Starting phenix.real_space_refine on Thu Mar 13 22:40:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gz3_34389/03_2025/8gz3_34389.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gz3_34389/03_2025/8gz3_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/cci-nas-00/data/ceres_data/8gz3_34389/03_2025/8gz3_34389.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gz3_34389/03_2025/8gz3_34389.map" model { file = "/net/cci-nas-00/data/ceres_data/8gz3_34389/03_2025/8gz3_34389.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gz3_34389/03_2025/8gz3_34389.cif" } 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. Time to flip 13 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 6.98, per 1000 atoms: 0.82 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 - 3.00 Amino acid : True - 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: 2.86 Conformation dependent library (CDL) restraints added in 1.3 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: 1.35 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: 3.37 Time building geometry restraints manager: 3.10 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: 0.00 - 2.78: 11305 2.78 - 5.56: 523 5.56 - 8.34: 100 8.34 - 11.11: 36 11.11 - 13.89: 5 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 3.040 nonbonded pdb=" O TYR N 100 " pdb=" OH TYR N 105 " model vdw 2.281 3.040 nonbonded pdb=" O THR N 32 " pdb=" NH2 ARG N 72 " model vdw 2.313 3.120 nonbonded pdb=" O ALA A 101 " pdb=" OG1 THR A 107 " model vdw 2.316 3.040 ... (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 Time spend for trying shortcut: 0.00 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: 153.630 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: 0.000 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 27.520 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.070 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: 0.020 Load rotamer database and sin/cos tables:3.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 185.480 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 11 poor density : 132 time to evaluate : 1.080 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: 0.2722 time to fit residues: 52.5478 Evaluate side-chains 94 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 89 time to evaluate : 0.758 ------------------------------------------------------------------------------- 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: 3.9990 chunk 90 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 60 optimal weight: 9.9990 chunk 48 optimal weight: 0.7980 chunk 93 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 108 optimal weight: 0.6980 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.3508 r_free = 0.3508 target = 0.143847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.133974 restraints weight = 10809.378| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 1.01 r_work: 0.3186 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8723 Z= 0.226 Angle : 0.656 13.131 11969 Z= 0.306 Chirality : 0.039 0.174 1420 Planarity : 0.005 0.075 1506 Dihedral : 12.047 179.563 1496 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Rotamer: Outliers : 2.69 % Allowed : 10.74 % 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: 0.41 (0.29), residues: 777 helix: 1.09 (0.25), residues: 376 sheet: -0.63 (0.44), residues: 129 loop : -0.26 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 337 HIS 0.005 0.001 HIS B 115 PHE 0.021 0.002 PHE B 62 TYR 0.013 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 109 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 0.865 Fit side-chains REVERT: A 8 MET cc_start: 0.8548 (mmt) cc_final: 0.8201 (mmt) REVERT: B 33 TYR cc_start: 0.8902 (m-80) cc_final: 0.8586 (m-80) REVERT: B 103 MET cc_start: 0.8978 (mtp) cc_final: 0.8769 (mtm) REVERT: B 246 GLN cc_start: 0.8424 (mm110) cc_final: 0.8208 (mm-40) REVERT: B 318 LYS cc_start: 0.8319 (mtpp) cc_final: 0.8034 (mtmm) REVERT: B 381 LYS cc_start: 0.7807 (mttt) cc_final: 0.7217 (tttm) REVERT: B 397 ASP cc_start: 0.7701 (p0) cc_final: 0.7392 (p0) REVERT: B 435 LYS cc_start: 0.8350 (mttt) cc_final: 0.8128 (mtmt) REVERT: B 508 LYS cc_start: 0.7590 (tmtt) cc_final: 0.6950 (tptp) REVERT: B 513 ARG cc_start: 0.7885 (mtt180) cc_final: 0.6605 (mtt180) REVERT: B 537 CYS cc_start: 0.8605 (t) cc_final: 0.8390 (t) REVERT: N 71 SER cc_start: 0.8471 (t) cc_final: 0.8159 (p) REVERT: N 103 ASN cc_start: 0.8245 (t0) cc_final: 0.7847 (t0) outliers start: 17 outliers final: 7 residues processed: 103 average time/residue: 0.2279 time to fit residues: 31.8252 Evaluate side-chains 87 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 80 time to evaluate : 0.748 ------------------------------------------------------------------------------- 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 436 LEU Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain N residue 101 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 38 optimal weight: 1.9990 chunk 70 optimal weight: 7.9990 chunk 27 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 89 optimal weight: 7.9990 chunk 105 optimal weight: 10.0000 chunk 0 optimal weight: 4.9990 chunk 97 optimal weight: 7.9990 chunk 99 optimal weight: 9.9990 chunk 115 optimal weight: 3.9990 chunk 80 optimal weight: 10.0000 overall best weight: 2.4986 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.135658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.120534 restraints weight = 11041.420| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.60 r_work: 0.2996 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 8723 Z= 0.421 Angle : 0.783 16.727 11969 Z= 0.361 Chirality : 0.043 0.190 1420 Planarity : 0.005 0.073 1506 Dihedral : 10.443 126.576 1488 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 4.27 % Allowed : 11.53 % Favored : 84.20 % 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: 0.13 (0.29), residues: 777 helix: 0.69 (0.25), residues: 377 sheet: -0.79 (0.45), residues: 129 loop : -0.10 (0.36), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 337 HIS 0.009 0.002 HIS B 115 PHE 0.017 0.002 PHE B 39 TYR 0.018 0.002 TYR B 29 ARG 0.011 0.001 ARG B 92 *********************** 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 105 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 78 time to evaluate : 0.779 Fit side-chains REVERT: A 35 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.7872 (mm-40) REVERT: A 58 LYS cc_start: 0.8356 (tttm) cc_final: 0.8136 (ttmt) REVERT: B 318 LYS cc_start: 0.8400 (mtpp) cc_final: 0.8149 (mtmm) REVERT: B 406 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8662 (mp) REVERT: B 508 LYS cc_start: 0.7722 (tmtt) cc_final: 0.6998 (tptp) REVERT: B 513 ARG cc_start: 0.7958 (mtt180) cc_final: 0.6993 (mtt180) REVERT: B 537 CYS cc_start: 0.8578 (t) cc_final: 0.8347 (t) REVERT: N 71 SER cc_start: 0.8579 (t) cc_final: 0.8322 (m) outliers start: 27 outliers final: 14 residues processed: 100 average time/residue: 0.2470 time to fit residues: 33.8055 Evaluate side-chains 84 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 68 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 86 ASN Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 96 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 406 LEU Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 449 HIS 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 B residue 561 VAL Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 48 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 18 optimal weight: 0.8980 chunk 81 optimal weight: 7.9990 chunk 75 optimal weight: 7.9990 chunk 23 optimal weight: 0.8980 chunk 85 optimal weight: 10.0000 chunk 48 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 111 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3458 r_free = 0.3458 target = 0.139761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.124066 restraints weight = 10831.961| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 1.57 r_work: 0.3071 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8723 Z= 0.183 Angle : 0.602 14.517 11969 Z= 0.273 Chirality : 0.036 0.175 1420 Planarity : 0.004 0.063 1506 Dihedral : 9.320 120.431 1488 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 2.37 % Allowed : 14.22 % Favored : 83.41 % 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: 0.60 (0.29), residues: 777 helix: 1.17 (0.26), residues: 375 sheet: -0.73 (0.45), residues: 128 loop : 0.07 (0.37), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 337 HIS 0.008 0.001 HIS B 449 PHE 0.015 0.001 PHE B 454 TYR 0.011 0.001 TYR B 280 ARG 0.004 0.000 ARG B 96 *********************** 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 89 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.765 Fit side-chains REVERT: A 35 GLN cc_start: 0.8687 (OUTLIER) cc_final: 0.8009 (mm-40) REVERT: A 58 LYS cc_start: 0.8355 (tttm) cc_final: 0.8150 (ttmt) REVERT: B 199 ARG cc_start: 0.6653 (tmt170) cc_final: 0.6050 (ttp80) REVERT: B 318 LYS cc_start: 0.8457 (mtpp) cc_final: 0.8192 (mtmm) REVERT: B 381 LYS cc_start: 0.7833 (mttt) cc_final: 0.7364 (tttm) REVERT: B 435 LYS cc_start: 0.8293 (mttt) cc_final: 0.7987 (mtmm) REVERT: B 508 LYS cc_start: 0.7652 (tmtt) cc_final: 0.6934 (tptp) REVERT: B 513 ARG cc_start: 0.7976 (mtt180) cc_final: 0.6959 (mtt180) REVERT: B 537 CYS cc_start: 0.8758 (t) cc_final: 0.8523 (t) outliers start: 15 outliers final: 4 residues processed: 81 average time/residue: 0.2423 time to fit residues: 26.5655 Evaluate side-chains 77 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLN 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 436 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 8.9990 chunk 16 optimal weight: 0.5980 chunk 79 optimal weight: 9.9990 chunk 93 optimal weight: 7.9990 chunk 8 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 27 optimal weight: 0.1980 chunk 54 optimal weight: 0.6980 chunk 101 optimal weight: 10.0000 chunk 30 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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 = 0.3472 r_free = 0.3472 target = 0.140895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.126063 restraints weight = 10829.035| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.54 r_work: 0.3097 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8723 Z= 0.161 Angle : 0.556 13.763 11969 Z= 0.253 Chirality : 0.035 0.165 1420 Planarity : 0.003 0.050 1506 Dihedral : 8.572 107.905 1488 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 2.53 % Allowed : 14.06 % Favored : 83.41 % 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: 0.79 (0.29), residues: 777 helix: 1.38 (0.26), residues: 379 sheet: -0.58 (0.45), residues: 118 loop : 0.01 (0.36), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 337 HIS 0.004 0.001 HIS B 115 PHE 0.013 0.001 PHE B 454 TYR 0.013 0.001 TYR N 80 ARG 0.002 0.000 ARG N 118 *********************** 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 95 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.754 Fit side-chains REVERT: A 35 GLN cc_start: 0.8711 (OUTLIER) cc_final: 0.7949 (mm-40) REVERT: A 58 LYS cc_start: 0.8271 (tttm) cc_final: 0.8067 (ttmt) REVERT: B 199 ARG cc_start: 0.6290 (tmt170) cc_final: 0.5720 (ttp80) REVERT: B 318 LYS cc_start: 0.8401 (mtpp) cc_final: 0.8123 (mtmm) REVERT: B 381 LYS cc_start: 0.7640 (mttt) cc_final: 0.7129 (tttm) REVERT: B 435 LYS cc_start: 0.8348 (mttt) cc_final: 0.8079 (mtmm) REVERT: B 508 LYS cc_start: 0.7552 (tmtt) cc_final: 0.6936 (tptp) REVERT: B 513 ARG cc_start: 0.7875 (mtt180) cc_final: 0.7080 (mtt-85) outliers start: 16 outliers final: 8 residues processed: 90 average time/residue: 0.2488 time to fit residues: 30.3433 Evaluate side-chains 83 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 86 ASN Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain N residue 96 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 116 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 100 optimal weight: 9.9990 chunk 91 optimal weight: 8.9990 chunk 90 optimal weight: 5.9990 chunk 114 optimal weight: 0.5980 chunk 106 optimal weight: 8.9990 chunk 118 optimal weight: 4.9990 chunk 111 optimal weight: 0.9980 chunk 68 optimal weight: 9.9990 chunk 81 optimal weight: 9.9990 overall best weight: 2.2784 ------------------------------------------------------------------------------- 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 = 0.3421 r_free = 0.3421 target = 0.136450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.123395 restraints weight = 10876.365| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 1.32 r_work: 0.3045 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 8723 Z= 0.383 Angle : 0.723 16.217 11969 Z= 0.327 Chirality : 0.041 0.182 1420 Planarity : 0.004 0.049 1506 Dihedral : 9.071 105.872 1488 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.69 % Allowed : 15.48 % Favored : 81.83 % 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: 0.95 (0.26), residues: 379 sheet: -0.64 (0.44), residues: 128 loop : 0.01 (0.37), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 337 HIS 0.008 0.002 HIS B 115 PHE 0.016 0.002 PHE B 215 TYR 0.016 0.002 TYR B 29 ARG 0.005 0.001 ARG B 73 *********************** 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 89 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 72 time to evaluate : 0.704 Fit side-chains REVERT: A 8 MET cc_start: 0.8868 (mmt) cc_final: 0.8526 (mmt) REVERT: A 35 GLN cc_start: 0.8713 (OUTLIER) cc_final: 0.7842 (mm-40) REVERT: A 58 LYS cc_start: 0.8477 (tttm) cc_final: 0.8179 (ttmt) REVERT: B 318 LYS cc_start: 0.8576 (mtpp) cc_final: 0.8252 (mtmt) REVERT: B 381 LYS cc_start: 0.7884 (mttt) cc_final: 0.7376 (tttm) REVERT: B 508 LYS cc_start: 0.7688 (tmtt) cc_final: 0.6927 (tptp) REVERT: B 513 ARG cc_start: 0.7909 (mtt180) cc_final: 0.7097 (mtt-85) outliers start: 17 outliers final: 10 residues processed: 81 average time/residue: 0.2426 time to fit residues: 26.5951 Evaluate side-chains 81 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 86 ASN 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 312 MET Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 449 HIS Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain N residue 28 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 81 optimal weight: 8.9990 chunk 96 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 111 optimal weight: 0.9990 chunk 88 optimal weight: 10.0000 chunk 70 optimal weight: 7.9990 chunk 113 optimal weight: 0.4980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3458 r_free = 0.3458 target = 0.139596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.126422 restraints weight = 10915.926| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 1.30 r_work: 0.3103 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8723 Z= 0.182 Angle : 0.578 13.940 11969 Z= 0.262 Chirality : 0.036 0.159 1420 Planarity : 0.003 0.045 1506 Dihedral : 8.622 107.262 1488 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 2.05 % Allowed : 16.11 % Favored : 81.83 % 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: 0.67 (0.29), residues: 777 helix: 1.27 (0.26), residues: 379 sheet: -0.57 (0.44), residues: 124 loop : -0.06 (0.37), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 337 HIS 0.004 0.001 HIS B 115 PHE 0.013 0.001 PHE B 454 TYR 0.011 0.001 TYR A 37 ARG 0.003 0.000 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 88 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.782 Fit side-chains REVERT: A 35 GLN cc_start: 0.8746 (OUTLIER) cc_final: 0.7972 (mm-40) REVERT: A 58 LYS cc_start: 0.8362 (tttm) cc_final: 0.8084 (ttmt) REVERT: B 199 ARG cc_start: 0.6541 (tmt170) cc_final: 0.5910 (ttp80) REVERT: B 318 LYS cc_start: 0.8551 (mtpp) cc_final: 0.8206 (mtmt) REVERT: B 381 LYS cc_start: 0.7803 (mttt) cc_final: 0.7214 (tttm) REVERT: B 508 LYS cc_start: 0.7665 (tmtt) cc_final: 0.6934 (tptp) REVERT: B 513 ARG cc_start: 0.7845 (mtt180) cc_final: 0.6739 (mtt180) outliers start: 13 outliers final: 9 residues processed: 83 average time/residue: 0.2249 time to fit residues: 25.4197 Evaluate side-chains 82 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLN 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 242 THR Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 561 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 0 optimal weight: 4.9990 chunk 89 optimal weight: 8.9990 chunk 98 optimal weight: 8.9990 chunk 87 optimal weight: 10.0000 chunk 56 optimal weight: 0.6980 chunk 116 optimal weight: 5.9990 chunk 84 optimal weight: 10.0000 chunk 29 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 109 optimal weight: 0.8980 chunk 118 optimal weight: 0.2980 overall best weight: 1.5782 ------------------------------------------------------------------------------- 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 = 0.3436 r_free = 0.3436 target = 0.137848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.123385 restraints weight = 11094.479| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 1.45 r_work: 0.3047 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 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 : 0.004 0.049 8723 Z= 0.278 Angle : 0.642 15.201 11969 Z= 0.289 Chirality : 0.038 0.159 1420 Planarity : 0.004 0.047 1506 Dihedral : 8.679 104.909 1488 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.37 % Allowed : 16.43 % 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: 0.58 (0.29), residues: 777 helix: 1.20 (0.26), residues: 379 sheet: -0.59 (0.44), residues: 122 loop : -0.13 (0.36), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 337 HIS 0.007 0.001 HIS B 115 PHE 0.014 0.002 PHE B 215 TYR 0.013 0.002 TYR B 29 ARG 0.005 0.001 ARG B 73 *********************** 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 87 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.752 Fit side-chains REVERT: A 12 GLU cc_start: 0.8447 (mp0) cc_final: 0.8215 (mp0) REVERT: A 35 GLN cc_start: 0.8772 (OUTLIER) cc_final: 0.7990 (mm-40) REVERT: A 58 LYS cc_start: 0.8436 (tttm) cc_final: 0.8169 (ttmt) REVERT: B 318 LYS cc_start: 0.8583 (mtpp) cc_final: 0.8240 (mtmt) REVERT: B 381 LYS cc_start: 0.7870 (mttt) cc_final: 0.7362 (tttm) REVERT: B 508 LYS cc_start: 0.7679 (tmtt) cc_final: 0.6915 (tptp) REVERT: B 513 ARG cc_start: 0.7853 (mtt180) cc_final: 0.6759 (mtt180) outliers start: 15 outliers final: 12 residues processed: 81 average time/residue: 0.2303 time to fit residues: 25.2723 Evaluate side-chains 85 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLN 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 242 THR Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 449 HIS Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain N residue 96 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 4 optimal weight: 0.7980 chunk 73 optimal weight: 7.9990 chunk 100 optimal weight: 10.0000 chunk 47 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 94 optimal weight: 10.0000 chunk 18 optimal weight: 0.7980 chunk 71 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.3453 r_free = 0.3453 target = 0.139212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.126065 restraints weight = 10961.153| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.27 r_work: 0.3105 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.3463 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= 0.207 Angle : 0.584 14.341 11969 Z= 0.263 Chirality : 0.036 0.149 1420 Planarity : 0.003 0.045 1506 Dihedral : 8.478 103.803 1488 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.90 % Allowed : 16.59 % Favored : 81.52 % 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: 0.72 (0.29), residues: 777 helix: 1.33 (0.26), residues: 379 sheet: -0.56 (0.44), residues: 124 loop : -0.07 (0.37), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 337 HIS 0.006 0.001 HIS B 115 PHE 0.012 0.001 PHE B 454 TYR 0.010 0.001 TYR B 280 ARG 0.004 0.000 ARG N 118 *********************** 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 89 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.719 Fit side-chains REVERT: A 8 MET cc_start: 0.8705 (mmt) cc_final: 0.8501 (mmt) REVERT: A 35 GLN cc_start: 0.8750 (OUTLIER) cc_final: 0.7807 (mm-40) REVERT: A 58 LYS cc_start: 0.8352 (tttm) cc_final: 0.8086 (ttmt) REVERT: B 318 LYS cc_start: 0.8528 (mtpp) cc_final: 0.8172 (mtmt) REVERT: B 381 LYS cc_start: 0.7741 (mttt) cc_final: 0.7184 (tttm) REVERT: B 508 LYS cc_start: 0.7672 (tmtt) cc_final: 0.6916 (tptp) REVERT: B 513 ARG cc_start: 0.7810 (mtt180) cc_final: 0.6895 (mtt-85) outliers start: 12 outliers final: 11 residues processed: 84 average time/residue: 0.2197 time to fit residues: 25.2276 Evaluate side-chains 86 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLN 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 242 THR Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain N residue 96 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 86 optimal weight: 9.9990 chunk 63 optimal weight: 2.9990 chunk 83 optimal weight: 9.9990 chunk 1 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 87 optimal weight: 10.0000 chunk 27 optimal weight: 3.9990 chunk 67 optimal weight: 9.9990 chunk 108 optimal weight: 0.7980 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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 = 0.3434 r_free = 0.3434 target = 0.137685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.123592 restraints weight = 10921.673| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 1.35 r_work: 0.3058 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 8723 Z= 0.292 Angle : 0.660 15.353 11969 Z= 0.297 Chirality : 0.038 0.151 1420 Planarity : 0.004 0.047 1506 Dihedral : 8.561 101.362 1488 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.21 % Allowed : 16.11 % 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: 0.56 (0.29), residues: 777 helix: 1.18 (0.26), residues: 379 sheet: -0.60 (0.44), residues: 122 loop : -0.14 (0.36), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 337 HIS 0.007 0.002 HIS B 115 PHE 0.015 0.002 PHE B 215 TYR 0.014 0.002 TYR B 29 ARG 0.004 0.001 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 85 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.732 Fit side-chains REVERT: A 35 GLN cc_start: 0.8787 (OUTLIER) cc_final: 0.7847 (mm-40) REVERT: A 58 LYS cc_start: 0.8448 (tttm) cc_final: 0.8171 (ttmt) REVERT: B 199 ARG cc_start: 0.6396 (tmt170) cc_final: 0.5691 (ttp80) REVERT: B 318 LYS cc_start: 0.8548 (mtpp) cc_final: 0.8199 (mtmt) REVERT: B 508 LYS cc_start: 0.7699 (tmtt) cc_final: 0.6915 (tptp) REVERT: B 513 ARG cc_start: 0.7814 (mtt180) cc_final: 0.6734 (mtt180) outliers start: 14 outliers final: 11 residues processed: 79 average time/residue: 0.2358 time to fit residues: 25.3106 Evaluate side-chains 83 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLN 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 242 THR Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 449 HIS Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain N residue 96 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 57 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 87 optimal weight: 10.0000 chunk 118 optimal weight: 0.0770 chunk 16 optimal weight: 0.9990 chunk 13 optimal weight: 0.0980 chunk 74 optimal weight: 6.9990 chunk 32 optimal weight: 0.9980 overall best weight: 0.6138 ------------------------------------------------------------------------------- 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 = 0.3468 r_free = 0.3468 target = 0.140490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.126528 restraints weight = 10955.572| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.39 r_work: 0.3088 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8723 Z= 0.162 Angle : 0.566 13.331 11969 Z= 0.255 Chirality : 0.035 0.145 1420 Planarity : 0.003 0.044 1506 Dihedral : 8.271 100.141 1488 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.90 % Allowed : 16.43 % 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: 0.83 (0.29), residues: 777 helix: 1.41 (0.26), residues: 380 sheet: -0.55 (0.43), residues: 120 loop : 0.01 (0.37), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 424 HIS 0.004 0.001 HIS B 115 PHE 0.012 0.001 PHE B 454 TYR 0.010 0.001 TYR A 37 ARG 0.004 0.000 ARG N 118 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4105.55 seconds wall clock time: 72 minutes 40.75 seconds (4360.75 seconds total)