Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 23:05:54 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gz3_34389/04_2023/8gz3_34389.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gz3_34389/04_2023/8gz3_34389.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gz3_34389/04_2023/8gz3_34389.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gz3_34389/04_2023/8gz3_34389.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gz3_34389/04_2023/8gz3_34389.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gz3_34389/04_2023/8gz3_34389.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= -0.007 sd= 0.191 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: 6 Type Number sf(0) Gaussians Fe 2 7.16 5 P 3 5.49 5 S 33 5.16 5 C 5476 2.51 5 N 1485 2.21 5 O 1543 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 456": "OD1" <-> "OD2" Residue "B PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 8542 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1030 Classifications: {'peptide': 134} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 128} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 4187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4187 Classifications: {'peptide': 529} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 506} Chain breaks: 3 Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 125 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 6, 'ARG:plan': 4, 'ASN:plan1': 5, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 80 Chain: "L" Number of atoms: 1055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1055 Classifications: {'peptide': 211} Incomplete info: {'truncation_to_alanine': 211} Link IDs: {'CIS': 1, 'TRANS': 209} Unresolved non-hydrogen bonds: 422 Unresolved non-hydrogen angles: 633 Unresolved non-hydrogen dihedrals: 211 Planarities with less than four sites: {'UNK:plan-1': 211} Unresolved non-hydrogen planarities: 211 Chain: "H" Number of atoms: 1070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1070 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 214} Link IDs: {'TRANS': 213} Chain breaks: 1 Unresolved non-hydrogen bonds: 428 Unresolved non-hydrogen angles: 642 Unresolved non-hydrogen dihedrals: 214 Planarities with less than four sites: {'UNK:plan-1': 214} Unresolved non-hydrogen planarities: 214 Chain: "N" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 945 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 3, 'TRANS': 122} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 216 Unusual residues: {'FAD': 1, 'HEM': 2, 'LBN': 1, 'NAG': 2} Classifications: {'undetermined': 6, 'water': 1} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 5.34, per 1000 atoms: 0.63 Number of scatterers: 8542 At special positions: 0 Unit cell: (72.8344, 80.2234, 184.725, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 2 26.01 S 33 16.00 P 3 15.00 O 1543 8.00 N 1485 7.00 C 5476 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 244 " - pdb=" SG CYS B 257 " distance=2.04 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.00 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=2, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " NAG-ASN " NAG B 604 " - " ASN B 132 " " NAG B 605 " - " ASN B 240 " " NAG C 1 " - " ASN B 149 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.89 Conformation dependent library (CDL) restraints added in 1.1 seconds 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2304 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 16 sheets defined 58.6% alpha, 40.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 5 through 31 removed outlier: 4.223A pdb=" N TRP A 9 " --> pdb=" O GLU A 5 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA A 16 " --> pdb=" O GLU A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 54 removed outlier: 4.212A pdb=" N GLY A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 80 removed outlier: 4.329A pdb=" N MET A 73 " --> pdb=" O GLY A 69 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL A 76 " --> pdb=" O TYR A 72 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N PHE A 80 " --> pdb=" O VAL A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 86 removed outlier: 3.652A pdb=" N ARG A 85 " --> pdb=" O GLY A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 99 Processing helix chain 'A' and resid 100 through 103 removed outlier: 3.705A pdb=" N PHE A 103 " --> pdb=" O PRO A 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 100 through 103' Processing helix chain 'A' and resid 104 through 128 removed outlier: 4.130A pdb=" N LEU A 109 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N GLY A 110 " --> pdb=" O ALA A 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 33 removed outlier: 3.519A pdb=" N TYR B 33 " --> pdb=" O TYR B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 40 removed outlier: 3.688A pdb=" N PHE B 39 " --> pdb=" O PRO B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 46 Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 50 through 69 Proline residue: B 56 - end of helix removed outlier: 3.562A pdb=" N MET B 65 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LEU B 68 " --> pdb=" O CYS B 64 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEU B 69 " --> pdb=" O MET B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 83 removed outlier: 3.723A pdb=" N SER B 82 " --> pdb=" O PHE B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 95 removed outlier: 3.895A pdb=" N GLN B 93 " --> pdb=" O ARG B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 131 removed outlier: 3.628A pdb=" N LYS B 102 " --> pdb=" O LEU B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 143 Processing helix chain 'B' and resid 163 through 173 Processing helix chain 'B' and resid 173 through 192 removed outlier: 3.848A pdb=" N ILE B 189 " --> pdb=" O CYS B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 201 Processing helix chain 'B' and resid 201 through 209 Processing helix chain 'B' and resid 211 through 221 removed outlier: 3.525A pdb=" N ILE B 221 " --> pdb=" O ILE B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 239 Processing helix chain 'B' and resid 240 through 245 Processing helix chain 'B' and resid 246 through 251 removed outlier: 5.159A pdb=" N SER B 249 " --> pdb=" O GLN B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 293 removed outlier: 3.630A pdb=" N TRP B 272 " --> pdb=" O MET B 268 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N GLY B 275 " --> pdb=" O LYS B 271 " (cutoff:3.500A) Proline residue: B 276 - end of helix Processing helix chain 'B' and resid 359 through 370 Processing helix chain 'B' and resid 395 through 400 Processing helix chain 'B' and resid 413 through 430 removed outlier: 3.757A pdb=" N ALA B 417 " --> pdb=" O VAL B 413 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N SER B 418 " --> pdb=" O THR B 414 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE B 419 " --> pdb=" O PRO B 415 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TRP B 424 " --> pdb=" O LEU B 420 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR B 425 " --> pdb=" O LYS B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 468 removed outlier: 3.634A pdb=" N ALA B 455 " --> pdb=" O PHE B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 527 removed outlier: 3.760A pdb=" N LYS B 521 " --> pdb=" O ASP B 517 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 554 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.752A pdb=" N UNK L 83 " --> pdb=" O UNK L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 127 removed outlier: 3.594A pdb=" N UNK L 127 " --> pdb=" O UNK L 123 " (cutoff:3.500A) Processing helix chain 'L' and resid 182 through 189 removed outlier: 4.033A pdb=" N UNK L 189 " --> pdb=" O UNK L 185 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 90 Processing helix chain 'H' and resid 191 through 197 removed outlier: 4.492A pdb=" N UNK H 195 " --> pdb=" O UNK H 191 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N UNK H 196 " --> pdb=" O UNK H 192 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.623A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'N' and resid 106 through 111 Processing sheet with id=AA1, first strand: chain 'B' and resid 229 through 231 Processing sheet with id=AA2, first strand: chain 'B' and resid 296 through 303 removed outlier: 5.420A pdb=" N ILE B 297 " --> pdb=" O LYS B 313 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N LYS B 313 " --> pdb=" O ILE B 297 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR B 307 " --> pdb=" O HIS B 303 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 338 through 341 Processing sheet with id=AA4, first strand: chain 'B' and resid 509 through 511 removed outlier: 6.176A pdb=" N ILE B 439 " --> pdb=" O SER B 475 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N ASN B 477 " --> pdb=" O ILE B 439 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N PHE B 441 " --> pdb=" O ASN B 477 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N TYR B 479 " --> pdb=" O PHE B 441 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N TRP B 443 " --> pdb=" O TYR B 479 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N VAL B 403 " --> pdb=" O GLY B 533 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N PHE B 535 " --> pdb=" O VAL B 403 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 509 through 511 removed outlier: 6.176A pdb=" N ILE B 439 " --> pdb=" O SER B 475 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N ASN B 477 " --> pdb=" O ILE B 439 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N PHE B 441 " --> pdb=" O ASN B 477 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N TYR B 479 " --> pdb=" O PHE B 441 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N TRP B 443 " --> pdb=" O TYR B 479 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.550A pdb=" N UNK L 35 " --> pdb=" O UNK L 47 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N UNK L 37 " --> pdb=" O UNK L 45 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 114 through 118 removed outlier: 5.185A pdb=" N UNK L 131 " --> pdb=" O UNK L 181 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N UNK L 181 " --> pdb=" O UNK L 131 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N UNK L 133 " --> pdb=" O UNK L 179 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N UNK L 179 " --> pdb=" O UNK L 133 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N UNK L 135 " --> pdb=" O UNK L 177 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N UNK L 177 " --> pdb=" O UNK L 135 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N UNK L 137 " --> pdb=" O UNK L 175 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N UNK L 175 " --> pdb=" O UNK L 137 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N UNK L 159 " --> pdb=" O SER N 101 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 153 through 155 removed outlier: 4.306A pdb=" N UNK L 148 " --> pdb=" O UNK L 155 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N UNK L 198 " --> pdb=" O UNK L 203 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N UNK L 203 " --> pdb=" O UNK L 198 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 4 through 8 Processing sheet with id=AB2, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.602A pdb=" N UNK H 50 " --> pdb=" O UNK H 37 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N UNK H 59 " --> pdb=" O UNK H 51 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 45 through 47 removed outlier: 3.594A pdb=" N UNK H 45 " --> pdb=" O UNK H 41 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N UNK H 108 " --> pdb=" O UNK H 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 126 through 130 removed outlier: 3.677A pdb=" N UNK H 150 " --> pdb=" O UNK H 181 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N UNK H 181 " --> pdb=" O UNK H 150 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N UNK H 180 " --> pdb=" O UNK H 176 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N UNK H 176 " --> pdb=" O UNK H 180 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N UNK H 182 " --> pdb=" O UNK H 174 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N UNK H 174 " --> pdb=" O UNK H 182 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N UNK H 184 " --> pdb=" O UNK H 172 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 156 through 160 Processing sheet with id=AB6, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB7, first strand: chain 'N' and resid 11 through 12 removed outlier: 3.724A pdb=" N ALA N 33 " --> pdb=" O THR N 99 " (cutoff:3.500A) 472 hydrogen bonds defined for protein. 1311 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: 3.01 Time building geometry restraints manager: 4.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.37: 3058 1.37 - 1.56: 5603 1.56 - 1.75: 8 1.75 - 1.93: 48 1.93 - 2.12: 6 Bond restraints: 8723 Sorted by residual: bond pdb=" CA TRP B 443 " pdb=" C TRP B 443 " ideal model delta sigma weight residual 1.523 1.459 0.063 1.23e-02 6.61e+03 2.65e+01 bond pdb=" CA LYS B 314 " pdb=" C LYS B 314 " ideal model delta sigma weight residual 1.520 1.459 0.061 1.20e-02 6.94e+03 2.62e+01 bond pdb=" CA SER B 333 " pdb=" C SER B 333 " ideal model delta sigma weight residual 1.520 1.465 0.054 1.12e-02 7.97e+03 2.37e+01 bond pdb=" C PRO B 339 " pdb=" O PRO B 339 " ideal model delta sigma weight residual 1.233 1.187 0.046 1.06e-02 8.90e+03 1.89e+01 bond pdb=" CA GLU B 309 " pdb=" C GLU B 309 " ideal model delta sigma weight residual 1.524 1.473 0.051 1.22e-02 6.72e+03 1.77e+01 ... (remaining 8718 not shown) Histogram of bond angle deviations from ideal: 86.62 - 104.75: 151 104.75 - 122.88: 11004 122.88 - 141.01: 810 141.01 - 159.14: 0 159.14 - 177.27: 4 Bond angle restraints: 11969 Sorted by residual: angle pdb=" N ASP B 360 " pdb=" CA ASP B 360 " pdb=" C ASP B 360 " ideal model delta sigma weight residual 111.07 122.65 -11.58 1.07e+00 8.73e-01 1.17e+02 angle pdb=" N PHE B 473 " pdb=" CA PHE B 473 " pdb=" C PHE B 473 " ideal model delta sigma weight residual 111.07 121.39 -10.32 1.07e+00 8.73e-01 9.31e+01 angle pdb=" N GLY B 560 " pdb=" CA GLY B 560 " pdb=" C GLY B 560 " ideal model delta sigma weight residual 111.93 122.35 -10.42 1.15e+00 7.56e-01 8.22e+01 angle pdb=" N GLU B 336 " pdb=" CA GLU B 336 " pdb=" C GLU B 336 " ideal model delta sigma weight residual 109.59 123.48 -13.89 1.61e+00 3.86e-01 7.45e+01 angle pdb=" N LEU B 211 " pdb=" CA LEU B 211 " pdb=" C LEU B 211 " ideal model delta sigma weight residual 113.20 103.52 9.68 1.21e+00 6.83e-01 6.40e+01 ... (remaining 11964 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.02: 4896 33.02 - 66.04: 66 66.04 - 99.06: 10 99.06 - 132.08: 3 132.08 - 165.09: 2 Dihedral angle restraints: 4977 sinusoidal: 1431 harmonic: 3546 Sorted by residual: dihedral pdb=" C2C HEM B 603 " pdb=" C3C HEM B 603 " pdb=" CAC HEM B 603 " pdb=" CBC HEM B 603 " ideal model delta sinusoidal sigma weight residual 0.00 -51.11 51.11 2 1.00e+01 1.00e-02 2.91e+01 dihedral pdb=" O5' FAD B 601 " pdb=" O3P FAD B 601 " pdb=" P FAD B 601 " pdb=" PA FAD B 601 " ideal model delta sinusoidal sigma weight residual 298.23 133.14 165.09 1 3.00e+01 1.11e-03 2.10e+01 dihedral pdb=" C LYS B 306 " pdb=" N LYS B 306 " pdb=" CA LYS B 306 " pdb=" CB LYS B 306 " ideal model delta harmonic sigma weight residual -122.60 -133.51 10.91 0 2.50e+00 1.60e-01 1.91e+01 ... (remaining 4974 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 1196 0.118 - 0.236: 171 0.236 - 0.355: 35 0.355 - 0.473: 15 0.473 - 0.591: 3 Chirality restraints: 1420 Sorted by residual: chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.30 -0.10 2.00e-02 2.50e+03 2.65e+01 chirality pdb=" C1 BMA C 3 " pdb=" O4 NAG C 2 " pdb=" C2 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.32 -0.08 2.00e-02 2.50e+03 1.74e+01 chirality pdb=" CA LYS B 306 " pdb=" N LYS B 306 " pdb=" C LYS B 306 " pdb=" CB LYS B 306 " both_signs ideal model delta sigma weight residual False 2.51 1.92 0.59 2.00e-01 2.50e+01 8.73e+00 ... (remaining 1417 not shown) Planarity restraints: 1509 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS B 119 " 0.023 2.00e-02 2.50e+03 4.56e-02 2.08e+01 pdb=" C HIS B 119 " -0.079 2.00e-02 2.50e+03 pdb=" O HIS B 119 " 0.029 2.00e-02 2.50e+03 pdb=" N LEU B 120 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY N 16 " 0.022 2.00e-02 2.50e+03 4.33e-02 1.88e+01 pdb=" C GLY N 16 " -0.075 2.00e-02 2.50e+03 pdb=" O GLY N 16 " 0.029 2.00e-02 2.50e+03 pdb=" N SER N 17 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA UNK L 84 " 0.021 2.00e-02 2.50e+03 4.23e-02 1.79e+01 pdb=" C UNK L 84 " -0.073 2.00e-02 2.50e+03 pdb=" O UNK L 84 " 0.028 2.00e-02 2.50e+03 pdb=" N UNK L 85 " 0.025 2.00e-02 2.50e+03 ... (remaining 1506 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 291 2.69 - 3.25: 8053 3.25 - 3.80: 13290 3.80 - 4.35: 16665 4.35 - 4.90: 28156 Nonbonded interactions: 66455 Sorted by model distance: nonbonded pdb=" NE2 HIS B 222 " pdb="FE HEM B 602 " model vdw 2.142 3.080 nonbonded pdb=" O GLY B 179 " pdb=" OG1 THR B 183 " model vdw 2.213 2.440 nonbonded pdb=" O TYR N 100 " pdb=" OH TYR N 105 " model vdw 2.281 2.440 nonbonded pdb=" O THR N 32 " pdb=" NH2 ARG N 72 " model vdw 2.313 2.520 nonbonded pdb=" O ALA A 101 " pdb=" OG1 THR A 107 " model vdw 2.316 2.440 ... (remaining 66450 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 'H' and resid 4 through 219) selection = chain 'L' } 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: 1.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 5.510 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 26.740 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.040 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: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 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 : 0.012 0.199 8723 Z= 0.752 Angle : 1.452 13.893 11969 Z= 0.816 Chirality : 0.098 0.591 1420 Planarity : 0.008 0.081 1506 Dihedral : 13.722 165.095 2667 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer Outliers : 1.74 % Cbeta Deviations : 0.26 % Peptide Plane: Cis-proline : 3.33 % 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: -0.20 (0.28), residues: 777 helix: 0.60 (0.25), residues: 377 sheet: -0.40 (0.44), residues: 123 loop : -0.88 (0.33), residues: 277 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 132 time to evaluate : 0.788 Fit side-chains outliers start: 11 outliers final: 5 residues processed: 141 average time/residue: 0.2308 time to fit residues: 43.3242 Evaluate side-chains 88 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 83 time to evaluate : 0.834 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 1 residues processed: 5 average time/residue: 0.0848 time to fit residues: 1.8249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 100 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 60 optimal weight: 8.9990 chunk 48 optimal weight: 0.9980 chunk 93 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 108 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.060 8723 Z= 0.248 Angle : 0.672 14.214 11969 Z= 0.314 Chirality : 0.038 0.174 1420 Planarity : 0.005 0.079 1506 Dihedral : 10.404 174.020 1330 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer Outliers : 2.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.40 (0.29), residues: 777 helix: 1.10 (0.25), residues: 379 sheet: -0.50 (0.44), residues: 128 loop : -0.38 (0.36), residues: 270 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 86 time to evaluate : 0.797 Fit side-chains outliers start: 14 outliers final: 7 residues processed: 95 average time/residue: 0.2276 time to fit residues: 29.5870 Evaluate side-chains 91 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 84 time to evaluate : 0.860 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1357 time to fit residues: 2.5663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 60 optimal weight: 0.2980 chunk 33 optimal weight: 0.9980 chunk 89 optimal weight: 7.9990 chunk 73 optimal weight: 8.9990 chunk 29 optimal weight: 0.9980 chunk 108 optimal weight: 0.0170 chunk 116 optimal weight: 0.9980 chunk 96 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 86 optimal weight: 10.0000 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 8723 Z= 0.162 Angle : 0.560 13.780 11969 Z= 0.258 Chirality : 0.035 0.147 1420 Planarity : 0.004 0.065 1506 Dihedral : 8.896 138.510 1330 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer Outliers : 1.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.73 (0.29), residues: 777 helix: 1.43 (0.26), residues: 378 sheet: -0.56 (0.41), residues: 139 loop : -0.16 (0.37), residues: 260 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 79 time to evaluate : 0.807 Fit side-chains outliers start: 12 outliers final: 3 residues processed: 87 average time/residue: 0.2631 time to fit residues: 30.1353 Evaluate side-chains 67 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 64 time to evaluate : 0.840 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0881 time to fit residues: 1.5302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 8.9990 chunk 81 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 51 optimal weight: 5.9990 chunk 72 optimal weight: 10.0000 chunk 108 optimal weight: 0.6980 chunk 115 optimal weight: 0.5980 chunk 102 optimal weight: 8.9990 chunk 30 optimal weight: 0.8980 chunk 95 optimal weight: 9.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 8723 Z= 0.224 Angle : 0.618 16.165 11969 Z= 0.277 Chirality : 0.037 0.149 1420 Planarity : 0.004 0.059 1506 Dihedral : 8.418 125.149 1330 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer Outliers : 1.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.74 (0.29), residues: 777 helix: 1.33 (0.26), residues: 380 sheet: -0.41 (0.43), residues: 128 loop : -0.09 (0.36), residues: 269 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 66 time to evaluate : 0.867 Fit side-chains outliers start: 11 outliers final: 5 residues processed: 72 average time/residue: 0.2359 time to fit residues: 23.4580 Evaluate side-chains 69 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 64 time to evaluate : 0.808 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1412 time to fit residues: 2.1461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 65 optimal weight: 7.9990 chunk 1 optimal weight: 0.6980 chunk 85 optimal weight: 10.0000 chunk 47 optimal weight: 2.9990 chunk 98 optimal weight: 10.0000 chunk 79 optimal weight: 9.9990 chunk 0 optimal weight: 3.9990 chunk 58 optimal weight: 9.9990 chunk 103 optimal weight: 9.9990 chunk 29 optimal weight: 4.9990 chunk 38 optimal weight: 0.4980 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 449 HIS ** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.066 8723 Z= 0.427 Angle : 0.774 18.370 11969 Z= 0.348 Chirality : 0.042 0.161 1420 Planarity : 0.005 0.051 1506 Dihedral : 8.503 117.983 1330 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer Outliers : 2.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.32 (0.29), residues: 777 helix: 0.81 (0.25), residues: 381 sheet: -0.58 (0.44), residues: 129 loop : -0.02 (0.38), residues: 267 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 65 time to evaluate : 0.773 Fit side-chains outliers start: 13 outliers final: 4 residues processed: 72 average time/residue: 0.2368 time to fit residues: 23.4705 Evaluate side-chains 64 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 60 time to evaluate : 0.823 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0882 time to fit residues: 1.6409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 103 optimal weight: 9.9990 chunk 22 optimal weight: 0.6980 chunk 67 optimal weight: 8.9990 chunk 28 optimal weight: 0.6980 chunk 115 optimal weight: 0.9990 chunk 95 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 9 optimal weight: 0.0470 chunk 38 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 111 optimal weight: 0.0980 overall best weight: 0.5080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 8723 Z= 0.142 Angle : 0.564 15.497 11969 Z= 0.250 Chirality : 0.034 0.155 1420 Planarity : 0.003 0.044 1506 Dihedral : 7.698 114.965 1330 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer Outliers : 1.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.30), residues: 777 helix: 1.43 (0.26), residues: 379 sheet: -0.30 (0.45), residues: 122 loop : 0.04 (0.37), residues: 276 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 69 time to evaluate : 0.884 Fit side-chains outliers start: 10 outliers final: 4 residues processed: 73 average time/residue: 0.2351 time to fit residues: 23.7385 Evaluate side-chains 68 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 64 time to evaluate : 0.882 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1750 time to fit residues: 2.1337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 12 optimal weight: 0.0870 chunk 65 optimal weight: 7.9990 chunk 84 optimal weight: 9.9990 chunk 96 optimal weight: 6.9990 chunk 64 optimal weight: 7.9990 chunk 114 optimal weight: 0.9980 chunk 71 optimal weight: 10.0000 chunk 69 optimal weight: 8.9990 chunk 52 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 chunk 45 optimal weight: 0.0980 overall best weight: 1.1960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 103 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 8723 Z= 0.224 Angle : 0.602 16.356 11969 Z= 0.268 Chirality : 0.036 0.143 1420 Planarity : 0.003 0.045 1506 Dihedral : 7.690 110.999 1330 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer Outliers : 0.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.88 (0.30), residues: 777 helix: 1.37 (0.26), residues: 380 sheet: -0.16 (0.45), residues: 122 loop : -0.02 (0.37), residues: 275 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 62 time to evaluate : 0.795 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 65 average time/residue: 0.2221 time to fit residues: 20.2709 Evaluate side-chains 63 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 60 time to evaluate : 0.796 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0810 time to fit residues: 1.4717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 68 optimal weight: 10.0000 chunk 34 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 72 optimal weight: 10.0000 chunk 78 optimal weight: 9.9990 chunk 56 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 90 optimal weight: 6.9990 chunk 104 optimal weight: 10.0000 chunk 109 optimal weight: 1.9990 chunk 100 optimal weight: 10.0000 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.3398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 8723 Z= 0.220 Angle : 0.600 16.259 11969 Z= 0.267 Chirality : 0.036 0.153 1420 Planarity : 0.003 0.045 1506 Dihedral : 7.645 106.812 1330 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer Outliers : 0.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.90 (0.30), residues: 777 helix: 1.38 (0.26), residues: 378 sheet: -0.05 (0.46), residues: 121 loop : -0.04 (0.37), residues: 278 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 60 time to evaluate : 0.858 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 61 average time/residue: 0.2320 time to fit residues: 19.8222 Evaluate side-chains 62 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 59 time to evaluate : 0.664 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1790 time to fit residues: 1.7409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 8.9990 chunk 109 optimal weight: 3.9990 chunk 64 optimal weight: 6.9990 chunk 46 optimal weight: 0.9980 chunk 83 optimal weight: 10.0000 chunk 32 optimal weight: 0.7980 chunk 96 optimal weight: 6.9990 chunk 101 optimal weight: 10.0000 chunk 70 optimal weight: 8.9990 chunk 113 optimal weight: 0.3980 chunk 68 optimal weight: 8.9990 overall best weight: 2.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.065 8723 Z= 0.433 Angle : 0.763 18.773 11969 Z= 0.341 Chirality : 0.042 0.150 1420 Planarity : 0.004 0.050 1506 Dihedral : 8.118 107.475 1330 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer Outliers : 0.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.42 (0.29), residues: 777 helix: 0.94 (0.26), residues: 378 sheet: -0.33 (0.45), residues: 122 loop : -0.18 (0.36), residues: 277 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 58 time to evaluate : 0.847 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 62 average time/residue: 0.2355 time to fit residues: 20.3397 Evaluate side-chains 61 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 58 time to evaluate : 0.874 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0872 time to fit residues: 1.6409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 53 optimal weight: 1.9990 chunk 78 optimal weight: 9.9990 chunk 118 optimal weight: 1.9990 chunk 109 optimal weight: 0.3980 chunk 94 optimal weight: 10.0000 chunk 9 optimal weight: 0.9990 chunk 72 optimal weight: 9.9990 chunk 57 optimal weight: 0.9990 chunk 74 optimal weight: 5.9990 chunk 100 optimal weight: 9.9990 chunk 28 optimal weight: 0.9990 overall best weight: 1.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.3515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 8723 Z= 0.216 Angle : 0.613 16.633 11969 Z= 0.272 Chirality : 0.036 0.155 1420 Planarity : 0.003 0.046 1506 Dihedral : 7.720 102.443 1330 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.74 (0.30), residues: 777 helix: 1.24 (0.26), residues: 378 sheet: -0.20 (0.46), residues: 122 loop : -0.06 (0.37), residues: 277 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.787 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.2481 time to fit residues: 20.3933 Evaluate side-chains 59 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.789 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 87 optimal weight: 9.9990 chunk 13 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 94 optimal weight: 10.0000 chunk 39 optimal weight: 0.5980 chunk 97 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 83 optimal weight: 10.0000 chunk 5 optimal weight: 0.7980 chunk 68 optimal weight: 9.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.138942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.126432 restraints weight = 10807.303| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.22 r_work: 0.3113 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.3545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 8723 Z= 0.224 Angle : 0.613 16.702 11969 Z= 0.272 Chirality : 0.036 0.152 1420 Planarity : 0.003 0.046 1506 Dihedral : 7.613 95.878 1330 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer Outliers : 0.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.81 (0.30), residues: 777 helix: 1.33 (0.26), residues: 378 sheet: -0.27 (0.44), residues: 132 loop : -0.01 (0.38), residues: 267 =============================================================================== Job complete usr+sys time: 1529.21 seconds wall clock time: 28 minutes 40.72 seconds (1720.72 seconds total)