Starting phenix.real_space_refine on Mon Aug 5 14:18:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8khr_37249/08_2024/8khr_37249.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8khr_37249/08_2024/8khr_37249.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8khr_37249/08_2024/8khr_37249.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8khr_37249/08_2024/8khr_37249.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8khr_37249/08_2024/8khr_37249.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8khr_37249/08_2024/8khr_37249.cif" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6549 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 5317 2.51 5 N 1418 2.21 5 O 1549 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H GLU 10": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 8320 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 1267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1267 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 16, 'TRANS': 156} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 152 Unresolved non-hydrogen angles: 199 Unresolved non-hydrogen dihedrals: 132 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 1, 'TYR:plan': 2, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 5, 'GLU:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 98 Chain: "H" Number of atoms: 704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 704 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 5, 'TRANS': 105} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 147 Unresolved non-hydrogen angles: 192 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 4, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 92 Chain: "L" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 703 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 8, 'TRANS': 98} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 139 Unresolved non-hydrogen angles: 176 Unresolved non-hydrogen dihedrals: 121 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 91 Chain: "A" Number of atoms: 4938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 650, 4938 Classifications: {'peptide': 650} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 26, 'TRANS': 623} Chain breaks: 1 Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 156 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 4, 'GLU:plan': 7, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 71 Chain: "B" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 708 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 1, 'TRANS': 95} Chain breaks: 2 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Time building chain proxies: 5.86, per 1000 atoms: 0.70 Number of scatterers: 8320 At special positions: 0 Unit cell: (84.645, 95.76, 146.205, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 36 16.00 O 1549 8.00 N 1418 7.00 C 5317 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS A 454 " - pdb=" SG CYS A 478 " distance=2.08 Simple disulfide: pdb=" SG CYS A 534 " - pdb=" SG CYS A 587 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.82 Conformation dependent library (CDL) restraints added in 1.6 seconds 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2116 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 11 sheets defined 30.7% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'C' and resid 66 through 71 Processing helix chain 'C' and resid 127 through 131 Processing helix chain 'C' and resid 148 through 155 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'A' and resid 40 through 47 removed outlier: 3.579A pdb=" N MET A 44 " --> pdb=" O TRP A 40 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N ALA A 45 " --> pdb=" O THR A 41 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS A 46 " --> pdb=" O GLU A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 60 Processing helix chain 'A' and resid 64 through 75 removed outlier: 4.011A pdb=" N ILE A 75 " --> pdb=" O ARG A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 131 Processing helix chain 'A' and resid 141 through 148 removed outlier: 4.088A pdb=" N VAL A 147 " --> pdb=" O PRO A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 189 No H-bonds generated for 'chain 'A' and resid 187 through 189' Processing helix chain 'A' and resid 212 through 215 removed outlier: 3.562A pdb=" N SER A 215 " --> pdb=" O SER A 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 212 through 215' Processing helix chain 'A' and resid 231 through 242 removed outlier: 4.373A pdb=" N TYR A 241 " --> pdb=" O ASN A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 256 Processing helix chain 'A' and resid 257 through 274 removed outlier: 3.557A pdb=" N MET A 274 " --> pdb=" O VAL A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 307 removed outlier: 3.715A pdb=" N LEU A 288 " --> pdb=" O ASP A 284 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 337 removed outlier: 3.631A pdb=" N GLY A 337 " --> pdb=" O GLY A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 359 removed outlier: 3.535A pdb=" N GLU A 349 " --> pdb=" O SER A 345 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR A 358 " --> pdb=" O MET A 354 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N VAL A 359 " --> pdb=" O LEU A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 364 Processing helix chain 'A' and resid 368 through 383 Processing helix chain 'A' and resid 391 through 407 removed outlier: 3.820A pdb=" N GLY A 395 " --> pdb=" O GLY A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 433 removed outlier: 4.140A pdb=" N HIS A 426 " --> pdb=" O PHE A 422 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N VAL A 427 " --> pdb=" O ILE A 423 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL A 428 " --> pdb=" O GLY A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 453 removed outlier: 3.685A pdb=" N LEU A 443 " --> pdb=" O GLN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 469 Processing helix chain 'A' and resid 470 through 474 removed outlier: 3.590A pdb=" N GLY A 473 " --> pdb=" O THR A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 493 Processing helix chain 'A' and resid 504 through 517 removed outlier: 4.316A pdb=" N ASN A 508 " --> pdb=" O ALA A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 646 Processing helix chain 'B' and resid 41 through 45 removed outlier: 3.596A pdb=" N ILE B 45 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 97 Processing helix chain 'B' and resid 98 through 100 No H-bonds generated for 'chain 'B' and resid 98 through 100' Processing helix chain 'B' and resid 101 through 112 Processing helix chain 'B' and resid 114 through 119 Processing sheet with id=AA1, first strand: chain 'C' and resid 162 through 163 removed outlier: 3.936A pdb=" N LEU C 162 " --> pdb=" O VAL C 195 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL C 195 " --> pdb=" O LEU C 162 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'H' and resid 46 through 47 Processing sheet with id=AA3, first strand: chain 'L' and resid 45 through 50 removed outlier: 4.599A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N CYS L 88 " --> pdb=" O GLN L 100 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN L 100 " --> pdb=" O CYS L 88 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE L 98 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 35 through 39 removed outlier: 3.820A pdb=" N VAL A 23 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE B 48 " --> pdb=" O LYS A 24 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR B 49 " --> pdb=" O SER B 63 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER B 63 " --> pdb=" O TYR B 49 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ARG B 78 " --> pdb=" O LEU B 64 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 100 through 102 removed outlier: 5.711A pdb=" N MET A 100 " --> pdb=" O CYS A 120 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LEU A 122 " --> pdb=" O MET A 100 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N VAL A 102 " --> pdb=" O LEU A 122 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 134 through 136 Processing sheet with id=AA7, first strand: chain 'A' and resid 167 through 170 removed outlier: 3.676A pdb=" N TYR A 157 " --> pdb=" O LYS A 341 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 177 through 178 removed outlier: 6.418A pdb=" N TYR A 224 " --> pdb=" O GLN A 220 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLN A 220 " --> pdb=" O TYR A 224 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N LEU A 226 " --> pdb=" O SER A 218 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 184 through 185 Processing sheet with id=AB1, first strand: chain 'A' and resid 541 through 546 removed outlier: 6.916A pdb=" N ILE A 554 " --> pdb=" O LEU A 542 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ILE A 544 " --> pdb=" O PHE A 552 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N PHE A 552 " --> pdb=" O ILE A 544 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL A 550 " --> pdb=" O PRO A 546 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU A 567 " --> pdb=" O ARG A 597 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 601 through 602 removed outlier: 5.037A pdb=" N TYR A 658 " --> pdb=" O ILE A 670 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU A 661 " --> pdb=" O ALA A 618 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA A 618 " --> pdb=" O LEU A 661 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N ASP A 623 " --> pdb=" O LEU A 628 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N LEU A 628 " --> pdb=" O ASP A 623 " (cutoff:3.500A) 272 hydrogen bonds defined for protein. 759 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: 2.22 Time building geometry restraints manager: 3.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2681 1.34 - 1.46: 1685 1.46 - 1.58: 4081 1.58 - 1.70: 0 1.70 - 1.82: 56 Bond restraints: 8503 Sorted by residual: bond pdb=" CA GLY A 209 " pdb=" C GLY A 209 " ideal model delta sigma weight residual 1.515 1.476 0.039 1.43e-02 4.89e+03 7.46e+00 bond pdb=" N SER A 588 " pdb=" CA SER A 588 " ideal model delta sigma weight residual 1.453 1.484 -0.031 1.22e-02 6.72e+03 6.37e+00 bond pdb=" C PHE A 292 " pdb=" N GLU A 293 " ideal model delta sigma weight residual 1.334 1.302 0.032 1.27e-02 6.20e+03 6.31e+00 bond pdb=" N CYS L 88 " pdb=" CA CYS L 88 " ideal model delta sigma weight residual 1.455 1.484 -0.028 1.21e-02 6.83e+03 5.51e+00 bond pdb=" N GLU C 160 " pdb=" CA GLU C 160 " ideal model delta sigma weight residual 1.457 1.488 -0.030 1.29e-02 6.01e+03 5.47e+00 ... (remaining 8498 not shown) Histogram of bond angle deviations from ideal: 100.18 - 106.95: 280 106.95 - 113.73: 4708 113.73 - 120.50: 3065 120.50 - 127.27: 3456 127.27 - 134.04: 94 Bond angle restraints: 11603 Sorted by residual: angle pdb=" N TYR B 115 " pdb=" CA TYR B 115 " pdb=" C TYR B 115 " ideal model delta sigma weight residual 111.14 100.82 10.32 1.08e+00 8.57e-01 9.13e+01 angle pdb=" C PHE A 292 " pdb=" N GLU A 293 " pdb=" CA GLU A 293 " ideal model delta sigma weight residual 120.63 110.99 9.64 1.36e+00 5.41e-01 5.02e+01 angle pdb=" N GLU A 293 " pdb=" CA GLU A 293 " pdb=" C GLU A 293 " ideal model delta sigma weight residual 111.03 103.55 7.48 1.11e+00 8.12e-01 4.54e+01 angle pdb=" C TYR B 115 " pdb=" CA TYR B 115 " pdb=" CB TYR B 115 " ideal model delta sigma weight residual 110.90 119.96 -9.06 1.58e+00 4.01e-01 3.29e+01 angle pdb=" C LEU A 288 " pdb=" N THR A 289 " pdb=" CA THR A 289 " ideal model delta sigma weight residual 120.44 113.01 7.43 1.30e+00 5.92e-01 3.27e+01 ... (remaining 11598 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 4322 17.88 - 35.76: 525 35.76 - 53.64: 151 53.64 - 71.53: 16 71.53 - 89.41: 7 Dihedral angle restraints: 5021 sinusoidal: 1726 harmonic: 3295 Sorted by residual: dihedral pdb=" CB CYS A 534 " pdb=" SG CYS A 534 " pdb=" SG CYS A 587 " pdb=" CB CYS A 587 " ideal model delta sinusoidal sigma weight residual -86.00 -38.00 -48.00 1 1.00e+01 1.00e-02 3.18e+01 dihedral pdb=" CA ARG L 92 " pdb=" C ARG L 92 " pdb=" N THR L 93 " pdb=" CA THR L 93 " ideal model delta harmonic sigma weight residual 180.00 162.87 17.13 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CA TYR L 94 " pdb=" C TYR L 94 " pdb=" N PRO L 95 " pdb=" CA PRO L 95 " ideal model delta harmonic sigma weight residual -180.00 -162.90 -17.10 0 5.00e+00 4.00e-02 1.17e+01 ... (remaining 5018 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1144 0.053 - 0.105: 181 0.105 - 0.158: 33 0.158 - 0.210: 1 0.210 - 0.263: 1 Chirality restraints: 1360 Sorted by residual: chirality pdb=" CA CYS L 23 " pdb=" N CYS L 23 " pdb=" C CYS L 23 " pdb=" CB CYS L 23 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CA ASN A 60 " pdb=" N ASN A 60 " pdb=" C ASN A 60 " pdb=" CB ASN A 60 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.24e-01 chirality pdb=" CA GLU A 293 " pdb=" N GLU A 293 " pdb=" C GLU A 293 " pdb=" CB GLU A 293 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.19e-01 ... (remaining 1357 not shown) Planarity restraints: 1482 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE C 159 " -0.012 2.00e-02 2.50e+03 2.36e-02 5.55e+00 pdb=" C ILE C 159 " 0.041 2.00e-02 2.50e+03 pdb=" O ILE C 159 " -0.015 2.00e-02 2.50e+03 pdb=" N GLU C 160 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 114 " 0.011 2.00e-02 2.50e+03 2.32e-02 5.37e+00 pdb=" C LEU B 114 " -0.040 2.00e-02 2.50e+03 pdb=" O LEU B 114 " 0.015 2.00e-02 2.50e+03 pdb=" N TYR B 115 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS L 23 " 0.009 2.00e-02 2.50e+03 1.89e-02 3.56e+00 pdb=" C CYS L 23 " -0.033 2.00e-02 2.50e+03 pdb=" O CYS L 23 " 0.012 2.00e-02 2.50e+03 pdb=" N ARG L 24 " 0.011 2.00e-02 2.50e+03 ... (remaining 1479 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 223 2.68 - 3.23: 7957 3.23 - 3.79: 12217 3.79 - 4.34: 15413 4.34 - 4.90: 25919 Nonbonded interactions: 61729 Sorted by model distance: nonbonded pdb=" O ASN A 60 " pdb=" ND2 ASN A 60 " model vdw 2.125 3.120 nonbonded pdb=" O SER A 251 " pdb=" OG1 THR A 255 " model vdw 2.252 3.040 nonbonded pdb=" OG1 THR A 186 " pdb=" OD1 ASP A 190 " model vdw 2.261 3.040 nonbonded pdb=" OE2 GLU C 106 " pdb=" OG1 THR C 108 " model vdw 2.291 3.040 nonbonded pdb=" OH TYR A 261 " pdb=" OE1 GLU A 293 " model vdw 2.300 3.040 ... (remaining 61724 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 6.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.020 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 25.590 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 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 : 0.003 0.040 8503 Z= 0.169 Angle : 0.635 10.317 11603 Z= 0.378 Chirality : 0.041 0.263 1360 Planarity : 0.004 0.045 1482 Dihedral : 16.934 89.407 2896 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 0.62 % Allowed : 35.89 % Favored : 63.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.26), residues: 1122 helix: 1.81 (0.31), residues: 299 sheet: -1.57 (0.41), residues: 180 loop : -1.98 (0.25), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP H 47 HIS 0.002 0.000 HIS B 103 PHE 0.008 0.001 PHE A 322 TYR 0.019 0.001 TYR H 32 ARG 0.003 0.000 ARG C 154 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 88 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 6 GLN cc_start: 0.7737 (mp10) cc_final: 0.7508 (tp-100) REVERT: L 42 ARG cc_start: 0.6940 (ttm170) cc_final: 0.6628 (mmt90) REVERT: A 494 MET cc_start: 0.7822 (ptm) cc_final: 0.7591 (ptp) REVERT: B 67 PRO cc_start: 0.7946 (Cg_endo) cc_final: 0.7662 (Cg_exo) REVERT: B 115 TYR cc_start: 0.8221 (OUTLIER) cc_final: 0.6580 (t80) outliers start: 5 outliers final: 2 residues processed: 90 average time/residue: 0.2256 time to fit residues: 28.8678 Evaluate side-chains 79 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 76 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain A residue 534 CYS Chi-restraints excluded: chain B residue 115 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 chunk 45 optimal weight: 0.3980 chunk 87 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 65 optimal weight: 0.5980 chunk 101 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.0992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8503 Z= 0.177 Angle : 0.546 6.618 11603 Z= 0.283 Chirality : 0.040 0.146 1360 Planarity : 0.004 0.046 1482 Dihedral : 4.341 47.439 1223 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer: Outliers : 3.22 % Allowed : 33.42 % Favored : 63.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.26), residues: 1122 helix: 2.02 (0.31), residues: 302 sheet: -1.54 (0.41), residues: 175 loop : -2.09 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 47 HIS 0.002 0.001 HIS A 239 PHE 0.008 0.001 PHE A 322 TYR 0.019 0.001 TYR C 111 ARG 0.003 0.000 ARG A 184 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 82 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 187 ILE cc_start: 0.7938 (mp) cc_final: 0.7449 (mm) REVERT: H 36 TRP cc_start: 0.6969 (m100) cc_final: 0.6625 (m100) REVERT: H 102 TYR cc_start: 0.5715 (OUTLIER) cc_final: 0.4113 (t80) REVERT: L 42 ARG cc_start: 0.6964 (ttm170) cc_final: 0.6661 (mmt90) REVERT: A 44 MET cc_start: 0.8507 (mmp) cc_final: 0.8276 (mmp) REVERT: A 494 MET cc_start: 0.7827 (ptm) cc_final: 0.7598 (ptp) REVERT: B 67 PRO cc_start: 0.8073 (Cg_endo) cc_final: 0.7732 (Cg_exo) outliers start: 26 outliers final: 11 residues processed: 101 average time/residue: 0.1865 time to fit residues: 27.3622 Evaluate side-chains 88 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 76 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain B residue 45 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 0.7980 chunk 31 optimal weight: 5.9990 chunk 84 optimal weight: 0.0970 chunk 69 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 chunk 110 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 34 optimal weight: 6.9990 chunk 81 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8503 Z= 0.163 Angle : 0.524 6.419 11603 Z= 0.271 Chirality : 0.039 0.141 1360 Planarity : 0.004 0.046 1482 Dihedral : 4.164 47.173 1220 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 3.84 % Allowed : 30.69 % Favored : 65.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.26), residues: 1122 helix: 2.10 (0.31), residues: 303 sheet: -1.58 (0.39), residues: 184 loop : -2.04 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP H 47 HIS 0.002 0.000 HIS A 407 PHE 0.008 0.001 PHE A 322 TYR 0.013 0.001 TYR A 336 ARG 0.002 0.000 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 77 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 51 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7364 (tm-30) REVERT: H 102 TYR cc_start: 0.5683 (OUTLIER) cc_final: 0.4043 (t80) REVERT: L 42 ARG cc_start: 0.6973 (ttm170) cc_final: 0.6681 (mmt90) REVERT: A 44 MET cc_start: 0.8521 (mmp) cc_final: 0.8250 (mmm) REVERT: A 494 MET cc_start: 0.7875 (ptm) cc_final: 0.7671 (ptp) REVERT: B 67 PRO cc_start: 0.8105 (Cg_endo) cc_final: 0.7784 (Cg_exo) outliers start: 31 outliers final: 17 residues processed: 101 average time/residue: 0.2236 time to fit residues: 32.1271 Evaluate side-chains 94 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 75 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 264 TYR Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain B residue 50 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 0.2980 chunk 52 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 96 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 90 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8503 Z= 0.152 Angle : 0.508 6.478 11603 Z= 0.261 Chirality : 0.039 0.140 1360 Planarity : 0.003 0.047 1482 Dihedral : 4.108 43.154 1220 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 4.46 % Allowed : 31.56 % Favored : 63.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.26), residues: 1122 helix: 2.08 (0.31), residues: 307 sheet: -1.63 (0.39), residues: 189 loop : -2.04 (0.24), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP H 47 HIS 0.002 0.000 HIS A 407 PHE 0.008 0.001 PHE A 322 TYR 0.012 0.001 TYR A 336 ARG 0.003 0.000 ARG B 105 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 73 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 51 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7360 (tm-30) REVERT: H 102 TYR cc_start: 0.5696 (OUTLIER) cc_final: 0.4040 (t80) REVERT: L 42 ARG cc_start: 0.6957 (ttm170) cc_final: 0.6661 (mmt90) REVERT: B 67 PRO cc_start: 0.8119 (Cg_endo) cc_final: 0.7822 (Cg_exo) outliers start: 36 outliers final: 21 residues processed: 101 average time/residue: 0.1793 time to fit residues: 26.0525 Evaluate side-chains 97 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 74 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 264 TYR Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 605 PHE Chi-restraints excluded: chain B residue 45 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 2.9990 chunk 1 optimal weight: 0.0050 chunk 80 optimal weight: 1.9990 chunk 44 optimal weight: 0.0980 chunk 92 optimal weight: 4.9990 chunk 74 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8503 Z= 0.152 Angle : 0.513 6.422 11603 Z= 0.261 Chirality : 0.039 0.153 1360 Planarity : 0.003 0.047 1482 Dihedral : 4.048 40.540 1220 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 4.46 % Allowed : 31.44 % Favored : 64.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.26), residues: 1122 helix: 2.13 (0.31), residues: 303 sheet: -1.68 (0.38), residues: 194 loop : -1.99 (0.24), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP H 47 HIS 0.002 0.000 HIS A 407 PHE 0.007 0.001 PHE A 322 TYR 0.012 0.001 TYR A 336 ARG 0.002 0.000 ARG B 105 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 74 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 51 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7312 (tm-30) REVERT: H 102 TYR cc_start: 0.5703 (OUTLIER) cc_final: 0.4021 (t80) REVERT: L 42 ARG cc_start: 0.6830 (ttm170) cc_final: 0.6535 (mmt90) REVERT: B 67 PRO cc_start: 0.8175 (Cg_endo) cc_final: 0.7895 (Cg_exo) outliers start: 36 outliers final: 21 residues processed: 102 average time/residue: 0.2154 time to fit residues: 30.4022 Evaluate side-chains 96 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 73 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 264 TYR Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 534 CYS Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 50 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 26 optimal weight: 6.9990 chunk 108 optimal weight: 1.9990 chunk 89 optimal weight: 0.0060 chunk 50 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 35 optimal weight: 10.0000 chunk 56 optimal weight: 0.7980 chunk 104 optimal weight: 0.7980 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8503 Z= 0.154 Angle : 0.509 6.776 11603 Z= 0.260 Chirality : 0.039 0.142 1360 Planarity : 0.003 0.047 1482 Dihedral : 4.033 41.053 1220 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 4.21 % Allowed : 31.19 % Favored : 64.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.26), residues: 1122 helix: 2.16 (0.31), residues: 306 sheet: -1.67 (0.38), residues: 194 loop : -1.98 (0.24), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP H 47 HIS 0.002 0.000 HIS A 407 PHE 0.007 0.001 PHE A 322 TYR 0.012 0.001 TYR A 336 ARG 0.003 0.000 ARG B 105 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 72 time to evaluate : 0.908 Fit side-chains REVERT: C 51 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7313 (tm-30) REVERT: C 187 ILE cc_start: 0.8151 (mp) cc_final: 0.7824 (mm) REVERT: H 6 GLN cc_start: 0.7664 (tp-100) cc_final: 0.7307 (mp10) REVERT: H 102 TYR cc_start: 0.5711 (OUTLIER) cc_final: 0.4027 (t80) REVERT: L 42 ARG cc_start: 0.6821 (ttm170) cc_final: 0.6527 (mmt90) REVERT: B 67 PRO cc_start: 0.8186 (Cg_endo) cc_final: 0.7922 (Cg_exo) outliers start: 34 outliers final: 23 residues processed: 100 average time/residue: 0.1929 time to fit residues: 27.2984 Evaluate side-chains 95 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 70 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 264 TYR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 534 CYS Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 50 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 91 optimal weight: 0.4980 chunk 60 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 67 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8503 Z= 0.167 Angle : 0.526 7.495 11603 Z= 0.266 Chirality : 0.039 0.143 1360 Planarity : 0.004 0.046 1482 Dihedral : 3.683 20.363 1216 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 3.84 % Allowed : 31.81 % Favored : 64.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.26), residues: 1122 helix: 2.17 (0.31), residues: 306 sheet: -1.68 (0.38), residues: 194 loop : -1.99 (0.24), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP H 47 HIS 0.002 0.000 HIS A 407 PHE 0.007 0.001 PHE A 322 TYR 0.012 0.001 TYR A 336 ARG 0.012 0.000 ARG C 154 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 71 time to evaluate : 0.891 Fit side-chains revert: symmetry clash REVERT: C 51 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7316 (tm-30) REVERT: H 6 GLN cc_start: 0.7699 (tp-100) cc_final: 0.7327 (mp10) REVERT: H 102 TYR cc_start: 0.5739 (OUTLIER) cc_final: 0.4030 (t80) REVERT: L 42 ARG cc_start: 0.6824 (ttm170) cc_final: 0.6535 (mmt90) REVERT: A 179 MET cc_start: 0.8277 (OUTLIER) cc_final: 0.7971 (ttt) REVERT: B 67 PRO cc_start: 0.8122 (Cg_endo) cc_final: 0.7863 (Cg_exo) outliers start: 31 outliers final: 24 residues processed: 94 average time/residue: 0.1911 time to fit residues: 25.7628 Evaluate side-chains 96 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 69 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 264 TYR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 534 CYS Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 50 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 2.9990 chunk 32 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 98 optimal weight: 0.4980 chunk 103 optimal weight: 10.0000 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 154 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8503 Z= 0.271 Angle : 0.578 6.563 11603 Z= 0.296 Chirality : 0.041 0.147 1360 Planarity : 0.004 0.048 1482 Dihedral : 4.038 21.368 1216 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.25 % Favored : 89.75 % Rotamer: Outliers : 4.46 % Allowed : 31.06 % Favored : 64.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.26), residues: 1122 helix: 1.89 (0.31), residues: 304 sheet: -1.83 (0.37), residues: 192 loop : -2.07 (0.24), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP H 47 HIS 0.003 0.001 HIS A 407 PHE 0.011 0.001 PHE B 118 TYR 0.019 0.001 TYR A 336 ARG 0.009 0.000 ARG C 154 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 70 time to evaluate : 0.914 Fit side-chains revert: symmetry clash REVERT: C 51 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7381 (tm-30) REVERT: C 77 LYS cc_start: 0.8261 (tmmt) cc_final: 0.7968 (tptt) REVERT: H 6 GLN cc_start: 0.7889 (tp-100) cc_final: 0.7551 (mp10) REVERT: H 102 TYR cc_start: 0.5872 (OUTLIER) cc_final: 0.4227 (t80) REVERT: L 42 ARG cc_start: 0.6848 (ttm170) cc_final: 0.6551 (mmt90) REVERT: A 179 MET cc_start: 0.8304 (OUTLIER) cc_final: 0.7992 (ttt) REVERT: B 67 PRO cc_start: 0.8167 (Cg_endo) cc_final: 0.7891 (Cg_exo) outliers start: 36 outliers final: 28 residues processed: 96 average time/residue: 0.1806 time to fit residues: 25.0132 Evaluate side-chains 101 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 70 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 264 TYR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 534 CYS Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 605 PHE Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 92 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 6.9990 chunk 100 optimal weight: 5.9990 chunk 103 optimal weight: 9.9990 chunk 60 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 78 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 90 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 66 optimal weight: 0.5980 chunk 106 optimal weight: 0.4980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8503 Z= 0.167 Angle : 0.539 8.452 11603 Z= 0.274 Chirality : 0.040 0.138 1360 Planarity : 0.003 0.047 1482 Dihedral : 3.857 20.220 1216 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 3.84 % Allowed : 31.68 % Favored : 64.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.26), residues: 1122 helix: 1.99 (0.31), residues: 300 sheet: -1.78 (0.37), residues: 194 loop : -2.00 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP H 47 HIS 0.002 0.000 HIS A 407 PHE 0.007 0.001 PHE H 29 TYR 0.013 0.001 TYR C 111 ARG 0.006 0.000 ARG C 154 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 70 time to evaluate : 0.974 Fit side-chains revert: symmetry clash REVERT: C 51 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7344 (tm-30) REVERT: C 77 LYS cc_start: 0.8225 (tmmt) cc_final: 0.7974 (tptt) REVERT: H 6 GLN cc_start: 0.7769 (tp-100) cc_final: 0.7430 (mp10) REVERT: H 29 PHE cc_start: 0.5935 (t80) cc_final: 0.4857 (m-80) REVERT: H 102 TYR cc_start: 0.5767 (OUTLIER) cc_final: 0.3856 (t80) REVERT: L 42 ARG cc_start: 0.6816 (ttm170) cc_final: 0.6526 (mmt90) REVERT: A 44 MET cc_start: 0.8503 (mmt) cc_final: 0.8135 (mmt) REVERT: A 179 MET cc_start: 0.8259 (OUTLIER) cc_final: 0.7946 (ttt) REVERT: B 67 PRO cc_start: 0.8160 (Cg_endo) cc_final: 0.7898 (Cg_exo) outliers start: 31 outliers final: 24 residues processed: 94 average time/residue: 0.1862 time to fit residues: 24.8975 Evaluate side-chains 95 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 68 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 264 TYR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 534 CYS Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 50 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 111 optimal weight: 0.8980 chunk 102 optimal weight: 0.4980 chunk 88 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8503 Z= 0.238 Angle : 0.563 8.804 11603 Z= 0.287 Chirality : 0.041 0.142 1360 Planarity : 0.004 0.047 1482 Dihedral : 3.961 20.876 1216 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.25 % Favored : 89.75 % Rotamer: Outliers : 3.71 % Allowed : 31.81 % Favored : 64.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.26), residues: 1122 helix: 1.87 (0.30), residues: 304 sheet: -1.84 (0.37), residues: 194 loop : -2.05 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP H 47 HIS 0.003 0.001 HIS A 407 PHE 0.010 0.001 PHE C 188 TYR 0.016 0.001 TYR A 336 ARG 0.005 0.000 ARG C 154 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 69 time to evaluate : 0.922 Fit side-chains revert: symmetry clash REVERT: C 51 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7384 (tm-30) REVERT: C 77 LYS cc_start: 0.8266 (tmmt) cc_final: 0.7935 (tptt) REVERT: H 6 GLN cc_start: 0.7841 (tp-100) cc_final: 0.7505 (mp10) REVERT: H 29 PHE cc_start: 0.5962 (t80) cc_final: 0.4920 (m-80) REVERT: H 102 TYR cc_start: 0.5843 (OUTLIER) cc_final: 0.3895 (t80) REVERT: L 42 ARG cc_start: 0.6815 (ttm170) cc_final: 0.6491 (mmt90) REVERT: A 179 MET cc_start: 0.8266 (OUTLIER) cc_final: 0.7948 (ttt) REVERT: B 67 PRO cc_start: 0.8174 (Cg_endo) cc_final: 0.7911 (Cg_exo) outliers start: 30 outliers final: 25 residues processed: 93 average time/residue: 0.1967 time to fit residues: 26.5869 Evaluate side-chains 97 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 69 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 264 TYR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 534 CYS Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 50 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 10.0000 chunk 81 optimal weight: 0.6980 chunk 13 optimal weight: 4.9990 chunk 24 optimal weight: 10.0000 chunk 88 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 16 optimal weight: 10.0000 chunk 78 optimal weight: 0.1980 chunk 5 optimal weight: 10.0000 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN ** L 90 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 = 0.3801 r_free = 0.3801 target = 0.101433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.074911 restraints weight = 22272.453| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 3.62 r_work: 0.3145 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 8503 Z= 0.454 Angle : 0.690 8.105 11603 Z= 0.355 Chirality : 0.045 0.164 1360 Planarity : 0.004 0.048 1482 Dihedral : 4.609 22.725 1216 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.12 % Favored : 87.88 % Rotamer: Outliers : 3.59 % Allowed : 31.68 % Favored : 64.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.25), residues: 1122 helix: 1.39 (0.29), residues: 306 sheet: -2.08 (0.37), residues: 187 loop : -2.30 (0.23), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP H 47 HIS 0.005 0.001 HIS A 154 PHE 0.018 0.002 PHE B 118 TYR 0.027 0.002 TYR A 336 ARG 0.004 0.001 ARG C 154 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1966.95 seconds wall clock time: 35 minutes 48.26 seconds (2148.26 seconds total)