Starting phenix.real_space_refine on Mon Apr 15 12:34:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mgz_23831/04_2024/7mgz_23831_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mgz_23831/04_2024/7mgz_23831.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mgz_23831/04_2024/7mgz_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_23831/04_2024/7mgz_23831_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mgz_23831/04_2024/7mgz_23831_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mgz_23831/04_2024/7mgz_23831.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mgz_23831/04_2024/7mgz_23831.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mgz_23831/04_2024/7mgz_23831_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mgz_23831/04_2024/7mgz_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-dev-5288/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: 15.07, per 1000 atoms: 0.43 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: 31.02 Conformation dependent library (CDL) restraints added in 3.4 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: 5.69 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: 13.79 Time building geometry restraints manager: 31.43 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: 14958 17.96 - 35.92: 986 35.92 - 53.88: 376 53.88 - 71.84: 176 71.84 - 89.80: 48 Dihedral angle restraints: 16544 sinusoidal: 9192 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 16541 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: 1.750 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: 7.620 Check model and map are aligned: 0.500 Set scattering table: 0.290 Process input model: 112.650 Find NCS groups from input model: 1.870 Set up NCS constraints: 0.150 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:11.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 136.730 ------------------------------------------------------------------------------- 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 : 2.682 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 REVERT: F 66 GLU cc_start: 0.8436 (mt-10) cc_final: 0.8066 (mt-10) REVERT: F 107 LEU cc_start: 0.7952 (mt) cc_final: 0.7639 (mt) REVERT: F 161 GLU cc_start: 0.8152 (tp30) cc_final: 0.7665 (mm-30) REVERT: F 335 LYS cc_start: 0.8294 (mttm) cc_final: 0.8040 (mtpt) REVERT: F 476 GLU cc_start: 0.8480 (mm-30) cc_final: 0.7263 (mm-30) REVERT: O 66 GLU cc_start: 0.8429 (mt-10) cc_final: 0.8018 (mt-10) REVERT: O 107 LEU cc_start: 0.8005 (mt) cc_final: 0.7630 (mt) REVERT: O 161 GLU cc_start: 0.8172 (tp30) cc_final: 0.7675 (mm-30) REVERT: O 335 LYS cc_start: 0.8289 (mttm) cc_final: 0.8052 (mtpt) REVERT: O 476 GLU cc_start: 0.8464 (mm-30) cc_final: 0.7244 (mm-30) REVERT: P 66 GLU cc_start: 0.8440 (mt-10) cc_final: 0.8097 (mt-10) REVERT: P 107 LEU cc_start: 0.7939 (mt) cc_final: 0.7644 (mt) REVERT: P 161 GLU cc_start: 0.8126 (tp30) cc_final: 0.7422 (mm-30) REVERT: P 335 LYS cc_start: 0.8296 (mttm) cc_final: 0.8033 (mtpt) REVERT: P 476 GLU cc_start: 0.8475 (mm-30) cc_final: 0.7277 (mm-30) REVERT: P 482 PHE cc_start: 0.8465 (m-80) cc_final: 0.8203 (m-80) REVERT: Q 66 GLU cc_start: 0.8423 (mt-10) cc_final: 0.8043 (mt-10) REVERT: Q 107 LEU cc_start: 0.7989 (mt) cc_final: 0.7626 (mt) REVERT: Q 161 GLU cc_start: 0.8170 (tp30) cc_final: 0.7696 (mm-30) REVERT: Q 335 LYS cc_start: 0.8277 (mttm) cc_final: 0.8076 (mttt) REVERT: Q 476 GLU cc_start: 0.8469 (mm-30) cc_final: 0.7254 (mm-30) REVERT: Q 482 PHE cc_start: 0.8396 (m-80) cc_final: 0.8132 (m-80) outliers start: 32 outliers final: 7 residues processed: 657 average time/residue: 2.7212 time to fit residues: 2013.2881 Evaluate side-chains 508 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 501 time to evaluate : 2.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 136 ASP Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain O residue 367 VAL Chi-restraints excluded: chain P residue 136 ASP Chi-restraints excluded: chain P residue 367 VAL Chi-restraints excluded: chain Q residue 136 ASP Chi-restraints excluded: chain Q residue 367 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 0.6980 chunk 163 optimal weight: 0.6980 chunk 90 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 chunk 110 optimal weight: 0.6980 chunk 87 optimal weight: 0.9980 chunk 169 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 126 optimal weight: 0.9980 chunk 196 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 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 99 ASN ** Q 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.3349 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= 0.248 Angle : 0.704 9.503 24292 Z= 0.371 Chirality : 0.067 1.315 2680 Planarity : 0.007 0.063 3100 Dihedral : 11.503 108.757 2526 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.91 % Allowed : 16.16 % Favored : 80.93 % 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: 0.04 (0.26), residues: 368 loop : -0.28 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP Q 387 HIS 0.007 0.002 HIS O 116 PHE 0.014 0.002 PHE P 233 TYR 0.011 0.002 TYR F 42 ARG 0.006 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 576 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 520 time to evaluate : 2.621 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: F 294 ARG cc_start: 0.7073 (mtm110) cc_final: 0.6863 (ptp-170) REVERT: F 322 GLU cc_start: 0.7763 (mt-10) cc_final: 0.7477 (mt-10) REVERT: F 335 LYS cc_start: 0.8142 (mttm) cc_final: 0.7924 (mttt) REVERT: F 389 ARG cc_start: 0.7186 (OUTLIER) cc_final: 0.6730 (mtm110) REVERT: F 475 GLU cc_start: 0.7839 (mt-10) cc_final: 0.7620 (mt-10) REVERT: F 476 GLU cc_start: 0.8435 (mm-30) cc_final: 0.8085 (mm-30) REVERT: O 288 MET cc_start: 0.7723 (mtp) cc_final: 0.7509 (mtm) REVERT: O 294 ARG cc_start: 0.7008 (mtm110) cc_final: 0.6672 (ptp-170) REVERT: O 322 GLU cc_start: 0.7714 (mt-10) cc_final: 0.7429 (mt-10) REVERT: O 387 TRP cc_start: 0.7655 (t-100) cc_final: 0.7357 (t-100) REVERT: O 389 ARG cc_start: 0.7192 (OUTLIER) cc_final: 0.6774 (mtm110) REVERT: O 475 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7658 (mt-10) REVERT: O 476 GLU cc_start: 0.8433 (mm-30) cc_final: 0.8089 (mm-30) REVERT: O 544 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8693 (mm) REVERT: P 79 ASP cc_start: 0.7216 (t0) cc_final: 0.6996 (t0) REVERT: P 294 ARG cc_start: 0.6864 (mtp180) cc_final: 0.6540 (ptp-170) REVERT: P 322 GLU cc_start: 0.7756 (mt-10) cc_final: 0.7332 (mt-10) REVERT: P 389 ARG cc_start: 0.7214 (OUTLIER) cc_final: 0.6789 (mtm110) REVERT: P 476 GLU cc_start: 0.8436 (mm-30) cc_final: 0.8086 (mm-30) REVERT: Q 286 LYS cc_start: 0.8245 (tptm) cc_final: 0.8001 (mmmt) REVERT: Q 294 ARG cc_start: 0.7036 (mtp180) cc_final: 0.6708 (ptp-170) REVERT: Q 353 ARG cc_start: 0.6893 (tpp80) cc_final: 0.6665 (ttm-80) REVERT: Q 389 ARG cc_start: 0.7218 (OUTLIER) cc_final: 0.6761 (mtm110) REVERT: Q 476 GLU cc_start: 0.8424 (mm-30) cc_final: 0.8097 (mm-30) REVERT: Q 544 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8660 (mm) outliers start: 56 outliers final: 14 residues processed: 533 average time/residue: 2.8778 time to fit residues: 1719.8742 Evaluate side-chains 441 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 421 time to evaluate : 2.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 136 ASP Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 389 ARG Chi-restraints excluded: chain F residue 503 ASP Chi-restraints excluded: chain O residue 136 ASP Chi-restraints excluded: chain O residue 291 ARG Chi-restraints excluded: chain O residue 367 VAL Chi-restraints excluded: chain O residue 389 ARG Chi-restraints excluded: chain O residue 503 ASP Chi-restraints excluded: chain O residue 544 LEU Chi-restraints excluded: chain P residue 136 ASP Chi-restraints excluded: chain P residue 367 VAL Chi-restraints excluded: chain P residue 389 ARG Chi-restraints excluded: chain P residue 503 ASP Chi-restraints excluded: chain Q residue 136 ASP Chi-restraints excluded: chain Q residue 367 VAL Chi-restraints excluded: chain Q residue 389 ARG Chi-restraints excluded: chain Q residue 503 ASP Chi-restraints excluded: chain Q residue 544 LEU 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: 0.9990 chunk 54 optimal weight: 1.9990 chunk 196 optimal weight: 2.9990 chunk 212 optimal weight: 0.0770 chunk 175 optimal weight: 0.0770 chunk 194 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 157 optimal weight: 0.4980 overall best weight: 0.4896 ------------------------------------------------------------------------------- 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 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 365 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.4075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17916 Z= 0.181 Angle : 0.606 10.905 24292 Z= 0.315 Chirality : 0.071 1.465 2680 Planarity : 0.005 0.039 3100 Dihedral : 9.233 106.192 2526 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.23 % Allowed : 18.04 % Favored : 79.73 % 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: -0.55 (0.17), residues: 2144 helix: -0.49 (0.16), residues: 924 sheet: 0.04 (0.25), residues: 384 loop : -0.15 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP O 387 HIS 0.008 0.001 HIS O 330 PHE 0.011 0.001 PHE F 163 TYR 0.012 0.001 TYR F 42 ARG 0.006 0.000 ARG O 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 501 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 458 time to evaluate : 2.603 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: F 389 ARG cc_start: 0.7231 (OUTLIER) cc_final: 0.6798 (mtm110) REVERT: F 402 MET cc_start: 0.8426 (ttp) cc_final: 0.8218 (ttp) REVERT: F 476 GLU cc_start: 0.8434 (mm-30) cc_final: 0.8183 (mm-30) REVERT: F 481 ARG cc_start: 0.7555 (mtt-85) cc_final: 0.7326 (mtt-85) REVERT: O 219 SER cc_start: 0.8677 (p) cc_final: 0.8437 (m) REVERT: O 294 ARG cc_start: 0.6954 (mtm110) cc_final: 0.6624 (ptp-170) REVERT: O 322 GLU cc_start: 0.7693 (mt-10) cc_final: 0.7397 (mt-10) REVERT: O 387 TRP cc_start: 0.7820 (t-100) cc_final: 0.7484 (t-100) REVERT: O 436 MET cc_start: 0.7505 (ttt) cc_final: 0.7118 (ttm) REVERT: O 481 ARG cc_start: 0.7554 (mtt-85) cc_final: 0.7335 (mtt-85) REVERT: O 502 GLN cc_start: 0.7932 (OUTLIER) cc_final: 0.7608 (mt0) REVERT: O 514 LEU cc_start: 0.8359 (tp) cc_final: 0.8156 (tt) REVERT: P 294 ARG cc_start: 0.6813 (mtp180) cc_final: 0.6564 (ptp-170) REVERT: P 322 GLU cc_start: 0.7699 (mt-10) cc_final: 0.7303 (mt-10) REVERT: P 402 MET cc_start: 0.8414 (ttp) cc_final: 0.8201 (ttp) REVERT: P 436 MET cc_start: 0.7525 (ttt) cc_final: 0.7108 (ttm) REVERT: P 476 GLU cc_start: 0.8437 (mm-30) cc_final: 0.8155 (mm-30) REVERT: P 481 ARG cc_start: 0.7572 (mtt-85) cc_final: 0.7229 (mtp180) REVERT: P 502 GLN cc_start: 0.7861 (OUTLIER) cc_final: 0.7635 (mt0) REVERT: Q 288 MET cc_start: 0.7698 (mtp) cc_final: 0.7470 (mtm) REVERT: Q 294 ARG cc_start: 0.6879 (mtp180) cc_final: 0.6669 (ptp-170) REVERT: Q 389 ARG cc_start: 0.7156 (OUTLIER) cc_final: 0.6757 (mtm110) REVERT: Q 402 MET cc_start: 0.8429 (ttp) cc_final: 0.8219 (ttp) REVERT: Q 436 MET cc_start: 0.7543 (ttt) cc_final: 0.7208 (ttm) REVERT: Q 476 GLU cc_start: 0.8440 (mm-30) cc_final: 0.8205 (mm-30) outliers start: 43 outliers final: 17 residues processed: 480 average time/residue: 2.8981 time to fit residues: 1557.7686 Evaluate side-chains 459 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 438 time to evaluate : 2.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 243 CYS Chi-restraints excluded: chain F residue 363 SER Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 389 ARG Chi-restraints excluded: chain F residue 503 ASP Chi-restraints excluded: chain O residue 136 ASP Chi-restraints excluded: chain O residue 243 CYS Chi-restraints excluded: chain O residue 291 ARG Chi-restraints excluded: chain O residue 367 VAL Chi-restraints excluded: chain O residue 389 ARG Chi-restraints excluded: chain O residue 502 GLN Chi-restraints excluded: chain O residue 503 ASP Chi-restraints excluded: chain P residue 243 CYS Chi-restraints excluded: chain P residue 367 VAL Chi-restraints excluded: chain P residue 389 ARG Chi-restraints excluded: chain P residue 502 GLN Chi-restraints excluded: chain P residue 503 ASP Chi-restraints excluded: chain Q residue 243 CYS Chi-restraints excluded: chain Q residue 367 VAL Chi-restraints excluded: chain Q residue 389 ARG Chi-restraints excluded: chain Q residue 503 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 194 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 chunk 21 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 197 optimal weight: 3.9990 chunk 208 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 186 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- 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 260 GLN F 365 HIS O 87 ASN O 240 GLN O 260 GLN O 365 HIS ** P 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 240 GLN P 260 GLN ** P 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 365 HIS Q 87 ASN Q 240 GLN Q 260 GLN Q 365 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.4524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 17916 Z= 0.345 Angle : 0.627 10.981 24292 Z= 0.324 Chirality : 0.071 1.449 2680 Planarity : 0.006 0.055 3100 Dihedral : 7.468 48.274 2520 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.91 % Allowed : 18.40 % Favored : 78.69 % 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: -0.43 (0.18), residues: 2144 helix: -0.32 (0.16), residues: 924 sheet: -0.05 (0.25), residues: 380 loop : -0.09 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP Q 387 HIS 0.008 0.002 HIS O 116 PHE 0.016 0.002 PHE Q 163 TYR 0.015 0.002 TYR P 292 ARG 0.005 0.001 ARG F 252 *********************** 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 471 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 415 time to evaluate : 2.634 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: F 288 MET cc_start: 0.7843 (mtp) cc_final: 0.7626 (mtm) REVERT: F 322 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7482 (mt-10) REVERT: F 389 ARG cc_start: 0.7175 (OUTLIER) cc_final: 0.6897 (mtm110) REVERT: F 481 ARG cc_start: 0.7692 (mtt-85) cc_final: 0.7428 (mtt-85) REVERT: O 291 ARG cc_start: 0.7775 (OUTLIER) cc_final: 0.7482 (mtp85) REVERT: O 294 ARG cc_start: 0.6998 (mtm110) cc_final: 0.6658 (ptp-170) REVERT: O 322 GLU cc_start: 0.7748 (mt-10) cc_final: 0.7451 (mt-10) REVERT: O 389 ARG cc_start: 0.7185 (OUTLIER) cc_final: 0.6831 (mtm110) REVERT: O 481 ARG cc_start: 0.7688 (mtt-85) cc_final: 0.7427 (mtt-85) REVERT: O 502 GLN cc_start: 0.7981 (OUTLIER) cc_final: 0.7568 (mt0) REVERT: P 294 ARG cc_start: 0.6827 (mtp180) cc_final: 0.6551 (ptp-170) REVERT: P 322 GLU cc_start: 0.7684 (mt-10) cc_final: 0.7357 (mt-10) REVERT: P 356 GLU cc_start: 0.7329 (tp30) cc_final: 0.6991 (mm-30) REVERT: P 389 ARG cc_start: 0.7160 (OUTLIER) cc_final: 0.6765 (mtm110) REVERT: P 481 ARG cc_start: 0.7725 (mtt-85) cc_final: 0.7418 (mtt-85) REVERT: Q 288 MET cc_start: 0.7767 (mtp) cc_final: 0.7520 (mtm) REVERT: Q 294 ARG cc_start: 0.6952 (mtp180) cc_final: 0.6702 (ptp-170) REVERT: Q 389 ARG cc_start: 0.7091 (OUTLIER) cc_final: 0.6742 (mtm110) REVERT: Q 391 GLN cc_start: 0.7321 (mp10) cc_final: 0.6954 (mp10) outliers start: 56 outliers final: 27 residues processed: 445 average time/residue: 2.9161 time to fit residues: 1454.0707 Evaluate side-chains 412 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 379 time to evaluate : 2.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 243 CYS Chi-restraints excluded: chain F residue 286 LYS Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain F residue 363 SER Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 389 ARG Chi-restraints excluded: chain F residue 503 ASP Chi-restraints excluded: chain F residue 547 SER Chi-restraints excluded: chain O residue 243 CYS Chi-restraints excluded: chain O residue 291 ARG Chi-restraints excluded: chain O residue 363 SER Chi-restraints excluded: chain O residue 367 VAL Chi-restraints excluded: chain O residue 389 ARG Chi-restraints excluded: chain O residue 502 GLN Chi-restraints excluded: chain O residue 503 ASP Chi-restraints excluded: chain O residue 547 SER Chi-restraints excluded: chain P residue 136 ASP Chi-restraints excluded: chain P residue 243 CYS Chi-restraints excluded: chain P residue 312 ASP Chi-restraints excluded: chain P residue 326 LEU Chi-restraints excluded: chain P residue 363 SER Chi-restraints excluded: chain P residue 367 VAL Chi-restraints excluded: chain P residue 389 ARG Chi-restraints excluded: chain P residue 458 GLN Chi-restraints excluded: chain P residue 502 GLN Chi-restraints excluded: chain P residue 503 ASP Chi-restraints excluded: chain P residue 547 SER Chi-restraints excluded: chain Q residue 243 CYS Chi-restraints excluded: chain Q residue 363 SER Chi-restraints excluded: chain Q residue 367 VAL Chi-restraints excluded: chain Q residue 389 ARG Chi-restraints excluded: chain Q residue 503 ASP Chi-restraints excluded: chain Q residue 547 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 173 optimal weight: 0.3980 chunk 118 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 155 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 178 optimal weight: 0.6980 chunk 144 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 106 optimal weight: 0.4980 chunk 187 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 365 HIS O 220 ASN O 240 GLN O 365 HIS P 220 ASN P 240 GLN ** P 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 365 HIS 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: 0.7713 moved from start: 0.4675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17916 Z= 0.190 Angle : 0.564 11.191 24292 Z= 0.289 Chirality : 0.070 1.467 2680 Planarity : 0.005 0.076 3100 Dihedral : 7.037 47.183 2520 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.70 % Allowed : 19.13 % Favored : 78.17 % 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: -0.05 (0.18), residues: 2144 helix: -0.02 (0.17), residues: 924 sheet: 0.07 (0.26), residues: 372 loop : 0.17 (0.22), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP Q 387 HIS 0.007 0.001 HIS F 235 PHE 0.010 0.001 PHE O 163 TYR 0.014 0.001 TYR F 42 ARG 0.007 0.001 ARG Q 353 *********************** 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 463 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 411 time to evaluate : 2.737 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: F 288 MET cc_start: 0.7757 (mtp) cc_final: 0.7533 (mtm) REVERT: F 322 GLU cc_start: 0.7665 (mt-10) cc_final: 0.7361 (mt-10) REVERT: F 411 ARG cc_start: 0.7445 (OUTLIER) cc_final: 0.6552 (mtt-85) REVERT: F 481 ARG cc_start: 0.7701 (mtt-85) cc_final: 0.7379 (mtt-85) REVERT: O 288 MET cc_start: 0.7777 (mtp) cc_final: 0.7576 (mtm) REVERT: O 294 ARG cc_start: 0.7006 (mtm110) cc_final: 0.6664 (ptp-170) REVERT: O 322 GLU cc_start: 0.7699 (mt-10) cc_final: 0.7385 (mt-10) REVERT: O 391 GLN cc_start: 0.7311 (mm110) cc_final: 0.6980 (mp-120) REVERT: O 481 ARG cc_start: 0.7677 (mtt-85) cc_final: 0.7357 (mtt-85) REVERT: O 502 GLN cc_start: 0.7986 (OUTLIER) cc_final: 0.7568 (mt0) REVERT: P 294 ARG cc_start: 0.6782 (mtp180) cc_final: 0.6523 (ptp-170) REVERT: P 322 GLU cc_start: 0.7628 (mt-10) cc_final: 0.7265 (mt-10) REVERT: P 356 GLU cc_start: 0.7286 (tp30) cc_final: 0.6953 (mm-30) REVERT: Q 288 MET cc_start: 0.7715 (mtp) cc_final: 0.7471 (mtm) REVERT: Q 353 ARG cc_start: 0.6818 (ttm-80) cc_final: 0.6617 (mtm-85) REVERT: Q 411 ARG cc_start: 0.7441 (OUTLIER) cc_final: 0.6609 (mtt-85) outliers start: 52 outliers final: 23 residues processed: 432 average time/residue: 2.8734 time to fit residues: 1388.9035 Evaluate side-chains 428 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 402 time to evaluate : 2.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 243 CYS Chi-restraints excluded: chain F residue 291 ARG Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain F residue 332 LEU Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 411 ARG Chi-restraints excluded: chain F residue 503 ASP Chi-restraints excluded: chain O residue 138 LEU Chi-restraints excluded: chain O residue 243 CYS Chi-restraints excluded: chain O residue 291 ARG Chi-restraints excluded: chain O residue 367 VAL Chi-restraints excluded: chain O residue 458 GLN Chi-restraints excluded: chain O residue 502 GLN Chi-restraints excluded: chain O residue 503 ASP Chi-restraints excluded: chain P residue 136 ASP Chi-restraints excluded: chain P residue 243 CYS Chi-restraints excluded: chain P residue 286 LYS Chi-restraints excluded: chain P residue 326 LEU Chi-restraints excluded: chain P residue 367 VAL Chi-restraints excluded: chain P residue 502 GLN Chi-restraints excluded: chain P residue 503 ASP Chi-restraints excluded: chain Q residue 243 CYS Chi-restraints excluded: chain Q residue 367 VAL Chi-restraints excluded: chain Q residue 411 ARG Chi-restraints excluded: chain Q residue 503 ASP Chi-restraints excluded: chain Q residue 547 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 70 optimal weight: 0.8980 chunk 188 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 122 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 208 optimal weight: 3.9990 chunk 173 optimal weight: 0.9980 chunk 96 optimal weight: 0.2980 chunk 17 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 365 HIS O 220 ASN ** O 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 365 HIS P 220 ASN P 240 GLN ** P 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 365 HIS Q 220 ASN Q 365 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.4849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17916 Z= 0.218 Angle : 0.557 11.171 24292 Z= 0.285 Chirality : 0.070 1.472 2680 Planarity : 0.005 0.061 3100 Dihedral : 6.942 47.580 2520 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.39 % Allowed : 20.22 % Favored : 77.39 % 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: 0.09 (0.18), residues: 2144 helix: 0.10 (0.17), residues: 924 sheet: 0.09 (0.26), residues: 372 loop : 0.27 (0.22), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP Q 387 HIS 0.007 0.001 HIS P 235 PHE 0.017 0.001 PHE F 482 TYR 0.013 0.001 TYR F 42 ARG 0.009 0.001 ARG P 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 444 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 398 time to evaluate : 2.165 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: F 220 ASN cc_start: 0.8209 (OUTLIER) cc_final: 0.7542 (p0) REVERT: F 288 MET cc_start: 0.7738 (mtp) cc_final: 0.7505 (mtm) REVERT: F 291 ARG cc_start: 0.7902 (OUTLIER) cc_final: 0.7701 (mtp85) REVERT: F 322 GLU cc_start: 0.7602 (mt-10) cc_final: 0.7357 (mt-10) REVERT: F 389 ARG cc_start: 0.7438 (OUTLIER) cc_final: 0.7051 (ttp-110) REVERT: F 411 ARG cc_start: 0.7429 (OUTLIER) cc_final: 0.6530 (mtt-85) REVERT: O 288 MET cc_start: 0.7802 (mtp) cc_final: 0.7593 (mtm) REVERT: O 294 ARG cc_start: 0.7042 (mtm110) cc_final: 0.6674 (ptp-170) REVERT: O 322 GLU cc_start: 0.7650 (mt-10) cc_final: 0.7376 (mt-10) REVERT: O 391 GLN cc_start: 0.7271 (mm110) cc_final: 0.6891 (mp-120) REVERT: O 502 GLN cc_start: 0.7992 (OUTLIER) cc_final: 0.7589 (mt0) REVERT: P 294 ARG cc_start: 0.6797 (mtp180) cc_final: 0.6515 (ptp-170) REVERT: P 356 GLU cc_start: 0.7332 (tp30) cc_final: 0.7015 (mm-30) REVERT: Q 288 MET cc_start: 0.7721 (mtp) cc_final: 0.7479 (mtm) REVERT: Q 389 ARG cc_start: 0.7336 (OUTLIER) cc_final: 0.7024 (ttp-110) REVERT: Q 411 ARG cc_start: 0.7449 (OUTLIER) cc_final: 0.6608 (mtt-85) outliers start: 46 outliers final: 24 residues processed: 416 average time/residue: 2.8410 time to fit residues: 1327.7088 Evaluate side-chains 421 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 390 time to evaluate : 2.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 220 ASN Chi-restraints excluded: chain F residue 243 CYS Chi-restraints excluded: chain F residue 286 LYS Chi-restraints excluded: chain F residue 291 ARG Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain F residue 332 LEU Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 389 ARG Chi-restraints excluded: chain F residue 411 ARG Chi-restraints excluded: chain F residue 547 SER Chi-restraints excluded: chain O residue 138 LEU Chi-restraints excluded: chain O residue 243 CYS Chi-restraints excluded: chain O residue 291 ARG Chi-restraints excluded: chain O residue 332 LEU Chi-restraints excluded: chain O residue 367 VAL Chi-restraints excluded: chain O residue 502 GLN Chi-restraints excluded: chain O residue 503 ASP Chi-restraints excluded: chain O residue 547 SER Chi-restraints excluded: chain P residue 243 CYS Chi-restraints excluded: chain P residue 326 LEU Chi-restraints excluded: chain P residue 363 SER Chi-restraints excluded: chain P residue 367 VAL Chi-restraints excluded: chain P residue 503 ASP Chi-restraints excluded: chain P residue 547 SER Chi-restraints excluded: chain Q residue 138 LEU Chi-restraints excluded: chain Q residue 243 CYS Chi-restraints excluded: chain Q residue 367 VAL Chi-restraints excluded: chain Q residue 389 ARG Chi-restraints excluded: chain Q residue 411 ARG Chi-restraints excluded: chain Q residue 503 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 201 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 119 optimal weight: 0.7980 chunk 152 optimal weight: 4.9990 chunk 118 optimal weight: 0.9980 chunk 175 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 208 optimal weight: 3.9990 chunk 130 optimal weight: 0.0970 chunk 126 optimal weight: 1.9990 chunk 96 optimal weight: 0.4980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 240 GLN 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 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 365 HIS Q 220 ASN Q 365 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.4897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17916 Z= 0.189 Angle : 0.549 11.201 24292 Z= 0.280 Chirality : 0.070 1.480 2680 Planarity : 0.005 0.054 3100 Dihedral : 6.796 47.882 2520 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.13 % Allowed : 20.63 % Favored : 77.23 % 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: 0.29 (0.18), residues: 2144 helix: 0.19 (0.17), residues: 924 sheet: 0.24 (0.26), residues: 364 loop : 0.44 (0.22), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP Q 387 HIS 0.007 0.001 HIS P 235 PHE 0.011 0.001 PHE P 163 TYR 0.013 0.001 TYR P 292 ARG 0.010 0.001 ARG O 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 437 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 396 time to evaluate : 2.770 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: F 288 MET cc_start: 0.7740 (mtp) cc_final: 0.7509 (mtm) REVERT: F 322 GLU cc_start: 0.7601 (mt-10) cc_final: 0.7342 (mt-10) REVERT: F 391 GLN cc_start: 0.7828 (mp10) cc_final: 0.7547 (mp10) REVERT: F 411 ARG cc_start: 0.7415 (OUTLIER) cc_final: 0.6515 (mtt-85) REVERT: O 288 MET cc_start: 0.7741 (mtp) cc_final: 0.7534 (mtm) REVERT: O 294 ARG cc_start: 0.7022 (mtm110) cc_final: 0.6650 (ptp-170) REVERT: O 322 GLU cc_start: 0.7617 (mt-10) cc_final: 0.7345 (mt-10) REVERT: O 391 GLN cc_start: 0.7271 (mm110) cc_final: 0.6880 (mp-120) REVERT: O 481 ARG cc_start: 0.7699 (mtt-85) cc_final: 0.7485 (mtp85) REVERT: O 502 GLN cc_start: 0.7994 (OUTLIER) cc_final: 0.7589 (mt0) REVERT: P 294 ARG cc_start: 0.6781 (mtp180) cc_final: 0.6496 (ptp-170) REVERT: P 356 GLU cc_start: 0.7314 (tp30) cc_final: 0.6967 (mm-30) REVERT: P 411 ARG cc_start: 0.7486 (OUTLIER) cc_final: 0.6574 (mtt-85) REVERT: Q 288 MET cc_start: 0.7709 (mtp) cc_final: 0.7454 (mtm) REVERT: Q 411 ARG cc_start: 0.7434 (OUTLIER) cc_final: 0.6573 (mtt-85) outliers start: 41 outliers final: 27 residues processed: 416 average time/residue: 2.9651 time to fit residues: 1379.7814 Evaluate side-chains 413 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 382 time to evaluate : 2.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 243 CYS Chi-restraints excluded: chain F residue 286 LYS Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain F residue 363 SER Chi-restraints excluded: chain F residue 411 ARG Chi-restraints excluded: chain F residue 547 SER Chi-restraints excluded: chain O residue 138 LEU Chi-restraints excluded: chain O residue 243 CYS Chi-restraints excluded: chain O residue 291 ARG Chi-restraints excluded: chain O residue 332 LEU Chi-restraints excluded: chain O residue 363 SER Chi-restraints excluded: chain O residue 502 GLN Chi-restraints excluded: chain O residue 503 ASP Chi-restraints excluded: chain O residue 547 SER Chi-restraints excluded: chain P residue 138 LEU Chi-restraints excluded: chain P residue 243 CYS Chi-restraints excluded: chain P residue 286 LYS Chi-restraints excluded: chain P residue 291 ARG Chi-restraints excluded: chain P residue 326 LEU Chi-restraints excluded: chain P residue 363 SER Chi-restraints excluded: chain P residue 411 ARG Chi-restraints excluded: chain P residue 503 ASP Chi-restraints excluded: chain P residue 547 SER Chi-restraints excluded: chain Q residue 138 LEU Chi-restraints excluded: chain Q residue 243 CYS Chi-restraints excluded: chain Q residue 332 LEU Chi-restraints excluded: chain Q residue 367 VAL Chi-restraints excluded: chain Q residue 389 ARG Chi-restraints excluded: chain Q residue 411 ARG Chi-restraints excluded: chain Q residue 503 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 128 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 141 optimal weight: 0.4980 chunk 102 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 163 optimal weight: 0.9980 chunk 189 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 240 GLN ** 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 O 461 ASN P 220 ASN ** P 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 365 HIS P 461 ASN Q 220 ASN Q 365 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.5002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17916 Z= 0.262 Angle : 0.567 11.198 24292 Z= 0.289 Chirality : 0.071 1.478 2680 Planarity : 0.005 0.058 3100 Dihedral : 6.825 49.900 2517 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.23 % Allowed : 20.95 % Favored : 76.82 % 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: 0.25 (0.18), residues: 2144 helix: 0.14 (0.17), residues: 920 sheet: 0.20 (0.26), residues: 364 loop : 0.46 (0.22), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP Q 387 HIS 0.006 0.001 HIS P 116 PHE 0.013 0.001 PHE Q 163 TYR 0.013 0.002 TYR P 292 ARG 0.009 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 428 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 385 time to evaluate : 3.268 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: F 288 MET cc_start: 0.7784 (mtp) cc_final: 0.7554 (mtm) REVERT: F 322 GLU cc_start: 0.7654 (mt-10) cc_final: 0.7395 (mt-10) REVERT: F 391 GLN cc_start: 0.7908 (mp10) cc_final: 0.7608 (mp10) REVERT: F 411 ARG cc_start: 0.7426 (OUTLIER) cc_final: 0.6534 (mtt-85) REVERT: F 502 GLN cc_start: 0.8183 (mm-40) cc_final: 0.7788 (mm-40) REVERT: O 288 MET cc_start: 0.7732 (mtp) cc_final: 0.7515 (mtm) REVERT: O 294 ARG cc_start: 0.7037 (mtm110) cc_final: 0.6640 (ptp-170) REVERT: O 322 GLU cc_start: 0.7631 (mt-10) cc_final: 0.7348 (mt-10) REVERT: O 391 GLN cc_start: 0.7390 (mm110) cc_final: 0.7061 (mp-120) REVERT: O 411 ARG cc_start: 0.7493 (OUTLIER) cc_final: 0.6553 (mtt-85) REVERT: O 514 LEU cc_start: 0.8353 (tp) cc_final: 0.8111 (tp) REVERT: P 294 ARG cc_start: 0.6803 (mtp180) cc_final: 0.6494 (ptp-170) REVERT: P 356 GLU cc_start: 0.7329 (tp30) cc_final: 0.6995 (mm-30) REVERT: P 411 ARG cc_start: 0.7503 (OUTLIER) cc_final: 0.6588 (mtt-85) REVERT: P 436 MET cc_start: 0.7697 (ttm) cc_final: 0.7324 (ttp) REVERT: Q 288 MET cc_start: 0.7733 (mtp) cc_final: 0.7488 (mtm) REVERT: Q 353 ARG cc_start: 0.6871 (ttm-80) cc_final: 0.6658 (mtm-85) REVERT: Q 411 ARG cc_start: 0.7424 (OUTLIER) cc_final: 0.6562 (mtt-85) REVERT: Q 481 ARG cc_start: 0.7855 (ptp-170) cc_final: 0.7526 (ptp-110) outliers start: 43 outliers final: 22 residues processed: 409 average time/residue: 3.0073 time to fit residues: 1375.0302 Evaluate side-chains 404 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 378 time to evaluate : 2.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 243 CYS Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain F residue 363 SER Chi-restraints excluded: chain F residue 411 ARG Chi-restraints excluded: chain O residue 138 LEU Chi-restraints excluded: chain O residue 243 CYS Chi-restraints excluded: chain O residue 291 ARG Chi-restraints excluded: chain O residue 363 SER Chi-restraints excluded: chain O residue 411 ARG Chi-restraints excluded: chain O residue 503 ASP Chi-restraints excluded: chain O residue 547 SER Chi-restraints excluded: chain P residue 138 LEU Chi-restraints excluded: chain P residue 243 CYS Chi-restraints excluded: chain P residue 326 LEU Chi-restraints excluded: chain P residue 363 SER Chi-restraints excluded: chain P residue 367 VAL Chi-restraints excluded: chain P residue 411 ARG Chi-restraints excluded: chain P residue 503 ASP Chi-restraints excluded: chain Q residue 138 LEU Chi-restraints excluded: chain Q residue 243 CYS Chi-restraints excluded: chain Q residue 316 SER Chi-restraints excluded: chain Q residue 363 SER Chi-restraints excluded: chain Q residue 411 ARG Chi-restraints excluded: chain Q residue 503 ASP Chi-restraints excluded: chain Q residue 547 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 199 optimal weight: 0.9980 chunk 181 optimal weight: 0.9990 chunk 194 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 152 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 chunk 175 optimal weight: 0.5980 chunk 183 optimal weight: 0.9990 chunk 193 optimal weight: 0.7980 chunk 127 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 240 GLN F 365 HIS F 461 ASN O 198 GLN O 220 ASN O 240 GLN O 365 HIS P 220 ASN P 240 GLN ** P 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 365 HIS P 458 GLN P 461 ASN Q 198 GLN Q 220 ASN Q 365 HIS Q 461 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.5080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17916 Z= 0.212 Angle : 0.561 11.247 24292 Z= 0.285 Chirality : 0.071 1.489 2680 Planarity : 0.005 0.063 3100 Dihedral : 6.730 53.678 2516 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.92 % Allowed : 21.41 % Favored : 76.66 % 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: 0.33 (0.18), residues: 2144 helix: 0.23 (0.17), residues: 920 sheet: 0.28 (0.27), residues: 352 loop : 0.44 (0.22), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP Q 387 HIS 0.006 0.001 HIS P 235 PHE 0.011 0.001 PHE P 163 TYR 0.012 0.001 TYR P 292 ARG 0.010 0.001 ARG O 481 *********************** REFINEMENT MACRO_CYCLE 9 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 426 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 389 time to evaluate : 2.656 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: F 288 MET cc_start: 0.7821 (mtp) cc_final: 0.7578 (mtm) REVERT: F 322 GLU cc_start: 0.7600 (mt-10) cc_final: 0.7340 (mt-10) REVERT: F 391 GLN cc_start: 0.7864 (mp10) cc_final: 0.7590 (mp10) REVERT: F 411 ARG cc_start: 0.7395 (OUTLIER) cc_final: 0.6498 (mtt-85) REVERT: F 502 GLN cc_start: 0.8168 (mm-40) cc_final: 0.7905 (mm-40) REVERT: O 288 MET cc_start: 0.7694 (mtp) cc_final: 0.7479 (mtm) REVERT: O 294 ARG cc_start: 0.7016 (mtm110) cc_final: 0.6640 (ptp-170) REVERT: O 322 GLU cc_start: 0.7566 (mt-10) cc_final: 0.7272 (mt-10) REVERT: O 391 GLN cc_start: 0.7402 (mm110) cc_final: 0.7067 (mp-120) REVERT: O 411 ARG cc_start: 0.7448 (OUTLIER) cc_final: 0.6523 (mtt-85) REVERT: O 514 LEU cc_start: 0.8341 (tp) cc_final: 0.8091 (tt) REVERT: P 294 ARG cc_start: 0.6821 (mtp180) cc_final: 0.6514 (ptp-170) REVERT: P 356 GLU cc_start: 0.7318 (tp30) cc_final: 0.6972 (mm-30) REVERT: P 411 ARG cc_start: 0.7491 (OUTLIER) cc_final: 0.6582 (mtt-85) REVERT: Q 235 HIS cc_start: 0.7927 (m90) cc_final: 0.7719 (m90) REVERT: Q 288 MET cc_start: 0.7722 (mtp) cc_final: 0.7473 (mtm) REVERT: Q 411 ARG cc_start: 0.7431 (OUTLIER) cc_final: 0.6556 (mtt-85) REVERT: Q 465 ARG cc_start: 0.7886 (ttt-90) cc_final: 0.7670 (ttt-90) outliers start: 37 outliers final: 22 residues processed: 410 average time/residue: 2.3930 time to fit residues: 1098.6219 Evaluate side-chains 406 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 380 time to evaluate : 1.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 243 CYS Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain F residue 363 SER Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 411 ARG Chi-restraints excluded: chain O residue 138 LEU Chi-restraints excluded: chain O residue 243 CYS Chi-restraints excluded: chain O residue 291 ARG Chi-restraints excluded: chain O residue 363 SER Chi-restraints excluded: chain O residue 367 VAL Chi-restraints excluded: chain O residue 411 ARG Chi-restraints excluded: chain O residue 503 ASP Chi-restraints excluded: chain P residue 138 LEU Chi-restraints excluded: chain P residue 243 CYS Chi-restraints excluded: chain P residue 316 SER Chi-restraints excluded: chain P residue 326 LEU Chi-restraints excluded: chain P residue 363 SER Chi-restraints excluded: chain P residue 367 VAL Chi-restraints excluded: chain P residue 411 ARG Chi-restraints excluded: chain P residue 503 ASP Chi-restraints excluded: chain Q residue 138 LEU Chi-restraints excluded: chain Q residue 243 CYS Chi-restraints excluded: chain Q residue 363 SER Chi-restraints excluded: chain Q residue 411 ARG Chi-restraints excluded: chain Q residue 503 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 205 optimal weight: 2.9990 chunk 125 optimal weight: 0.7980 chunk 97 optimal weight: 0.6980 chunk 142 optimal weight: 0.9990 chunk 215 optimal weight: 1.9990 chunk 198 optimal weight: 0.8980 chunk 171 optimal weight: 0.4980 chunk 17 optimal weight: 0.9980 chunk 132 optimal weight: 0.6980 chunk 105 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 365 HIS O 198 GLN O 220 ASN ** O 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 365 HIS P 220 ASN P 240 GLN ** P 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 365 HIS Q 198 GLN Q 220 ASN Q 365 HIS Q 461 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.5140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17916 Z= 0.201 Angle : 0.552 11.237 24292 Z= 0.280 Chirality : 0.071 1.491 2680 Planarity : 0.005 0.062 3100 Dihedral : 6.680 57.700 2516 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.56 % Allowed : 22.45 % 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: 0.37 (0.18), residues: 2144 helix: 0.26 (0.17), residues: 924 sheet: 0.30 (0.27), residues: 352 loop : 0.47 (0.22), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP Q 387 HIS 0.006 0.001 HIS P 235 PHE 0.011 0.001 PHE Q 482 TYR 0.012 0.001 TYR F 292 ARG 0.010 0.001 ARG P 481 ********************** REFINEMENT MACRO_CYCLE 10 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 420 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 390 time to evaluate : 3.141 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: F 288 MET cc_start: 0.7800 (mtp) cc_final: 0.7562 (mtm) REVERT: F 322 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7381 (mt-10) REVERT: F 391 GLN cc_start: 0.7920 (mp10) cc_final: 0.7643 (mp10) REVERT: F 411 ARG cc_start: 0.7402 (OUTLIER) cc_final: 0.6522 (mtt-85) REVERT: F 502 GLN cc_start: 0.8084 (mm-40) cc_final: 0.7844 (mm-40) REVERT: O 294 ARG cc_start: 0.6992 (mtm110) cc_final: 0.6610 (ptp-170) REVERT: O 322 GLU cc_start: 0.7563 (mt-10) cc_final: 0.7264 (mt-10) REVERT: O 411 ARG cc_start: 0.7439 (OUTLIER) cc_final: 0.6514 (mtt-85) REVERT: O 514 LEU cc_start: 0.8282 (tp) cc_final: 0.8038 (tt) REVERT: P 294 ARG cc_start: 0.6860 (mtp180) cc_final: 0.6527 (ptp-170) REVERT: P 356 GLU cc_start: 0.7360 (tp30) cc_final: 0.7012 (mm-30) REVERT: P 411 ARG cc_start: 0.7483 (OUTLIER) cc_final: 0.6569 (mtt-85) REVERT: Q 288 MET cc_start: 0.7707 (mtp) cc_final: 0.7463 (mtm) REVERT: Q 411 ARG cc_start: 0.7403 (OUTLIER) cc_final: 0.6521 (mtt-85) REVERT: Q 436 MET cc_start: 0.7454 (ttp) cc_final: 0.7235 (ttp) REVERT: Q 465 ARG cc_start: 0.7950 (ttt-90) cc_final: 0.7732 (ttt-90) outliers start: 30 outliers final: 21 residues processed: 406 average time/residue: 2.8836 time to fit residues: 1314.4919 Evaluate side-chains 404 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 379 time to evaluate : 2.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 243 CYS Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain F residue 363 SER Chi-restraints excluded: chain F residue 411 ARG Chi-restraints excluded: chain O residue 138 LEU Chi-restraints excluded: chain O residue 243 CYS Chi-restraints excluded: chain O residue 291 ARG Chi-restraints excluded: chain O residue 363 SER Chi-restraints excluded: chain O residue 367 VAL Chi-restraints excluded: chain O residue 411 ARG Chi-restraints excluded: chain O residue 503 ASP Chi-restraints excluded: chain P residue 138 LEU Chi-restraints excluded: chain P residue 243 CYS Chi-restraints excluded: chain P residue 326 LEU Chi-restraints excluded: chain P residue 363 SER Chi-restraints excluded: chain P residue 367 VAL Chi-restraints excluded: chain P residue 411 ARG Chi-restraints excluded: chain P residue 503 ASP Chi-restraints excluded: chain Q residue 138 LEU Chi-restraints excluded: chain Q residue 243 CYS Chi-restraints excluded: chain Q residue 363 SER Chi-restraints excluded: chain Q residue 367 VAL Chi-restraints excluded: chain Q residue 411 ARG Chi-restraints excluded: chain Q residue 461 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 158 optimal weight: 3.9990 chunk 25 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 chunk 171 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 176 optimal weight: 1.9990 chunk 21 optimal weight: 0.1980 chunk 31 optimal weight: 0.5980 chunk 150 optimal weight: 0.0570 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 365 HIS F 390 ASN O 198 GLN O 240 GLN P 240 GLN ** P 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 365 HIS Q 198 GLN Q 220 ASN Q 365 HIS Q 390 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.149991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.115516 restraints weight = 58825.900| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 1.94 r_work: 0.3064 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.5156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.266 17916 Z= 0.228 Angle : 0.732 59.199 24292 Z= 0.415 Chirality : 0.073 1.488 2680 Planarity : 0.005 0.062 3100 Dihedral : 6.672 57.723 2516 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.46 % Allowed : 23.13 % Favored : 75.42 % Cbeta Deviations : 0.05 % 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: 0.37 (0.18), residues: 2144 helix: 0.26 (0.17), residues: 924 sheet: 0.30 (0.27), residues: 352 loop : 0.47 (0.22), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP Q 387 HIS 0.006 0.001 HIS P 235 PHE 0.011 0.001 PHE P 163 TYR 0.011 0.001 TYR P 42 ARG 0.007 0.000 ARG P 481 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19251.80 seconds wall clock time: 340 minutes 17.81 seconds (20417.81 seconds total)