Starting phenix.real_space_refine on Mon Mar 11 15:33:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gz3_34389/03_2024/8gz3_34389.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gz3_34389/03_2024/8gz3_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_34389/03_2024/8gz3_34389.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gz3_34389/03_2024/8gz3_34389.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gz3_34389/03_2024/8gz3_34389.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gz3_34389/03_2024/8gz3_34389.pdb" } resolution = 3.3 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= -0.007 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-dev-5265/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 dihedrals: 9 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: 10 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 5.47, per 1000 atoms: 0.64 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: 3.71 Conformation dependent library (CDL) restraints added in 1.2 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: 1.25 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: 3.11 Time building geometry restraints manager: 3.94 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: 5034 33.02 - 66.04: 70 66.04 - 99.06: 19 99.06 - 132.08: 7 132.08 - 165.09: 2 Dihedral angle restraints: 5132 sinusoidal: 1586 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 5129 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: 2.050 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: 0.010 Extract box with map and model: 5.090 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 26.990 Find NCS groups from input model: 0.310 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.620 ------------------------------------------------------------------------------- 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 : 15.002 165.095 2822 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 % Allowed : 8.53 % Favored : 89.73 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP B 361 HIS 0.007 0.002 HIS B 239 PHE 0.025 0.003 PHE B 62 TYR 0.020 0.003 TYR B 476 ARG 0.009 0.001 ARG B 31 *********************** 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 : 0.772 Fit side-chains REVERT: A 73 MET cc_start: 0.8197 (mmm) cc_final: 0.7861 (mmm) REVERT: B 92 ARG cc_start: 0.7449 (mtp180) cc_final: 0.7229 (mtt-85) REVERT: B 203 GLU cc_start: 0.8167 (tt0) cc_final: 0.7753 (pm20) REVERT: B 234 GLU cc_start: 0.7225 (tt0) cc_final: 0.6967 (mp0) REVERT: B 246 GLN cc_start: 0.8374 (mm110) cc_final: 0.8108 (mm-40) REVERT: B 465 MET cc_start: 0.9042 (mmt) cc_final: 0.8805 (mmt) REVERT: B 513 ARG cc_start: 0.7976 (mtt180) cc_final: 0.6964 (mtt-85) REVERT: B 537 CYS cc_start: 0.9172 (t) cc_final: 0.8887 (t) REVERT: N 65 LYS cc_start: 0.8711 (ttmm) cc_final: 0.8487 (tttm) REVERT: N 71 SER cc_start: 0.7953 (t) cc_final: 0.7361 (p) outliers start: 11 outliers final: 5 residues processed: 141 average time/residue: 0.2294 time to fit residues: 43.1535 Evaluate side-chains 94 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 89 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ASN Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 330 PRO Chi-restraints excluded: chain B residue 530 THR 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: 0.8980 chunk 30 optimal weight: 0.6980 chunk 60 optimal weight: 9.9990 chunk 48 optimal weight: 0.9990 chunk 93 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 108 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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: 0.7513 moved from start: 0.1866 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= 0.236 Angle : 0.652 13.589 11969 Z= 0.303 Chirality : 0.038 0.169 1420 Planarity : 0.005 0.075 1506 Dihedral : 12.047 177.868 1496 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Rotamer: Outliers : 2.53 % Allowed : 10.90 % Favored : 86.57 % 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: 0.34 (0.29), residues: 777 helix: 1.07 (0.25), residues: 380 sheet: -0.57 (0.44), residues: 128 loop : -0.44 (0.36), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 337 HIS 0.005 0.001 HIS B 115 PHE 0.021 0.002 PHE B 62 TYR 0.014 0.002 TYR N 104 ARG 0.003 0.001 ARG N 118 *********************** 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 108 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 92 time to evaluate : 0.803 Fit side-chains REVERT: A 8 MET cc_start: 0.8259 (mmt) cc_final: 0.7925 (mmt) REVERT: B 33 TYR cc_start: 0.8936 (m-80) cc_final: 0.8697 (m-80) REVERT: B 92 ARG cc_start: 0.7438 (mtp180) cc_final: 0.7230 (mtt-85) REVERT: B 103 MET cc_start: 0.8797 (mtp) cc_final: 0.8580 (mtm) REVERT: B 112 SER cc_start: 0.8928 (t) cc_final: 0.8710 (m) REVERT: B 203 GLU cc_start: 0.8223 (tt0) cc_final: 0.7830 (pm20) REVERT: B 246 GLN cc_start: 0.8440 (mm110) cc_final: 0.8104 (mm-40) REVERT: B 318 LYS cc_start: 0.8322 (mtpp) cc_final: 0.8009 (mtmm) REVERT: B 381 LYS cc_start: 0.7989 (mttt) cc_final: 0.7170 (tttm) REVERT: B 435 LYS cc_start: 0.8374 (mttt) cc_final: 0.7987 (mtmt) REVERT: B 508 LYS cc_start: 0.7625 (tmtt) cc_final: 0.6948 (tptp) REVERT: B 513 ARG cc_start: 0.7961 (mtt180) cc_final: 0.6557 (mtt180) REVERT: B 537 CYS cc_start: 0.8987 (t) cc_final: 0.8443 (t) REVERT: N 65 LYS cc_start: 0.8834 (ttmm) cc_final: 0.8573 (tttm) REVERT: N 71 SER cc_start: 0.8222 (t) cc_final: 0.7600 (p) REVERT: N 103 ASN cc_start: 0.8317 (t0) cc_final: 0.7855 (t0) outliers start: 16 outliers final: 8 residues processed: 102 average time/residue: 0.2363 time to fit residues: 32.4178 Evaluate side-chains 95 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 87 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 349 ASP Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 474 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 60 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 89 optimal weight: 7.9990 chunk 73 optimal weight: 8.9990 chunk 29 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 chunk 116 optimal weight: 0.9980 chunk 96 optimal weight: 6.9990 chunk 107 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 86 optimal weight: 9.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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: 0.7548 moved from start: 0.2436 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 : 0.616 15.488 11969 Z= 0.281 Chirality : 0.037 0.169 1420 Planarity : 0.004 0.065 1506 Dihedral : 10.041 142.397 1488 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 3.16 % Allowed : 11.69 % Favored : 85.15 % 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: 0.53 (0.29), residues: 777 helix: 1.26 (0.26), residues: 379 sheet: -0.67 (0.42), residues: 139 loop : -0.25 (0.37), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 337 HIS 0.006 0.001 HIS B 115 PHE 0.014 0.002 PHE B 366 TYR 0.012 0.001 TYR B 201 ARG 0.005 0.000 ARG B 287 *********************** 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 104 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 84 time to evaluate : 0.728 Fit side-chains REVERT: A 58 LYS cc_start: 0.7723 (tttm) cc_final: 0.7461 (ttmt) REVERT: B 33 TYR cc_start: 0.8950 (m-80) cc_final: 0.8745 (m-80) REVERT: B 203 GLU cc_start: 0.8279 (tt0) cc_final: 0.7871 (pm20) REVERT: B 246 GLN cc_start: 0.8458 (mm110) cc_final: 0.8099 (mm-40) REVERT: B 318 LYS cc_start: 0.8360 (mtpp) cc_final: 0.8088 (mtmm) REVERT: B 381 LYS cc_start: 0.7926 (mttt) cc_final: 0.7144 (tttm) REVERT: B 435 LYS cc_start: 0.8382 (mttt) cc_final: 0.8004 (mtmt) REVERT: B 459 GLN cc_start: 0.8225 (mt0) cc_final: 0.7586 (pp30) REVERT: B 508 LYS cc_start: 0.7553 (tmtt) cc_final: 0.6878 (tptp) REVERT: B 513 ARG cc_start: 0.7965 (mtt180) cc_final: 0.6915 (mtt180) REVERT: B 537 CYS cc_start: 0.9003 (t) cc_final: 0.8412 (t) REVERT: N 65 LYS cc_start: 0.8873 (ttmm) cc_final: 0.8585 (tttm) REVERT: N 71 SER cc_start: 0.8330 (t) cc_final: 0.8006 (m) REVERT: N 103 ASN cc_start: 0.8382 (t0) cc_final: 0.7837 (t0) outliers start: 20 outliers final: 12 residues processed: 96 average time/residue: 0.2668 time to fit residues: 33.7450 Evaluate side-chains 85 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 73 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 349 ASP Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 550 SER Chi-restraints excluded: chain B residue 552 SER Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 101 SER 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: 9.9990 chunk 56 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 72 optimal weight: 9.9990 chunk 108 optimal weight: 0.7980 chunk 115 optimal weight: 0.7980 chunk 102 optimal weight: 8.9990 chunk 30 optimal weight: 0.6980 chunk 95 optimal weight: 8.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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: 0.7554 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8723 Z= 0.201 Angle : 0.592 15.529 11969 Z= 0.264 Chirality : 0.036 0.168 1420 Planarity : 0.004 0.058 1506 Dihedral : 9.119 137.881 1488 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 3.63 % Allowed : 12.01 % Favored : 84.36 % 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: 0.70 (0.29), residues: 777 helix: 1.35 (0.26), residues: 379 sheet: -0.57 (0.43), residues: 128 loop : -0.13 (0.36), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 337 HIS 0.006 0.001 HIS B 115 PHE 0.015 0.001 PHE B 454 TYR 0.012 0.001 TYR B 201 ARG 0.012 0.001 ARG B 92 *********************** 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 99 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 76 time to evaluate : 0.890 Fit side-chains REVERT: A 58 LYS cc_start: 0.7787 (tttm) cc_final: 0.7489 (ttmt) REVERT: B 199 ARG cc_start: 0.6107 (tmt170) cc_final: 0.5493 (ttp80) REVERT: B 203 GLU cc_start: 0.8308 (tt0) cc_final: 0.7862 (pm20) REVERT: B 246 GLN cc_start: 0.8484 (mm110) cc_final: 0.8121 (mm-40) REVERT: B 318 LYS cc_start: 0.8357 (mtpp) cc_final: 0.8072 (mtmm) REVERT: B 381 LYS cc_start: 0.7826 (mttt) cc_final: 0.7033 (tttm) REVERT: B 435 LYS cc_start: 0.8406 (mttt) cc_final: 0.7963 (mtmm) REVERT: B 508 LYS cc_start: 0.7539 (tmtt) cc_final: 0.6857 (tptp) REVERT: B 513 ARG cc_start: 0.7920 (mtt180) cc_final: 0.6609 (mtt180) REVERT: B 537 CYS cc_start: 0.9009 (t) cc_final: 0.8440 (t) REVERT: N 65 LYS cc_start: 0.8865 (ttmm) cc_final: 0.8590 (tttm) REVERT: N 71 SER cc_start: 0.8351 (t) cc_final: 0.7830 (p) REVERT: N 103 ASN cc_start: 0.8304 (t0) cc_final: 0.7735 (t0) outliers start: 23 outliers final: 12 residues processed: 91 average time/residue: 0.2526 time to fit residues: 30.3171 Evaluate side-chains 86 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 74 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 349 ASP Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 550 SER Chi-restraints excluded: chain B residue 552 SER Chi-restraints excluded: chain N residue 101 SER 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: 4.9990 chunk 85 optimal weight: 10.0000 chunk 47 optimal weight: 0.9990 chunk 98 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 0 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 103 optimal weight: 9.9990 chunk 29 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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: 0.7644 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.090 8723 Z= 0.633 Angle : 0.908 19.333 11969 Z= 0.411 Chirality : 0.049 0.205 1420 Planarity : 0.006 0.057 1506 Dihedral : 9.695 118.496 1488 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 4.11 % Allowed : 13.90 % Favored : 81.99 % 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: -0.03 (0.29), residues: 777 helix: 0.55 (0.25), residues: 376 sheet: -0.91 (0.43), residues: 127 loop : -0.12 (0.37), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP B 337 HIS 0.011 0.003 HIS A 94 PHE 0.022 0.003 PHE B 563 TYR 0.023 0.003 TYR B 152 ARG 0.008 0.001 ARG B 73 *********************** 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 93 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 67 time to evaluate : 0.807 Fit side-chains REVERT: A 8 MET cc_start: 0.8445 (mmt) cc_final: 0.8106 (mmt) REVERT: A 58 LYS cc_start: 0.8032 (tttm) cc_final: 0.7564 (ttmt) REVERT: B 203 GLU cc_start: 0.8375 (tt0) cc_final: 0.7846 (pm20) REVERT: B 246 GLN cc_start: 0.8410 (mm110) cc_final: 0.8178 (mm-40) REVERT: B 318 LYS cc_start: 0.8471 (mtpp) cc_final: 0.8147 (mtmm) REVERT: B 397 ASP cc_start: 0.8376 (p0) cc_final: 0.7927 (p0) REVERT: B 513 ARG cc_start: 0.7933 (mtt180) cc_final: 0.6913 (mtt180) REVERT: N 65 LYS cc_start: 0.9007 (ttmm) cc_final: 0.8761 (tttt) REVERT: N 71 SER cc_start: 0.8462 (t) cc_final: 0.7939 (p) REVERT: N 106 SER cc_start: 0.8959 (t) cc_final: 0.8749 (p) outliers start: 26 outliers final: 19 residues processed: 85 average time/residue: 0.2159 time to fit residues: 25.2653 Evaluate side-chains 86 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 67 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ASN Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 349 ASP Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 449 HIS Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 550 SER Chi-restraints excluded: chain B residue 552 SER Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 48 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 103 optimal weight: 10.0000 chunk 22 optimal weight: 0.8980 chunk 67 optimal weight: 7.9990 chunk 28 optimal weight: 0.9990 chunk 115 optimal weight: 0.9990 chunk 95 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 9 optimal weight: 0.0570 chunk 38 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 111 optimal weight: 0.9980 overall best weight: 0.7498 ------------------------------------------------------------------------------- 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: 0.7577 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8723 Z= 0.174 Angle : 0.614 16.212 11969 Z= 0.272 Chirality : 0.036 0.170 1420 Planarity : 0.003 0.049 1506 Dihedral : 9.057 113.784 1488 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 2.69 % Allowed : 15.64 % Favored : 81.67 % 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: 0.49 (0.29), residues: 777 helix: 1.13 (0.26), residues: 377 sheet: -0.80 (0.43), residues: 121 loop : -0.07 (0.37), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 337 HIS 0.016 0.002 HIS B 449 PHE 0.014 0.001 PHE B 454 TYR 0.011 0.001 TYR B 280 ARG 0.003 0.000 ARG N 118 *********************** 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 96 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 79 time to evaluate : 0.795 Fit side-chains REVERT: A 8 MET cc_start: 0.8347 (mmt) cc_final: 0.8074 (mmt) REVERT: A 58 LYS cc_start: 0.7835 (tttm) cc_final: 0.7422 (ttmt) REVERT: B 199 ARG cc_start: 0.5995 (tmt170) cc_final: 0.5298 (ttp80) REVERT: B 203 GLU cc_start: 0.8231 (tt0) cc_final: 0.7854 (pm20) REVERT: B 246 GLN cc_start: 0.8441 (mm110) cc_final: 0.8189 (mm-40) REVERT: B 318 LYS cc_start: 0.8461 (mtpp) cc_final: 0.8133 (mtmm) REVERT: B 397 ASP cc_start: 0.8304 (p0) cc_final: 0.7730 (p0) REVERT: B 459 GLN cc_start: 0.8336 (mt0) cc_final: 0.7680 (pp30) REVERT: B 508 LYS cc_start: 0.7669 (tmtt) cc_final: 0.6900 (tptp) REVERT: B 513 ARG cc_start: 0.7889 (mtt180) cc_final: 0.6572 (mtt180) REVERT: B 537 CYS cc_start: 0.8993 (t) cc_final: 0.8390 (t) REVERT: N 65 LYS cc_start: 0.8913 (ttmm) cc_final: 0.8648 (tttt) REVERT: N 71 SER cc_start: 0.8356 (t) cc_final: 0.7842 (p) outliers start: 17 outliers final: 10 residues processed: 89 average time/residue: 0.2462 time to fit residues: 29.6216 Evaluate side-chains 83 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 73 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LYS Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 349 ASP Chi-restraints excluded: chain B residue 428 CYS Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 550 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 12 optimal weight: 3.9990 chunk 65 optimal weight: 8.9990 chunk 84 optimal weight: 9.9990 chunk 96 optimal weight: 6.9990 chunk 64 optimal weight: 7.9990 chunk 114 optimal weight: 0.8980 chunk 71 optimal weight: 9.9990 chunk 69 optimal weight: 8.9990 chunk 52 optimal weight: 0.0670 chunk 70 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 overall best weight: 2.9924 ------------------------------------------------------------------------------- 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: 0.7631 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.071 8723 Z= 0.470 Angle : 0.802 18.848 11969 Z= 0.358 Chirality : 0.044 0.177 1420 Planarity : 0.005 0.060 1506 Dihedral : 9.361 113.726 1488 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.00 % Allowed : 15.64 % Favored : 81.36 % 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: 0.06 (0.29), residues: 777 helix: 0.71 (0.26), residues: 379 sheet: -0.91 (0.43), residues: 121 loop : -0.25 (0.36), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 337 HIS 0.009 0.002 HIS B 115 PHE 0.017 0.003 PHE B 215 TYR 0.018 0.002 TYR B 152 ARG 0.007 0.001 ARG N 118 *********************** 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 86 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 67 time to evaluate : 0.788 Fit side-chains REVERT: A 58 LYS cc_start: 0.8018 (tttm) cc_final: 0.7593 (ttmt) REVERT: B 199 ARG cc_start: 0.5896 (tmt170) cc_final: 0.5110 (ttp80) REVERT: B 203 GLU cc_start: 0.8334 (tt0) cc_final: 0.7873 (pm20) REVERT: B 246 GLN cc_start: 0.8345 (mm110) cc_final: 0.8104 (mm-40) REVERT: B 318 LYS cc_start: 0.8482 (mtpp) cc_final: 0.8171 (mtmt) REVERT: B 397 ASP cc_start: 0.8343 (p0) cc_final: 0.7869 (p0) REVERT: B 459 GLN cc_start: 0.8325 (mt0) cc_final: 0.7705 (pp30) REVERT: B 513 ARG cc_start: 0.7902 (mtt180) cc_final: 0.6821 (mtt180) REVERT: B 537 CYS cc_start: 0.8970 (t) cc_final: 0.8356 (t) REVERT: N 65 LYS cc_start: 0.8990 (ttmm) cc_final: 0.8772 (tttt) REVERT: N 71 SER cc_start: 0.8455 (t) cc_final: 0.7907 (p) outliers start: 19 outliers final: 14 residues processed: 80 average time/residue: 0.2312 time to fit residues: 25.2490 Evaluate side-chains 80 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 66 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LYS Chi-restraints excluded: chain A residue 86 ASN Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 349 ASP Chi-restraints excluded: chain B residue 428 CYS Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 550 SER Chi-restraints excluded: chain N residue 28 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 68 optimal weight: 8.9990 chunk 34 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 72 optimal weight: 9.9990 chunk 78 optimal weight: 9.9990 chunk 56 optimal weight: 0.6980 chunk 10 optimal weight: 0.0470 chunk 90 optimal weight: 5.9990 chunk 104 optimal weight: 10.0000 chunk 109 optimal weight: 0.0970 chunk 100 optimal weight: 9.9990 overall best weight: 0.5276 ------------------------------------------------------------------------------- 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: 0.7567 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8723 Z= 0.152 Angle : 0.581 15.634 11969 Z= 0.258 Chirality : 0.035 0.158 1420 Planarity : 0.003 0.048 1506 Dihedral : 8.681 105.488 1488 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 2.05 % Allowed : 16.75 % Favored : 81.20 % 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: 0.56 (0.29), residues: 777 helix: 1.24 (0.26), residues: 377 sheet: -0.73 (0.44), residues: 121 loop : -0.14 (0.37), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 424 HIS 0.004 0.001 HIS B 115 PHE 0.013 0.001 PHE B 454 TYR 0.010 0.001 TYR B 280 ARG 0.007 0.000 ARG N 118 *********************** 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 78 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 65 time to evaluate : 0.834 Fit side-chains REVERT: A 8 MET cc_start: 0.8289 (mmt) cc_final: 0.7942 (mmt) REVERT: A 12 GLU cc_start: 0.8175 (mp0) cc_final: 0.7949 (mp0) REVERT: A 58 LYS cc_start: 0.7818 (tttm) cc_final: 0.7442 (ttmt) REVERT: B 199 ARG cc_start: 0.5865 (tmt170) cc_final: 0.5100 (ttp80) REVERT: B 203 GLU cc_start: 0.8229 (tt0) cc_final: 0.7827 (pm20) REVERT: B 246 GLN cc_start: 0.8403 (mm110) cc_final: 0.8165 (mm-40) REVERT: B 318 LYS cc_start: 0.8489 (mtpp) cc_final: 0.8075 (mtmt) REVERT: B 397 ASP cc_start: 0.8284 (p0) cc_final: 0.7709 (p0) REVERT: B 459 GLN cc_start: 0.8388 (mt0) cc_final: 0.7768 (pp30) REVERT: B 513 ARG cc_start: 0.7826 (mtt180) cc_final: 0.6599 (mtt180) REVERT: B 537 CYS cc_start: 0.8988 (t) cc_final: 0.8391 (t) REVERT: N 65 LYS cc_start: 0.8894 (ttmm) cc_final: 0.8617 (tttt) REVERT: N 71 SER cc_start: 0.8377 (t) cc_final: 0.7881 (p) outliers start: 13 outliers final: 10 residues processed: 73 average time/residue: 0.2417 time to fit residues: 23.8880 Evaluate side-chains 74 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 64 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LYS Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 349 ASP Chi-restraints excluded: chain B residue 428 CYS Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 550 SER Chi-restraints excluded: chain B residue 551 ILE 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: 9.9990 chunk 46 optimal weight: 0.9990 chunk 83 optimal weight: 10.0000 chunk 32 optimal weight: 3.9990 chunk 96 optimal weight: 6.9990 chunk 101 optimal weight: 10.0000 chunk 70 optimal weight: 8.9990 chunk 113 optimal weight: 0.0040 chunk 68 optimal weight: 9.9990 overall best weight: 3.2000 ------------------------------------------------------------------------------- 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: 0.7632 moved from start: 0.3439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.073 8723 Z= 0.484 Angle : 0.797 18.764 11969 Z= 0.356 Chirality : 0.044 0.165 1420 Planarity : 0.005 0.063 1506 Dihedral : 9.107 103.115 1488 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.90 % Allowed : 17.22 % Favored : 80.88 % 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: 0.09 (0.29), residues: 777 helix: 0.77 (0.26), residues: 379 sheet: -0.98 (0.43), residues: 121 loop : -0.24 (0.36), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 337 HIS 0.009 0.002 HIS B 115 PHE 0.017 0.003 PHE B 563 TYR 0.018 0.002 TYR B 152 ARG 0.008 0.001 ARG B 73 *********************** 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 78 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 66 time to evaluate : 1.140 Fit side-chains REVERT: A 58 LYS cc_start: 0.8051 (tttm) cc_final: 0.7616 (ttmt) REVERT: B 199 ARG cc_start: 0.5805 (tmt170) cc_final: 0.4973 (ttp80) REVERT: B 203 GLU cc_start: 0.8301 (tt0) cc_final: 0.7825 (pm20) REVERT: B 246 GLN cc_start: 0.8344 (mm110) cc_final: 0.8100 (mm-40) REVERT: B 318 LYS cc_start: 0.8500 (mtpp) cc_final: 0.8181 (mtmt) REVERT: B 397 ASP cc_start: 0.8380 (p0) cc_final: 0.7827 (p0) REVERT: B 401 TYR cc_start: 0.8367 (m-10) cc_final: 0.8162 (m-80) REVERT: B 459 GLN cc_start: 0.8311 (mt0) cc_final: 0.7651 (pp30) REVERT: B 513 ARG cc_start: 0.7885 (mtt180) cc_final: 0.6629 (mtt180) REVERT: B 537 CYS cc_start: 0.8984 (t) cc_final: 0.8362 (t) REVERT: N 65 LYS cc_start: 0.8988 (ttmm) cc_final: 0.8771 (tttt) REVERT: N 71 SER cc_start: 0.8481 (t) cc_final: 0.7939 (p) outliers start: 12 outliers final: 10 residues processed: 74 average time/residue: 0.2483 time to fit residues: 25.0798 Evaluate side-chains 74 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 64 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LYS Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 349 ASP Chi-restraints excluded: chain B residue 428 CYS Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 550 SER Chi-restraints excluded: chain N residue 28 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 53 optimal weight: 0.9990 chunk 78 optimal weight: 9.9990 chunk 118 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 chunk 94 optimal weight: 9.9990 chunk 9 optimal weight: 0.0020 chunk 72 optimal weight: 10.0000 chunk 57 optimal weight: 0.7980 chunk 74 optimal weight: 5.9990 chunk 100 optimal weight: 10.0000 chunk 28 optimal weight: 0.0980 overall best weight: 0.5792 ------------------------------------------------------------------------------- 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: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8723 Z= 0.148 Angle : 0.579 15.578 11969 Z= 0.256 Chirality : 0.035 0.152 1420 Planarity : 0.003 0.048 1506 Dihedral : 8.475 99.880 1488 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 1.58 % Allowed : 17.85 % Favored : 80.57 % 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: 0.56 (0.30), residues: 777 helix: 1.23 (0.26), residues: 377 sheet: -0.78 (0.44), residues: 122 loop : -0.10 (0.37), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 424 HIS 0.004 0.001 HIS B 115 PHE 0.012 0.001 PHE B 454 TYR 0.011 0.001 TYR B 280 ARG 0.007 0.000 ARG N 118 ********************** 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 74 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 64 time to evaluate : 0.840 Fit side-chains REVERT: A 8 MET cc_start: 0.8266 (mmt) cc_final: 0.8008 (mmt) REVERT: A 58 LYS cc_start: 0.7877 (tttm) cc_final: 0.7481 (ttmt) REVERT: B 199 ARG cc_start: 0.5963 (tmt170) cc_final: 0.5181 (ttp80) REVERT: B 203 GLU cc_start: 0.8229 (tt0) cc_final: 0.7827 (pm20) REVERT: B 246 GLN cc_start: 0.8380 (mm110) cc_final: 0.8148 (mm-40) REVERT: B 318 LYS cc_start: 0.8469 (mtpp) cc_final: 0.8204 (mtmt) REVERT: B 397 ASP cc_start: 0.8320 (p0) cc_final: 0.8096 (p0) REVERT: B 459 GLN cc_start: 0.8364 (mt0) cc_final: 0.7754 (pp30) REVERT: B 508 LYS cc_start: 0.7683 (tmtt) cc_final: 0.6891 (tptp) REVERT: B 537 CYS cc_start: 0.8986 (t) cc_final: 0.8393 (t) REVERT: N 65 LYS cc_start: 0.8886 (ttmm) cc_final: 0.8614 (tttt) REVERT: N 71 SER cc_start: 0.8408 (t) cc_final: 0.7882 (p) outliers start: 10 outliers final: 10 residues processed: 70 average time/residue: 0.2383 time to fit residues: 22.8039 Evaluate side-chains 74 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 64 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 349 ASP Chi-restraints excluded: chain B residue 428 CYS Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 550 SER Chi-restraints excluded: chain N residue 28 THR 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: 0.4980 chunk 26 optimal weight: 4.9990 chunk 94 optimal weight: 10.0000 chunk 39 optimal weight: 0.9980 chunk 97 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 83 optimal weight: 9.9990 chunk 5 optimal weight: 0.1980 chunk 68 optimal weight: 9.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 = 0.3442 r_free = 0.3442 target = 0.138298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.121868 restraints weight = 10853.421| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.67 r_work: 0.3031 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 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 0.042 8723 Z= 0.212 Angle : 0.601 16.199 11969 Z= 0.267 Chirality : 0.036 0.146 1420 Planarity : 0.003 0.049 1506 Dihedral : 8.367 96.249 1488 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.90 % Allowed : 17.54 % Favored : 80.57 % 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: 0.64 (0.30), residues: 777 helix: 1.29 (0.26), residues: 377 sheet: -0.71 (0.44), residues: 122 loop : -0.07 (0.37), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 337 HIS 0.005 0.001 HIS B 115 PHE 0.013 0.002 PHE B 215 TYR 0.011 0.001 TYR B 280 ARG 0.007 0.000 ARG N 118 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1527.38 seconds wall clock time: 28 minutes 36.55 seconds (1716.55 seconds total)