgz_23831/12_2023/7mgz_23831_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mgz_23831/12_2023/7mgz_23831_trim_updated.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.263 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: 7 Type Number sf(0) Gaussians P 24 5.49 5 Mg 8 5.21 5 S 92 5.16 5 C 11104 2.51 5 N 2992 2.21 5 O 3316 1.98 5 H 17316 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 46": "OD1" <-> "OD2" Residue "F GLU 54": "OE1" <-> "OE2" Residue "F ASP 62": "OD1" <-> "OD2" Residue "F ASP 79": "OD1" <-> "OD2" Residue "F TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 135": "OE1" <-> "OE2" Residue "F GLU 139": "OE1" <-> "OE2" Residue "F GLU 173": "OE1" <-> "OE2" Residue "F GLU 203": "OE1" <-> "OE2" Residue "F GLU 287": "OE1" <-> "OE2" Residue "F TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 297": "OE1" <-> "OE2" Residue "F GLU 322": "OE1" <-> "OE2" Residue "F GLU 333": "OE1" <-> "OE2" Residue "F GLU 349": "OE1" <-> "OE2" Residue "F GLU 350": "OE1" <-> "OE2" Residue "F GLU 356": "OE1" <-> "OE2" Residue "F PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 482": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 505": "OE1" <-> "OE2" Residue "F PHE 520": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 525": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 540": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O ASP 46": "OD1" <-> "OD2" Residue "O GLU 54": "OE1" <-> "OE2" Residue "O ASP 62": "OD1" <-> "OD2" Residue "O ASP 79": "OD1" <-> "OD2" Residue "O TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O GLU 135": "OE1" <-> "OE2" Residue "O GLU 139": "OE1" <-> "OE2" Residue "O GLU 173": "OE1" <-> "OE2" Residue "O GLU 203": "OE1" <-> "OE2" Residue "O GLU 287": "OE1" <-> "OE2" Residue "O TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O GLU 297": "OE1" <-> "OE2" Residue "O GLU 322": "OE1" <-> "OE2" Residue "O GLU 333": "OE1" <-> "OE2" Residue "O GLU 349": "OE1" <-> "OE2" Residue "O GLU 350": "OE1" <-> "OE2" Residue "O GLU 356": "OE1" <-> "OE2" Residue "O PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O PHE 482": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O GLU 505": "OE1" <-> "OE2" Residue "O PHE 520": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O TYR 525": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O TYR 540": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P ASP 46": "OD1" <-> "OD2" Residue "P GLU 54": "OE1" <-> "OE2" Residue "P ASP 62": "OD1" <-> "OD2" Residue "P ASP 79": "OD1" <-> "OD2" Residue "P TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P GLU 135": "OE1" <-> "OE2" Residue "P GLU 139": "OE1" <-> "OE2" Residue "P GLU 173": "OE1" <-> "OE2" Residue "P GLU 203": "OE1" <-> "OE2" Residue "P GLU 287": "OE1" <-> "OE2" Residue "P TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P GLU 297": "OE1" <-> "OE2" Residue "P GLU 322": "OE1" <-> "OE2" Residue "P GLU 333": "OE1" <-> "OE2" Residue "P GLU 349": "OE1" <-> "OE2" Residue "P GLU 350": "OE1" <-> "OE2" Residue "P GLU 356": "OE1" <-> "OE2" Residue "P PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P PHE 482": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P GLU 505": "OE1" <-> "OE2" Residue "P PHE 520": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P TYR 525": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P TYR 540": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q ASP 46": "OD1" <-> "OD2" Residue "Q GLU 54": "OE1" <-> "OE2" Residue "Q ASP 62": "OD1" <-> "OD2" Residue "Q ASP 79": "OD1" <-> "OD2" Residue "Q TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q GLU 135": "OE1" <-> "OE2" Residue "Q GLU 139": "OE1" <-> "OE2" Residue "Q GLU 173": "OE1" <-> "OE2" Residue "Q GLU 203": "OE1" <-> "OE2" Residue "Q GLU 287": "OE1" <-> "OE2" Residue "Q TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q GLU 297": "OE1" <-> "OE2" Residue "Q GLU 322": "OE1" <-> "OE2" Residue "Q GLU 333": "OE1" <-> "OE2" Residue "Q GLU 349": "OE1" <-> "OE2" Residue "Q GLU 350": "OE1" <-> "OE2" Residue "Q GLU 356": "OE1" <-> "OE2" Residue "Q PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q PHE 482": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q GLU 505": "OE1" <-> "OE2" Residue "Q PHE 520": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q TYR 525": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q TYR 540": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 34852 Number of models: 1 Model: "" Number of chains: 8 Chain: "F" Number of atoms: 8631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 8631 Classifications: {'peptide': 542} Modifications used: {'ACID-GLU': 2, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 513} Chain breaks: 2 Chain: "O" Number of atoms: 8631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 8631 Classifications: {'peptide': 542} Modifications used: {'ACID-GLU': 2, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 513} Chain breaks: 2 Chain: "P" Number of atoms: 8631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 8631 Classifications: {'peptide': 542} Modifications used: {'ACID-GLU': 2, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 513} Chain breaks: 2 Chain: "Q" Number of atoms: 8631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 8631 Classifications: {'peptide': 542} Modifications used: {'ACID-GLU': 2, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 513} Chain breaks: 2 Chain: "F" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 82 Unusual residues: {' MG': 2, 'ANP': 1, 'UTP': 1} Inner-chain residues flagged as termini: ['pdbres="GLN F 602 "'] Classifications: {'peptide': 1, 'undetermined': 4} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {None: 4} Chain: "O" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 82 Unusual residues: {' MG': 2, 'ANP': 1, 'UTP': 1} Inner-chain residues flagged as termini: ['pdbres="GLN O 602 "'] Classifications: {'peptide': 1, 'undetermined': 4} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {None: 4} Chain: "P" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 82 Unusual residues: {' MG': 2, 'ANP': 1, 'UTP': 1} Inner-chain residues flagged as termini: ['pdbres="GLN P 603 "'] Classifications: {'peptide': 1, 'undetermined': 4} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {None: 4} Chain: "Q" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 82 Unusual residues: {' MG': 2, 'ANP': 1, 'UTP': 1} Inner-chain residues flagged as termini: ['pdbres="GLN Q 603 "'] Classifications: {'peptide': 1, 'undetermined': 4} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {None: 4} Time building chain proxies: 16.14, per 1000 atoms: 0.46 Number of scatterers: 34852 At special positions: 0 Unit cell: (127.05, 135.45, 87.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 92 16.00 P 24 15.00 Mg 8 11.99 O 3316 8.00 N 2992 7.00 C 11104 6.00 H 17316 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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=0, symmetry=0 Time building additional restraints: 30.73 Conformation dependent library (CDL) restraints added in 3.6 seconds 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4016 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 96 helices and 16 sheets defined 41.3% alpha, 14.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.51 Creating SS restraints... Processing helix chain 'F' and resid 16 through 29 Processing helix chain 'F' and resid 69 through 78 removed outlier: 3.845A pdb=" N TYR F 74 " --> pdb=" O LEU F 71 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG F 76 " --> pdb=" O ASN F 73 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU F 78 " --> pdb=" O GLU F 75 " (cutoff:3.500A) Processing helix chain 'F' and resid 84 through 86 No H-bonds generated for 'chain 'F' and resid 84 through 86' Processing helix chain 'F' and resid 90 through 102 Processing helix chain 'F' and resid 116 through 129 Processing helix chain 'F' and resid 154 through 169 removed outlier: 3.604A pdb=" N MET F 157 " --> pdb=" O ILE F 154 " (cutoff:3.500A) Proline residue: F 158 - end of helix removed outlier: 3.596A pdb=" N GLU F 161 " --> pdb=" O PRO F 158 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLN F 167 " --> pdb=" O ARG F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 174 No H-bonds generated for 'chain 'F' and resid 172 through 174' Processing helix chain 'F' and resid 195 through 206 Processing helix chain 'F' and resid 224 through 234 Processing helix chain 'F' and resid 238 through 240 No H-bonds generated for 'chain 'F' and resid 238 through 240' Processing helix chain 'F' and resid 250 through 260 Proline residue: F 254 - end of helix removed outlier: 3.617A pdb=" N LEU F 257 " --> pdb=" O PRO F 254 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN F 260 " --> pdb=" O LEU F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 262 through 269 removed outlier: 4.156A pdb=" N ARG F 268 " --> pdb=" O ASP F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 294 removed outlier: 3.560A pdb=" N MET F 288 " --> pdb=" O TRP F 285 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA F 289 " --> pdb=" O LYS F 286 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP F 293 " --> pdb=" O ASP F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 311 through 327 removed outlier: 6.557A pdb=" N SER F 316 " --> pdb=" O SER F 313 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS F 319 " --> pdb=" O SER F 316 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N HIS F 323 " --> pdb=" O ALA F 320 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA F 325 " --> pdb=" O GLU F 322 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU F 326 " --> pdb=" O HIS F 323 " (cutoff:3.500A) Processing helix chain 'F' and resid 339 through 342 Processing helix chain 'F' and resid 346 through 348 No H-bonds generated for 'chain 'F' and resid 346 through 348' Processing helix chain 'F' and resid 351 through 363 Processing helix chain 'F' and resid 378 through 390 Processing helix chain 'F' and resid 399 through 412 removed outlier: 3.875A pdb=" N LEU F 404 " --> pdb=" O GLY F 401 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL F 407 " --> pdb=" O LEU F 404 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE F 409 " --> pdb=" O VAL F 406 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASN F 412 " --> pdb=" O PHE F 409 " (cutoff:3.500A) Processing helix chain 'F' and resid 463 through 467 Processing helix chain 'F' and resid 489 through 493 Processing helix chain 'F' and resid 527 through 530 Processing helix chain 'F' and resid 538 through 547 Processing helix chain 'F' and resid 551 through 554 No H-bonds generated for 'chain 'F' and resid 551 through 554' Processing helix chain 'O' and resid 16 through 29 Processing helix chain 'O' and resid 69 through 78 removed outlier: 3.845A pdb=" N TYR O 74 " --> pdb=" O LEU O 71 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG O 76 " --> pdb=" O ASN O 73 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU O 78 " --> pdb=" O GLU O 75 " (cutoff:3.500A) Processing helix chain 'O' and resid 84 through 86 No H-bonds generated for 'chain 'O' and resid 84 through 86' Processing helix chain 'O' and resid 90 through 102 Processing helix chain 'O' and resid 116 through 129 Processing helix chain 'O' and resid 154 through 169 removed outlier: 3.604A pdb=" N MET O 157 " --> pdb=" O ILE O 154 " (cutoff:3.500A) Proline residue: O 158 - end of helix removed outlier: 3.596A pdb=" N GLU O 161 " --> pdb=" O PRO O 158 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLN O 167 " --> pdb=" O ARG O 164 " (cutoff:3.500A) Processing helix chain 'O' and resid 172 through 174 No H-bonds generated for 'chain 'O' and resid 172 through 174' Processing helix chain 'O' and resid 195 through 206 Processing helix chain 'O' and resid 224 through 234 Processing helix chain 'O' and resid 238 through 240 No H-bonds generated for 'chain 'O' and resid 238 through 240' Processing helix chain 'O' and resid 250 through 260 Proline residue: O 254 - end of helix removed outlier: 3.617A pdb=" N LEU O 257 " --> pdb=" O PRO O 254 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN O 260 " --> pdb=" O LEU O 257 " (cutoff:3.500A) Processing helix chain 'O' and resid 262 through 269 removed outlier: 4.156A pdb=" N ARG O 268 " --> pdb=" O ASP O 264 " (cutoff:3.500A) Processing helix chain 'O' and resid 281 through 294 removed outlier: 3.560A pdb=" N MET O 288 " --> pdb=" O TRP O 285 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA O 289 " --> pdb=" O LYS O 286 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP O 293 " --> pdb=" O ASP O 290 " (cutoff:3.500A) Processing helix chain 'O' and resid 311 through 327 removed outlier: 6.558A pdb=" N SER O 316 " --> pdb=" O SER O 313 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS O 319 " --> pdb=" O SER O 316 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N HIS O 323 " --> pdb=" O ALA O 320 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA O 325 " --> pdb=" O GLU O 322 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU O 326 " --> pdb=" O HIS O 323 " (cutoff:3.500A) Processing helix chain 'O' and resid 339 through 342 Processing helix chain 'O' and resid 346 through 348 No H-bonds generated for 'chain 'O' and resid 346 through 348' Processing helix chain 'O' and resid 351 through 363 Processing helix chain 'O' and resid 378 through 390 Processing helix chain 'O' and resid 399 through 412 removed outlier: 3.875A pdb=" N LEU O 404 " --> pdb=" O GLY O 401 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL O 407 " --> pdb=" O LEU O 404 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE O 409 " --> pdb=" O VAL O 406 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASN O 412 " --> pdb=" O PHE O 409 " (cutoff:3.500A) Processing helix chain 'O' and resid 463 through 467 Processing helix chain 'O' and resid 489 through 493 Processing helix chain 'O' and resid 527 through 530 Processing helix chain 'O' and resid 538 through 547 Processing helix chain 'O' and resid 551 through 554 No H-bonds generated for 'chain 'O' and resid 551 through 554' Processing helix chain 'P' and resid 16 through 29 Processing helix chain 'P' and resid 69 through 78 removed outlier: 3.845A pdb=" N TYR P 74 " --> pdb=" O LEU P 71 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG P 76 " --> pdb=" O ASN P 73 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU P 78 " --> pdb=" O GLU P 75 " (cutoff:3.500A) Processing helix chain 'P' and resid 84 through 86 No H-bonds generated for 'chain 'P' and resid 84 through 86' Processing helix chain 'P' and resid 90 through 102 Processing helix chain 'P' and resid 116 through 129 Processing helix chain 'P' and resid 154 through 169 removed outlier: 3.604A pdb=" N MET P 157 " --> pdb=" O ILE P 154 " (cutoff:3.500A) Proline residue: P 158 - end of helix removed outlier: 3.596A pdb=" N GLU P 161 " --> pdb=" O PRO P 158 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLN P 167 " --> pdb=" O ARG P 164 " (cutoff:3.500A) Processing helix chain 'P' and resid 172 through 174 No H-bonds generated for 'chain 'P' and resid 172 through 174' Processing helix chain 'P' and resid 195 through 206 Processing helix chain 'P' and resid 224 through 234 Processing helix chain 'P' and resid 238 through 240 No H-bonds generated for 'chain 'P' and resid 238 through 240' Processing helix chain 'P' and resid 250 through 260 Proline residue: P 254 - end of helix removed outlier: 3.616A pdb=" N LEU P 257 " --> pdb=" O PRO P 254 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN P 260 " --> pdb=" O LEU P 257 " (cutoff:3.500A) Processing helix chain 'P' and resid 262 through 269 removed outlier: 4.156A pdb=" N ARG P 268 " --> pdb=" O ASP P 264 " (cutoff:3.500A) Processing helix chain 'P' and resid 281 through 294 removed outlier: 3.559A pdb=" N MET P 288 " --> pdb=" O TRP P 285 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA P 289 " --> pdb=" O LYS P 286 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP P 293 " --> pdb=" O ASP P 290 " (cutoff:3.500A) Processing helix chain 'P' and resid 311 through 327 removed outlier: 6.557A pdb=" N SER P 316 " --> pdb=" O SER P 313 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS P 319 " --> pdb=" O SER P 316 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N HIS P 323 " --> pdb=" O ALA P 320 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA P 325 " --> pdb=" O GLU P 322 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU P 326 " --> pdb=" O HIS P 323 " (cutoff:3.500A) Processing helix chain 'P' and resid 339 through 342 Processing helix chain 'P' and resid 346 through 348 No H-bonds generated for 'chain 'P' and resid 346 through 348' Processing helix chain 'P' and resid 351 through 363 Processing helix chain 'P' and resid 378 through 390 Processing helix chain 'P' and resid 399 through 412 removed outlier: 3.875A pdb=" N LEU P 404 " --> pdb=" O GLY P 401 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL P 407 " --> pdb=" O LEU P 404 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE P 409 " --> pdb=" O VAL P 406 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASN P 412 " --> pdb=" O PHE P 409 " (cutoff:3.500A) Processing helix chain 'P' and resid 463 through 467 Processing helix chain 'P' and resid 489 through 493 Processing helix chain 'P' and resid 527 through 530 Processing helix chain 'P' and resid 538 through 547 Processing helix chain 'P' and resid 551 through 554 No H-bonds generated for 'chain 'P' and resid 551 through 554' Processing helix chain 'Q' and resid 16 through 29 Processing helix chain 'Q' and resid 69 through 78 removed outlier: 3.845A pdb=" N TYR Q 74 " --> pdb=" O LEU Q 71 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG Q 76 " --> pdb=" O ASN Q 73 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU Q 78 " --> pdb=" O GLU Q 75 " (cutoff:3.500A) Processing helix chain 'Q' and resid 84 through 86 No H-bonds generated for 'chain 'Q' and resid 84 through 86' Processing helix chain 'Q' and resid 90 through 102 Processing helix chain 'Q' and resid 116 through 129 Processing helix chain 'Q' and resid 154 through 169 removed outlier: 3.604A pdb=" N MET Q 157 " --> pdb=" O ILE Q 154 " (cutoff:3.500A) Proline residue: Q 158 - end of helix removed outlier: 3.596A pdb=" N GLU Q 161 " --> pdb=" O PRO Q 158 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLN Q 167 " --> pdb=" O ARG Q 164 " (cutoff:3.500A) Processing helix chain 'Q' and resid 172 through 174 No H-bonds generated for 'chain 'Q' and resid 172 through 174' Processing helix chain 'Q' and resid 195 through 206 Processing helix chain 'Q' and resid 224 through 234 Processing helix chain 'Q' and resid 238 through 240 No H-bonds generated for 'chain 'Q' and resid 238 through 240' Processing helix chain 'Q' and resid 250 through 260 Proline residue: Q 254 - end of helix removed outlier: 3.616A pdb=" N LEU Q 257 " --> pdb=" O PRO Q 254 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN Q 260 " --> pdb=" O LEU Q 257 " (cutoff:3.500A) Processing helix chain 'Q' and resid 262 through 269 removed outlier: 4.157A pdb=" N ARG Q 268 " --> pdb=" O ASP Q 264 " (cutoff:3.500A) Processing helix chain 'Q' and resid 281 through 294 removed outlier: 3.559A pdb=" N MET Q 288 " --> pdb=" O TRP Q 285 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA Q 289 " --> pdb=" O LYS Q 286 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP Q 293 " --> pdb=" O ASP Q 290 " (cutoff:3.500A) Processing helix chain 'Q' and resid 311 through 327 removed outlier: 6.557A pdb=" N SER Q 316 " --> pdb=" O SER Q 313 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS Q 319 " --> pdb=" O SER Q 316 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N HIS Q 323 " --> pdb=" O ALA Q 320 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA Q 325 " --> pdb=" O GLU Q 322 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU Q 326 " --> pdb=" O HIS Q 323 " (cutoff:3.500A) Processing helix chain 'Q' and resid 339 through 342 Processing helix chain 'Q' and resid 346 through 348 No H-bonds generated for 'chain 'Q' and resid 346 through 348' Processing helix chain 'Q' and resid 351 through 363 Processing helix chain 'Q' and resid 378 through 390 Processing helix chain 'Q' and resid 399 through 412 removed outlier: 3.875A pdb=" N LEU Q 404 " --> pdb=" O GLY Q 401 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL Q 407 " --> pdb=" O LEU Q 404 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE Q 409 " --> pdb=" O VAL Q 406 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASN Q 412 " --> pdb=" O PHE Q 409 " (cutoff:3.500A) Processing helix chain 'Q' and resid 463 through 467 Processing helix chain 'Q' and resid 489 through 493 Processing helix chain 'Q' and resid 527 through 530 Processing helix chain 'Q' and resid 538 through 547 Processing helix chain 'Q' and resid 551 through 554 No H-bonds generated for 'chain 'Q' and resid 551 through 554' Processing sheet with id= A, first strand: chain 'F' and resid 241 through 245 removed outlier: 6.365A pdb=" N VAL F 214 " --> pdb=" O ILE F 242 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N VAL F 244 " --> pdb=" O VAL F 214 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N CYS F 216 " --> pdb=" O VAL F 244 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N TYR F 3 " --> pdb=" O CYS F 176 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N ILE F 178 " --> pdb=" O TYR F 3 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N LEU F 5 " --> pdb=" O ILE F 178 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N VAL F 180 " --> pdb=" O LEU F 5 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N THR F 7 " --> pdb=" O VAL F 180 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N LEU F 182 " --> pdb=" O THR F 7 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLY F 8 " --> pdb=" O LEU F 147 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'F' and resid 331 through 338 removed outlier: 6.904A pdb=" N GLY F 366 " --> pdb=" O ALA F 302 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N VAL F 304 " --> pdb=" O GLY F 366 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N LEU F 368 " --> pdb=" O VAL F 304 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N VAL F 369 " --> pdb=" O PRO F 394 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LEU F 396 " --> pdb=" O VAL F 369 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'F' and resid 433 through 435 Processing sheet with id= D, first strand: chain 'F' and resid 473 through 478 Processing sheet with id= E, first strand: chain 'O' and resid 241 through 245 removed outlier: 6.365A pdb=" N VAL O 214 " --> pdb=" O ILE O 242 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N VAL O 244 " --> pdb=" O VAL O 214 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N CYS O 216 " --> pdb=" O VAL O 244 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N TYR O 3 " --> pdb=" O CYS O 176 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N ILE O 178 " --> pdb=" O TYR O 3 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N LEU O 5 " --> pdb=" O ILE O 178 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N VAL O 180 " --> pdb=" O LEU O 5 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N THR O 7 " --> pdb=" O VAL O 180 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N LEU O 182 " --> pdb=" O THR O 7 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLY O 8 " --> pdb=" O LEU O 147 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'O' and resid 331 through 338 removed outlier: 6.905A pdb=" N GLY O 366 " --> pdb=" O ALA O 302 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N VAL O 304 " --> pdb=" O GLY O 366 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N LEU O 368 " --> pdb=" O VAL O 304 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N VAL O 369 " --> pdb=" O PRO O 394 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LEU O 396 " --> pdb=" O VAL O 369 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'O' and resid 433 through 435 Processing sheet with id= H, first strand: chain 'O' and resid 473 through 478 Processing sheet with id= I, first strand: chain 'P' and resid 241 through 245 removed outlier: 6.365A pdb=" N VAL P 214 " --> pdb=" O ILE P 242 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N VAL P 244 " --> pdb=" O VAL P 214 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N CYS P 216 " --> pdb=" O VAL P 244 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N TYR P 3 " --> pdb=" O CYS P 176 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N ILE P 178 " --> pdb=" O TYR P 3 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N LEU P 5 " --> pdb=" O ILE P 178 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N VAL P 180 " --> pdb=" O LEU P 5 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N THR P 7 " --> pdb=" O VAL P 180 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N LEU P 182 " --> pdb=" O THR P 7 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLY P 8 " --> pdb=" O LEU P 147 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'P' and resid 331 through 338 removed outlier: 6.905A pdb=" N GLY P 366 " --> pdb=" O ALA P 302 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N VAL P 304 " --> pdb=" O GLY P 366 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N LEU P 368 " --> pdb=" O VAL P 304 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N VAL P 369 " --> pdb=" O PRO P 394 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU P 396 " --> pdb=" O VAL P 369 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'P' and resid 433 through 435 Processing sheet with id= L, first strand: chain 'P' and resid 473 through 478 Processing sheet with id= M, first strand: chain 'Q' and resid 241 through 245 removed outlier: 6.365A pdb=" N VAL Q 214 " --> pdb=" O ILE Q 242 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N VAL Q 244 " --> pdb=" O VAL Q 214 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N CYS Q 216 " --> pdb=" O VAL Q 244 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N TYR Q 3 " --> pdb=" O CYS Q 176 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N ILE Q 178 " --> pdb=" O TYR Q 3 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N LEU Q 5 " --> pdb=" O ILE Q 178 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N VAL Q 180 " --> pdb=" O LEU Q 5 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N THR Q 7 " --> pdb=" O VAL Q 180 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N LEU Q 182 " --> pdb=" O THR Q 7 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLY Q 8 " --> pdb=" O LEU Q 147 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'Q' and resid 331 through 338 removed outlier: 6.905A pdb=" N GLY Q 366 " --> pdb=" O ALA Q 302 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N VAL Q 304 " --> pdb=" O GLY Q 366 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N LEU Q 368 " --> pdb=" O VAL Q 304 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N VAL Q 369 " --> pdb=" O PRO Q 394 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LEU Q 396 " --> pdb=" O VAL Q 369 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'Q' and resid 433 through 435 Processing sheet with id= P, first strand: chain 'Q' and resid 473 through 478 608 hydrogen bonds defined for protein. 1320 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: 13.52 Time building geometry restraints manager: 31.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.85 - 1.05: 3780 1.05 - 1.24: 15856 1.24 - 1.43: 5192 1.43 - 1.62: 10240 1.62 - 1.82: 164 Bond restraints: 35232 Sorted by residual: bond pdb=" C4' UTP Q 602 " pdb=" O4' UTP Q 602 " ideal model delta sigma weight residual 1.320 1.537 -0.217 2.00e-02 2.50e+03 1.18e+02 bond pdb=" C4' UTP F 601 " pdb=" O4' UTP F 601 " ideal model delta sigma weight residual 1.320 1.536 -0.216 2.00e-02 2.50e+03 1.17e+02 bond pdb=" C4' UTP O 601 " pdb=" O4' UTP O 601 " ideal model delta sigma weight residual 1.320 1.536 -0.216 2.00e-02 2.50e+03 1.17e+02 bond pdb=" C4' UTP P 602 " pdb=" O4' UTP P 602 " ideal model delta sigma weight residual 1.320 1.536 -0.216 2.00e-02 2.50e+03 1.17e+02 bond pdb=" C1' UTP F 601 " pdb=" O4' UTP F 601 " ideal model delta sigma weight residual 1.553 1.359 0.194 2.00e-02 2.50e+03 9.46e+01 ... (remaining 35227 not shown) Histogram of bond angle deviations from ideal: 72.73 - 85.48: 12 85.48 - 98.23: 68 98.23 - 110.98: 35346 110.98 - 123.73: 26202 123.73 - 136.48: 2156 Bond angle restraints: 63784 Sorted by residual: angle pdb=" CG1 VAL Q 487 " pdb=" CB VAL Q 487 " pdb=" HB VAL Q 487 " ideal model delta sigma weight residual 108.00 72.73 35.27 3.00e+00 1.11e-01 1.38e+02 angle pdb=" CG1 VAL F 487 " pdb=" CB VAL F 487 " pdb=" HB VAL F 487 " ideal model delta sigma weight residual 108.00 72.73 35.27 3.00e+00 1.11e-01 1.38e+02 angle pdb=" CG1 VAL P 487 " pdb=" CB VAL P 487 " pdb=" HB VAL P 487 " ideal model delta sigma weight residual 108.00 72.73 35.27 3.00e+00 1.11e-01 1.38e+02 angle pdb=" CG1 VAL O 487 " pdb=" CB VAL O 487 " pdb=" HB VAL O 487 " ideal model delta sigma weight residual 108.00 72.73 35.27 3.00e+00 1.11e-01 1.38e+02 angle pdb=" CA VAL F 487 " pdb=" CB VAL F 487 " pdb=" HB VAL F 487 " ideal model delta sigma weight residual 109.00 75.36 33.64 3.00e+00 1.11e-01 1.26e+02 ... (remaining 63779 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 14686 17.96 - 35.92: 914 35.92 - 53.88: 268 53.88 - 71.84: 132 71.84 - 89.80: 48 Dihedral angle restraints: 16048 sinusoidal: 8696 harmonic: 7352 Sorted by residual: dihedral pdb=" CA LYS Q 460 " pdb=" C LYS Q 460 " pdb=" N ASN Q 461 " pdb=" CA ASN Q 461 " ideal model delta harmonic sigma weight residual -180.00 -153.23 -26.77 0 5.00e+00 4.00e-02 2.87e+01 dihedral pdb=" CA LYS P 460 " pdb=" C LYS P 460 " pdb=" N ASN P 461 " pdb=" CA ASN P 461 " ideal model delta harmonic sigma weight residual -180.00 -153.25 -26.75 0 5.00e+00 4.00e-02 2.86e+01 dihedral pdb=" CA LYS F 460 " pdb=" C LYS F 460 " pdb=" N ASN F 461 " pdb=" CA ASN F 461 " ideal model delta harmonic sigma weight residual -180.00 -153.25 -26.75 0 5.00e+00 4.00e-02 2.86e+01 ... (remaining 16045 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.161: 2313 0.161 - 0.321: 352 0.321 - 0.482: 11 0.482 - 0.643: 0 0.643 - 0.803: 4 Chirality restraints: 2680 Sorted by residual: chirality pdb=" CB VAL Q 487 " pdb=" CA VAL Q 487 " pdb=" CG1 VAL Q 487 " pdb=" CG2 VAL Q 487 " both_signs ideal model delta sigma weight residual False -2.63 -1.83 -0.80 2.00e-01 2.50e+01 1.61e+01 chirality pdb=" CB VAL O 487 " pdb=" CA VAL O 487 " pdb=" CG1 VAL O 487 " pdb=" CG2 VAL O 487 " both_signs ideal model delta sigma weight residual False -2.63 -1.83 -0.80 2.00e-01 2.50e+01 1.61e+01 chirality pdb=" CB VAL P 487 " pdb=" CA VAL P 487 " pdb=" CG1 VAL P 487 " pdb=" CG2 VAL P 487 " both_signs ideal model delta sigma weight residual False -2.63 -1.83 -0.80 2.00e-01 2.50e+01 1.61e+01 ... (remaining 2677 not shown) Planarity restraints: 5144 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN P 603 " -0.156 2.00e-02 2.50e+03 1.70e-01 4.33e+02 pdb=" CD GLN P 603 " 0.015 2.00e-02 2.50e+03 pdb=" OE1 GLN P 603 " 0.146 2.00e-02 2.50e+03 pdb=" NE2 GLN P 603 " 0.001 2.00e-02 2.50e+03 pdb="HE21 GLN P 603 " 0.249 2.00e-02 2.50e+03 pdb="HE22 GLN P 603 " -0.255 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN Q 603 " -0.156 2.00e-02 2.50e+03 1.70e-01 4.33e+02 pdb=" CD GLN Q 603 " 0.015 2.00e-02 2.50e+03 pdb=" OE1 GLN Q 603 " 0.146 2.00e-02 2.50e+03 pdb=" NE2 GLN Q 603 " 0.001 2.00e-02 2.50e+03 pdb="HE21 GLN Q 603 " 0.249 2.00e-02 2.50e+03 pdb="HE22 GLN Q 603 " -0.255 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN O 602 " 0.156 2.00e-02 2.50e+03 1.70e-01 4.32e+02 pdb=" CD GLN O 602 " -0.015 2.00e-02 2.50e+03 pdb=" OE1 GLN O 602 " -0.146 2.00e-02 2.50e+03 pdb=" NE2 GLN O 602 " -0.002 2.00e-02 2.50e+03 pdb="HE21 GLN O 602 " -0.248 2.00e-02 2.50e+03 pdb="HE22 GLN O 602 " 0.255 2.00e-02 2.50e+03 ... (remaining 5141 not shown) Histogram of nonbonded interaction distances: 1.01 - 1.73: 92 1.73 - 2.44: 15256 2.44 - 3.16: 115664 3.16 - 3.88: 153344 3.88 - 4.60: 240465 Nonbonded interactions: 524821 Sorted by model distance: nonbonded pdb=" HE2 MET O 448 " pdb=" HG3 ARG O 481 " model vdw 1.008 2.440 nonbonded pdb=" HE2 MET P 448 " pdb=" HG3 ARG P 481 " model vdw 1.008 2.440 nonbonded pdb=" HE2 MET F 448 " pdb=" HG3 ARG F 481 " model vdw 1.008 2.440 nonbonded pdb=" HE2 MET Q 448 " pdb=" HG3 ARG Q 481 " model vdw 1.008 2.440 nonbonded pdb=" HG3 MET Q 448 " pdb=" HG2 ARG Q 481 " model vdw 1.236 2.440 ... (remaining 524816 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 'F' and resid 1 through 555) selection = (chain 'O' and resid 1 through 555) selection = (chain 'P' and resid 1 through 555) selection = (chain 'Q' and resid 1 through 555) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.480 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: 0.530 Extract box with map and model: 7.670 Check model and map are aligned: 0.510 Set scattering table: 0.300 Process input model: 113.810 Find NCS groups from input model: 1.840 Set up NCS constraints: 0.130 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:10.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 137.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 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 : 0.014 0.217 17916 Z= 0.938 Angle : 2.034 14.805 24292 Z= 1.329 Chirality : 0.111 0.803 2680 Planarity : 0.018 0.174 3100 Dihedral : 16.599 89.798 6804 Min Nonbonded Distance : 1.574 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.36 % Favored : 96.46 % Rotamer: Outliers : 1.66 % Allowed : 7.28 % Favored : 91.06 % Cbeta Deviations : 0.40 % Peptide Plane: Cis-proline : 3.57 % 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 (0.16), residues: 2144 helix: -1.39 (0.14), residues: 912 sheet: -0.17 (0.28), residues: 320 loop : -0.49 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.021 TRP P 285 HIS 0.014 0.004 HIS F 439 PHE 0.057 0.014 PHE Q 233 TYR 0.122 0.022 TYR P 292 ARG 0.012 0.002 ARG F 389 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 681 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 649 time to evaluate : 2.820 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 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 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: 32 outliers final: 7 residues processed: 657 average time/residue: 2.6774 time to fit residues: 1979.6554 Evaluate side-chains 502 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 495 time to evaluate : 2.669 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 3 residues processed: 7 average time/residue: 0.4445 time to fit residues: 8.8547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 0.7980 chunk 163 optimal weight: 0.6980 chunk 90 optimal weight: 0.8980 chunk 55 optimal weight: 0.6980 chunk 110 optimal weight: 0.6980 chunk 87 optimal weight: 0.9990 chunk 169 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 126 optimal weight: 0.9980 chunk 196 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 87 ASN F 99 ASN ** F 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 87 ASN O 99 ASN ** O 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 87 ASN P 99 ASN ** P 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 87 ASN Q 99 ASN ** Q 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17916 Z= 0.266 Angle : 0.705 9.700 24292 Z= 0.370 Chirality : 0.068 1.346 2680 Planarity : 0.007 0.063 3100 Dihedral : 10.795 53.200 2516 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.96 % Allowed : 17.00 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.89 (0.17), residues: 2144 helix: -0.88 (0.15), residues: 924 sheet: 0.09 (0.26), residues: 368 loop : -0.29 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP P 358 HIS 0.007 0.002 HIS O 116 PHE 0.013 0.002 PHE P 233 TYR 0.011 0.002 TYR F 42 ARG 0.007 0.001 ARG F 294 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 508 time to evaluate : 2.427 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: 57 outliers final: 9 residues processed: 525 average time/residue: 2.8204 time to fit residues: 1659.6664 Evaluate side-chains 433 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 424 time to evaluate : 2.838 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 8 residues processed: 1 average time/residue: 2.2799 time to fit residues: 6.2333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 109 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 163 optimal weight: 1.9990 chunk 133 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 196 optimal weight: 2.9990 chunk 212 optimal weight: 0.6980 chunk 175 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 157 optimal weight: 0.7980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 365 HIS ** O 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 365 HIS P 365 HIS Q 365 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.4208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17916 Z= 0.263 Angle : 0.629 11.075 24292 Z= 0.328 Chirality : 0.071 1.473 2680 Planarity : 0.006 0.062 3100 Dihedral : 8.235 49.294 2516 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.98 % Allowed : 18.50 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.70 (0.17), residues: 2144 helix: -0.63 (0.15), residues: 924 sheet: 0.01 (0.25), residues: 384 loop : -0.22 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP O 387 HIS 0.006 0.002 HIS F 116 PHE 0.014 0.001 PHE P 163 TYR 0.013 0.001 TYR O 42 ARG 0.007 0.001 ARG P 481 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 456 time to evaluate : 2.847 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 14 residues processed: 482 average time/residue: 2.8968 time to fit residues: 1564.6186 Evaluate side-chains 415 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 401 time to evaluate : 2.814 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 12 residues processed: 2 average time/residue: 0.4602 time to fit residues: 5.1191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 194 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 197 optimal weight: 2.9990 chunk 208 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 186 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 365 HIS O 220 ASN O 240 GLN O 365 HIS P 240 GLN P 365 HIS Q 220 ASN Q 240 GLN ** Q 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 365 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.4584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 17916 Z= 0.344 Angle : 0.622 11.040 24292 Z= 0.321 Chirality : 0.071 1.447 2680 Planarity : 0.005 0.050 3100 Dihedral : 7.523 49.924 2516 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.70 % Allowed : 19.65 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.54 (0.18), residues: 2144 helix: -0.47 (0.16), residues: 924 sheet: -0.10 (0.25), residues: 384 loop : -0.08 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP Q 387 HIS 0.008 0.002 HIS O 116 PHE 0.015 0.002 PHE P 163 TYR 0.014 0.002 TYR F 42 ARG 0.006 0.001 ARG P 481 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 400 time to evaluate : 2.880 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: 52 outliers final: 30 residues processed: 431 average time/residue: 2.9510 time to fit residues: 1424.8656 Evaluate side-chains 408 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 378 time to evaluate : 3.004 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 22 residues processed: 8 average time/residue: 1.7063 time to fit residues: 20.3287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 173 optimal weight: 0.5980 chunk 118 optimal weight: 1.9990 chunk 3 optimal weight: 0.0470 chunk 155 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 178 optimal weight: 0.6980 chunk 144 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 chunk 187 optimal weight: 0.0970 chunk 52 optimal weight: 0.6980 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 365 HIS O 220 ASN O 240 GLN O 365 HIS P 240 GLN P 365 HIS Q 220 ASN Q 240 GLN Q 329 ASN ** Q 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 365 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.4726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 17916 Z= 0.165 Angle : 0.559 11.197 24292 Z= 0.286 Chirality : 0.070 1.469 2680 Planarity : 0.005 0.051 3100 Dihedral : 7.009 48.503 2516 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.39 % Allowed : 19.80 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.13 (0.18), residues: 2144 helix: -0.14 (0.17), residues: 932 sheet: 0.06 (0.26), residues: 372 loop : 0.18 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP Q 387 HIS 0.007 0.001 HIS P 235 PHE 0.010 0.001 PHE P 163 TYR 0.012 0.001 TYR F 42 ARG 0.007 0.001 ARG P 481 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 410 time to evaluate : 2.908 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: 46 outliers final: 19 residues processed: 437 average time/residue: 2.8938 time to fit residues: 1421.1439 Evaluate side-chains 418 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 399 time to evaluate : 3.041 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 15 residues processed: 4 average time/residue: 1.1453 time to fit residues: 9.8786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 70 optimal weight: 0.9980 chunk 188 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 122 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 208 optimal weight: 0.9980 chunk 173 optimal weight: 0.8980 chunk 96 optimal weight: 0.0040 chunk 17 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 overall best weight: 0.9794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 220 ASN F 240 GLN ** F 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 365 HIS O 220 ASN ** O 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 365 HIS P 220 ASN P 240 GLN P 365 HIS Q 220 ASN ** Q 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 365 HIS Q 391 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.4870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 17916 Z= 0.257 Angle : 0.563 11.179 24292 Z= 0.288 Chirality : 0.071 1.473 2680 Planarity : 0.005 0.052 3100 Dihedral : 6.949 49.285 2516 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.03 % Allowed : 21.05 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.06 (0.18), residues: 2144 helix: -0.08 (0.17), residues: 932 sheet: 0.07 (0.26), residues: 372 loop : 0.24 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP Q 387 HIS 0.006 0.001 HIS P 235 PHE 0.019 0.001 PHE P 482 TYR 0.013 0.001 TYR F 292 ARG 0.008 0.001 ARG F 481 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 402 time to evaluate : 2.929 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: 39 outliers final: 26 residues processed: 424 average time/residue: 2.8794 time to fit residues: 1369.2478 Evaluate side-chains 411 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 385 time to evaluate : 2.823 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 21 residues processed: 5 average time/residue: 1.0558 time to fit residues: 10.7209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 201 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 119 optimal weight: 0.8980 chunk 152 optimal weight: 4.9990 chunk 118 optimal weight: 0.9990 chunk 175 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 208 optimal weight: 2.9990 chunk 130 optimal weight: 0.6980 chunk 126 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 220 ASN F 240 GLN ** F 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 365 HIS F 461 ASN O 220 ASN ** O 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 365 HIS P 220 ASN ** P 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 365 HIS P 461 ASN Q 220 ASN ** Q 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 365 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.4967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17916 Z= 0.217 Angle : 0.561 11.224 24292 Z= 0.285 Chirality : 0.070 1.480 2680 Planarity : 0.005 0.043 3100 Dihedral : 6.823 49.619 2516 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.08 % Allowed : 21.67 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.11 (0.18), residues: 2144 helix: 0.07 (0.17), residues: 924 sheet: 0.08 (0.26), residues: 372 loop : 0.36 (0.22), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP O 387 HIS 0.006 0.001 HIS F 235 PHE 0.021 0.001 PHE P 482 TYR 0.012 0.001 TYR P 292 ARG 0.007 0.001 ARG F 481 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 403 time to evaluate : 2.939 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: 40 outliers final: 25 residues processed: 429 average time/residue: 3.0027 time to fit residues: 1451.3275 Evaluate side-chains 426 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 401 time to evaluate : 2.891 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 22 residues processed: 3 average time/residue: 1.3618 time to fit residues: 8.8916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 128 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 132 optimal weight: 0.8980 chunk 141 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 163 optimal weight: 0.4980 chunk 189 optimal weight: 0.0570 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 220 ASN ** F 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 365 HIS O 220 ASN ** O 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 365 HIS O 461 ASN P 220 ASN P 240 GLN P 365 HIS Q 220 ASN ** Q 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 365 HIS Q 461 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.5055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17916 Z= 0.189 Angle : 0.547 11.236 24292 Z= 0.279 Chirality : 0.070 1.487 2680 Planarity : 0.005 0.057 3100 Dihedral : 6.712 51.457 2516 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.03 % Allowed : 21.99 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.22 (0.18), residues: 2144 helix: 0.16 (0.17), residues: 924 sheet: 0.11 (0.26), residues: 372 loop : 0.44 (0.22), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP Q 387 HIS 0.006 0.001 HIS F 235 PHE 0.021 0.001 PHE P 482 TYR 0.012 0.001 TYR P 292 ARG 0.010 0.001 ARG F 481 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 409 time to evaluate : 3.150 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: 39 outliers final: 23 residues processed: 432 average time/residue: 2.4402 time to fit residues: 1182.5413 Evaluate side-chains 412 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 389 time to evaluate : 1.939 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 18 residues processed: 5 average time/residue: 1.1412 time to fit residues: 9.3527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 199 optimal weight: 1.9990 chunk 181 optimal weight: 0.9980 chunk 194 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 152 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 175 optimal weight: 0.6980 chunk 183 optimal weight: 0.8980 chunk 193 optimal weight: 0.5980 chunk 127 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: