Starting phenix.real_space_refine on Fri Dec 8 09:23:15 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dzy_8942/12_2023/6dzy_8942_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dzy_8942/12_2023/6dzy_8942.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dzy_8942/12_2023/6dzy_8942_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dzy_8942/12_2023/6dzy_8942_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dzy_8942/12_2023/6dzy_8942_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dzy_8942/12_2023/6dzy_8942.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dzy_8942/12_2023/6dzy_8942.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dzy_8942/12_2023/6dzy_8942_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dzy_8942/12_2023/6dzy_8942_neut_updated.pdb" } resolution = 4.1 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= 0.003 sd= 1.383 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 99 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 40 5.16 5 C 5117 2.51 5 N 1249 2.21 5 O 1436 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 79": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 7842 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4282 Classifications: {'peptide': 537} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 514} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 913 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "L" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 830 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 5, 'TRANS': 101} Chain: "V" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1744 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 8, 'TRANS': 212} Chain breaks: 1 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {'HJM': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.82, per 1000 atoms: 0.61 Number of scatterers: 7842 At special positions: 0 Unit cell: (90.828, 103.356, 120.06, 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 40 16.00 O 1436 8.00 N 1249 7.00 C 5117 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 200 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 115 " distance=2.03 Simple disulfide: pdb=" SG CYS L 43 " - pdb=" SG CYS L 112 " distance=2.03 Simple disulfide: pdb=" SG CYS V 37 " - pdb=" SG CYS V 111 " distance=2.03 Simple disulfide: pdb=" SG CYS V 172 " - pdb=" SG CYS V 237 " 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 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG B 1 " - " ASN A 208 " Time building additional restraints: 3.15 Conformation dependent library (CDL) restraints added in 1.4 seconds 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1804 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 37 helices and 9 sheets defined 42.6% alpha, 13.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.52 Creating SS restraints... Processing helix chain 'A' and resid 85 through 96 Processing helix chain 'A' and resid 99 through 109 removed outlier: 3.574A pdb=" N PHE A 105 " --> pdb=" O ASN A 101 " (cutoff:3.500A) Proline residue: A 106 - end of helix Processing helix chain 'A' and resid 114 through 127 removed outlier: 4.391A pdb=" N LEU A 119 " --> pdb=" O ALA A 116 " (cutoff:3.500A) Proline residue: A 120 - end of helix removed outlier: 4.179A pdb=" N MET A 124 " --> pdb=" O TYR A 121 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE A 127 " --> pdb=" O MET A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 143 removed outlier: 3.873A pdb=" N GLU A 136 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TYR A 142 " --> pdb=" O ALA A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 154 removed outlier: 3.805A pdb=" N ILE A 154 " --> pdb=" O TRP A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 191 removed outlier: 3.630A pdb=" N LYS A 159 " --> pdb=" O PRO A 156 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N GLY A 160 " --> pdb=" O ILE A 157 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY A 162 " --> pdb=" O LYS A 159 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE A 167 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE A 168 " --> pdb=" O ILE A 165 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA A 173 " --> pdb=" O PHE A 170 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N TYR A 176 " --> pdb=" O ALA A 173 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ASN A 177 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N THR A 178 " --> pdb=" O TYR A 175 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE A 179 " --> pdb=" O TYR A 176 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N MET A 180 " --> pdb=" O ASN A 177 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU A 184 " --> pdb=" O ALA A 181 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR A 185 " --> pdb=" O TRP A 182 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ILE A 188 " --> pdb=" O TYR A 185 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE A 191 " --> pdb=" O ILE A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 227 through 234 Processing helix chain 'A' and resid 239 through 241 No H-bonds generated for 'chain 'A' and resid 239 through 241' Processing helix chain 'A' and resid 253 through 271 removed outlier: 3.784A pdb=" N MET A 260 " --> pdb=" O ALA A 256 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE A 270 " --> pdb=" O ILE A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 301 removed outlier: 3.632A pdb=" N GLY A 278 " --> pdb=" O VAL A 274 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N LYS A 279 " --> pdb=" O LYS A 275 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL A 280 " --> pdb=" O THR A 276 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N VAL A 283 " --> pdb=" O LYS A 279 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N THR A 286 " --> pdb=" O TRP A 282 " (cutoff:3.500A) Proline residue: A 288 - end of helix removed outlier: 4.060A pdb=" N ARG A 298 " --> pdb=" O VAL A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 313 Processing helix chain 'A' and resid 317 through 321 Processing helix chain 'A' and resid 323 through 337 removed outlier: 3.514A pdb=" N PHE A 334 " --> pdb=" O ALA A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 350 removed outlier: 3.594A pdb=" N SER A 349 " --> pdb=" O LEU A 345 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N TYR A 350 " --> pdb=" O ALA A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 390 removed outlier: 3.643A pdb=" N VAL A 363 " --> pdb=" O GLN A 359 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE A 379 " --> pdb=" O SER A 375 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N TYR A 385 " --> pdb=" O THR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 416 removed outlier: 3.506A pdb=" N TYR A 410 " --> pdb=" O LEU A 406 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ALA A 411 " --> pdb=" O PHE A 407 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA A 415 " --> pdb=" O ALA A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 453 removed outlier: 3.702A pdb=" N PHE A 428 " --> pdb=" O ALA A 424 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE A 432 " --> pdb=" O PHE A 428 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU A 443 " --> pdb=" O SER A 439 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU A 444 " --> pdb=" O PHE A 440 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL A 446 " --> pdb=" O GLY A 442 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU A 453 " --> pdb=" O ALA A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 458 No H-bonds generated for 'chain 'A' and resid 455 through 458' Processing helix chain 'A' and resid 462 through 483 removed outlier: 3.624A pdb=" N VAL A 466 " --> pdb=" O ARG A 462 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU A 467 " --> pdb=" O GLU A 463 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL A 479 " --> pdb=" O PHE A 475 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N THR A 480 " --> pdb=" O GLY A 476 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU A 481 " --> pdb=" O SER A 477 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N PHE A 483 " --> pdb=" O VAL A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 496 removed outlier: 3.704A pdb=" N LEU A 491 " --> pdb=" O TYR A 487 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU A 494 " --> pdb=" O LYS A 490 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N TYR A 495 " --> pdb=" O LEU A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 513 Processing helix chain 'A' and resid 518 through 529 removed outlier: 3.885A pdb=" N MET A 528 " --> pdb=" O ASP A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 542 Processing helix chain 'A' and resid 544 through 556 removed outlier: 4.355A pdb=" N ILE A 552 " --> pdb=" O PHE A 548 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE A 553 " --> pdb=" O LEU A 549 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE A 556 " --> pdb=" O ILE A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 599 removed outlier: 4.228A pdb=" N PHE A 586 " --> pdb=" O GLY A 582 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ILE A 587 " --> pdb=" O THR A 583 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N CYS A 588 " --> pdb=" O SER A 584 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ILE A 589 " --> pdb=" O SER A 585 " (cutoff:3.500A) Proline residue: A 590 - end of helix Processing helix chain 'A' and resid 604 through 612 removed outlier: 3.582A pdb=" N ILE A 608 " --> pdb=" O PHE A 604 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER A 611 " --> pdb=" O ARG A 607 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 50 No H-bonds generated for 'chain 'H' and resid 48 through 50' Processing helix chain 'H' and resid 83 through 85 No H-bonds generated for 'chain 'H' and resid 83 through 85' Processing helix chain 'H' and resid 107 through 109 No H-bonds generated for 'chain 'H' and resid 107 through 109' Processing helix chain 'H' and resid 121 through 123 No H-bonds generated for 'chain 'H' and resid 121 through 123' Processing helix chain 'L' and resid 104 through 106 No H-bonds generated for 'chain 'L' and resid 104 through 106' Processing helix chain 'V' and resid 44 through 46 No H-bonds generated for 'chain 'V' and resid 44 through 46' Processing helix chain 'V' and resid 77 through 79 No H-bonds generated for 'chain 'V' and resid 77 through 79' Processing helix chain 'V' and resid 89 through 91 No H-bonds generated for 'chain 'V' and resid 89 through 91' Processing helix chain 'V' and resid 103 through 105 No H-bonds generated for 'chain 'V' and resid 103 through 105' Processing helix chain 'V' and resid 229 through 231 No H-bonds generated for 'chain 'V' and resid 229 through 231' Processing sheet with id= A, first strand: chain 'H' and resid 22 through 25 removed outlier: 3.652A pdb=" N GLN H 22 " --> pdb=" O SER H 44 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N SER H 44 " --> pdb=" O GLN H 22 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR H 97 " --> pdb=" O ASP H 92 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'H' and resid 134 through 136 removed outlier: 3.567A pdb=" N VAL H 112 " --> pdb=" O GLN H 58 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA H 116 " --> pdb=" O ASN H 54 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY H 68 " --> pdb=" O TRP H 55 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N LYS H 57 " --> pdb=" O TRP H 66 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N TRP H 66 " --> pdb=" O LYS H 57 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'L' and resid 24 through 27 removed outlier: 4.248A pdb=" N SER L 27 " --> pdb=" O SER L 42 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N SER L 42 " --> pdb=" O SER L 27 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA L 39 " --> pdb=" O ILE L 99 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE L 41 " --> pdb=" O LEU L 97 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE L 95 " --> pdb=" O CYS L 43 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'L' and resid 30 through 32 removed outlier: 6.686A pdb=" N LYS L 127 " --> pdb=" O LEU L 31 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR L 126 " --> pdb=" O TYR L 110 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL L 128 " --> pdb=" O ALA L 108 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE L 111 " --> pdb=" O PHE L 60 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N TRP L 59 " --> pdb=" O ILE L 72 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE L 72 " --> pdb=" O TRP L 59 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N GLN L 61 " --> pdb=" O LEU L 70 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N LEU L 70 " --> pdb=" O GLN L 61 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'V' and resid 18 through 21 removed outlier: 3.562A pdb=" N THR V 86 " --> pdb=" O TYR V 95 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'V' and resid 72 through 75 removed outlier: 6.551A pdb=" N TRP V 51 " --> pdb=" O ILE V 63 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'V' and resid 107 through 109 Processing sheet with id= H, first strand: chain 'V' and resid 153 through 155 removed outlier: 3.627A pdb=" N ASP V 219 " --> pdb=" O SER V 216 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'V' and resid 182 through 184 removed outlier: 3.890A pdb=" N ALA V 183 " --> pdb=" O GLN V 238 " (cutoff:3.500A) 289 hydrogen bonds defined for protein. 753 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: 2.02 Time building geometry restraints manager: 3.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 1194 1.27 - 1.41: 2235 1.41 - 1.54: 4523 1.54 - 1.68: 58 1.68 - 1.82: 59 Bond restraints: 8069 Sorted by residual: bond pdb=" C3 HJM A 701 " pdb=" C5 HJM A 701 " ideal model delta sigma weight residual 2.040 1.547 0.493 2.00e-02 2.50e+03 6.08e+02 bond pdb=" C1 HJM A 701 " pdb=" C2 HJM A 701 " ideal model delta sigma weight residual 0.996 1.489 -0.493 2.00e-02 2.50e+03 6.07e+02 bond pdb=" C2 HJM A 701 " pdb=" C8 HJM A 701 " ideal model delta sigma weight residual 1.918 1.504 0.414 2.00e-02 2.50e+03 4.28e+02 bond pdb=" C11 HJM A 701 " pdb=" C12 HJM A 701 " ideal model delta sigma weight residual 1.966 1.570 0.396 2.00e-02 2.50e+03 3.91e+02 bond pdb=" C11 HJM A 701 " pdb=" C8 HJM A 701 " ideal model delta sigma weight residual 1.753 1.363 0.390 2.00e-02 2.50e+03 3.81e+02 ... (remaining 8064 not shown) Histogram of bond angle deviations from ideal: 99.18 - 106.97: 242 106.97 - 114.77: 4606 114.77 - 122.56: 5048 122.56 - 130.36: 1038 130.36 - 138.15: 50 Bond angle restraints: 10984 Sorted by residual: angle pdb=" N TYR V 119 " pdb=" CA TYR V 119 " pdb=" CB TYR V 119 " ideal model delta sigma weight residual 111.62 138.15 -26.53 1.43e+00 4.89e-01 3.44e+02 angle pdb=" C TYR A 176 " pdb=" N ASN A 177 " pdb=" CA ASN A 177 " ideal model delta sigma weight residual 120.29 133.18 -12.89 1.42e+00 4.96e-01 8.23e+01 angle pdb=" N TYR V 119 " pdb=" CA TYR V 119 " pdb=" C TYR V 119 " ideal model delta sigma weight residual 111.30 99.18 12.12 1.36e+00 5.41e-01 7.94e+01 angle pdb=" N TYR A 176 " pdb=" CA TYR A 176 " pdb=" C TYR A 176 " ideal model delta sigma weight residual 111.36 120.93 -9.57 1.09e+00 8.42e-01 7.70e+01 angle pdb=" C SER A 532 " pdb=" N PRO A 533 " pdb=" CA PRO A 533 " ideal model delta sigma weight residual 121.00 130.13 -9.13 1.16e+00 7.43e-01 6.19e+01 ... (remaining 10979 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.07: 4554 21.07 - 42.13: 93 42.13 - 63.20: 26 63.20 - 84.27: 7 84.27 - 105.33: 12 Dihedral angle restraints: 4692 sinusoidal: 1846 harmonic: 2846 Sorted by residual: dihedral pdb=" N TYR V 119 " pdb=" C TYR V 119 " pdb=" CA TYR V 119 " pdb=" CB TYR V 119 " ideal model delta harmonic sigma weight residual 122.80 151.95 -29.15 0 2.50e+00 1.60e-01 1.36e+02 dihedral pdb=" CA GLU L 47 " pdb=" C GLU L 47 " pdb=" N SER L 48 " pdb=" CA SER L 48 " ideal model delta harmonic sigma weight residual 0.00 38.41 -38.41 0 5.00e+00 4.00e-02 5.90e+01 dihedral pdb=" C TYR V 119 " pdb=" N TYR V 119 " pdb=" CA TYR V 119 " pdb=" CB TYR V 119 " ideal model delta harmonic sigma weight residual -122.60 -139.33 16.73 0 2.50e+00 1.60e-01 4.48e+01 ... (remaining 4689 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.079: 1214 1.079 - 2.158: 0 2.158 - 3.237: 0 3.237 - 4.317: 0 4.317 - 5.396: 1 Chirality restraints: 1215 Sorted by residual: chirality pdb=" N1 HJM A 701 " pdb=" C1 HJM A 701 " pdb=" C7 HJM A 701 " pdb=" C9 HJM A 701 " both_signs ideal model delta sigma weight residual False -3.09 2.30 -5.40 2.00e-01 2.50e+01 7.28e+02 chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-02 2.50e+03 1.20e+02 chirality pdb=" CA TYR V 119 " pdb=" N TYR V 119 " pdb=" C TYR V 119 " pdb=" CB TYR V 119 " both_signs ideal model delta sigma weight residual False 2.51 1.45 1.06 2.00e-01 2.50e+01 2.79e+01 ... (remaining 1212 not shown) Planarity restraints: 1355 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 2 " -0.345 2.00e-02 2.50e+03 2.98e-01 1.11e+03 pdb=" C7 NAG B 2 " 0.080 2.00e-02 2.50e+03 pdb=" C8 NAG B 2 " -0.077 2.00e-02 2.50e+03 pdb=" N2 NAG B 2 " 0.528 2.00e-02 2.50e+03 pdb=" O7 NAG B 2 " -0.187 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 1 " -0.322 2.00e-02 2.50e+03 2.73e-01 9.35e+02 pdb=" C7 NAG B 1 " 0.083 2.00e-02 2.50e+03 pdb=" C8 NAG B 1 " -0.182 2.00e-02 2.50e+03 pdb=" N2 NAG B 1 " 0.477 2.00e-02 2.50e+03 pdb=" O7 NAG B 1 " -0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" O HJM A 701 " 0.166 2.00e-02 2.50e+03 8.51e-02 2.17e+02 pdb=" C11 HJM A 701 " 0.113 2.00e-02 2.50e+03 pdb=" C12 HJM A 701 " -0.117 2.00e-02 2.50e+03 pdb=" C13 HJM A 701 " 0.002 2.00e-02 2.50e+03 pdb=" C15 HJM A 701 " -0.043 2.00e-02 2.50e+03 pdb=" C16 HJM A 701 " -0.127 2.00e-02 2.50e+03 pdb=" C17 HJM A 701 " -0.021 2.00e-02 2.50e+03 pdb=" C18 HJM A 701 " -0.029 2.00e-02 2.50e+03 pdb=" C19 HJM A 701 " -0.039 2.00e-02 2.50e+03 pdb=" C2 HJM A 701 " 0.054 2.00e-02 2.50e+03 pdb=" C8 HJM A 701 " 0.085 2.00e-02 2.50e+03 pdb=" N2 HJM A 701 " -0.045 2.00e-02 2.50e+03 ... (remaining 1352 not shown) Histogram of nonbonded interaction distances: 1.39 - 2.09: 3 2.09 - 2.79: 1981 2.79 - 3.49: 10557 3.49 - 4.20: 18751 4.20 - 4.90: 32292 Nonbonded interactions: 63584 Sorted by model distance: nonbonded pdb=" O TRP A 220 " pdb=" CG2 VAL V 116 " model vdw 1.386 3.460 nonbonded pdb=" CD1 ILE A 327 " pdb=" CE2 PHE A 551 " model vdw 1.638 3.760 nonbonded pdb=" CB PRO V 118 " pdb=" CD1 TYR V 120 " model vdw 1.909 3.740 nonbonded pdb=" OE1 GLU A 494 " pdb=" O2B LMT A 702 " model vdw 2.093 2.440 nonbonded pdb=" O GLU A 229 " pdb=" OG1 THR A 233 " model vdw 2.126 2.440 ... (remaining 63579 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 6.100 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 24.730 Find NCS groups from input model: 0.210 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: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6273 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 : 0.015 0.493 8069 Z= 1.019 Angle : 0.947 26.534 10984 Z= 0.542 Chirality : 0.167 5.396 1215 Planarity : 0.013 0.298 1354 Dihedral : 12.085 105.335 2873 Min Nonbonded Distance : 1.386 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.70 % Favored : 95.19 % Rotamer: Outliers : 1.32 % Allowed : 0.60 % Favored : 98.07 % Cbeta Deviations : 0.44 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -2.99 (0.24), residues: 978 helix: -2.35 (0.21), residues: 357 sheet: -2.11 (0.35), residues: 157 loop : -1.46 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 52 HIS 0.006 0.001 HIS A 235 PHE 0.014 0.002 PHE A 213 TYR 0.017 0.001 TYR A 176 ARG 0.003 0.001 ARG V 245 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 471 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 8 residues processed: 478 average time/residue: 0.2040 time to fit residues: 129.5571 Evaluate side-chains 339 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 331 time to evaluate : 0.861 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 8 outliers final: 1 residues processed: 8 average time/residue: 0.1705 time to fit residues: 2.9985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 81 optimal weight: 10.0000 chunk 73 optimal weight: 4.9990 chunk 40 optimal weight: 0.5980 chunk 25 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 HIS A 211 ASN A 235 HIS ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 391 ASN L 61 GLN V 239 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6800 moved from start: 0.4469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 8069 Z= 0.330 Angle : 0.802 11.006 10984 Z= 0.407 Chirality : 0.050 0.351 1215 Planarity : 0.006 0.119 1354 Dihedral : 9.406 68.043 1178 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.60 % Favored : 95.30 % Rotamer: Outliers : 0.24 % Allowed : 2.77 % Favored : 96.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.61 (0.26), residues: 978 helix: -0.69 (0.23), residues: 375 sheet: -1.08 (0.35), residues: 172 loop : -1.27 (0.32), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP V 62 HIS 0.007 0.002 HIS V 240 PHE 0.037 0.003 PHE V 220 TYR 0.037 0.003 TYR V 48 ARG 0.004 0.001 ARG V 117 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 399 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 400 average time/residue: 0.1897 time to fit residues: 106.0692 Evaluate side-chains 319 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 319 time to evaluate : 0.932 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 48 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 59 optimal weight: 9.9990 chunk 24 optimal weight: 0.9980 chunk 88 optimal weight: 9.9990 chunk 95 optimal weight: 7.9990 chunk 78 optimal weight: 5.9990 chunk 87 optimal weight: 10.0000 chunk 30 optimal weight: 8.9990 chunk 70 optimal weight: 0.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 HIS ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 176 GLN V 187 GLN ** V 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6893 moved from start: 0.5420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8069 Z= 0.275 Angle : 0.702 13.783 10984 Z= 0.359 Chirality : 0.046 0.340 1215 Planarity : 0.005 0.100 1354 Dihedral : 7.182 59.596 1178 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 17.06 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.60 % Favored : 95.30 % Rotamer: Outliers : 0.12 % Allowed : 2.41 % Favored : 97.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.28 (0.26), residues: 978 helix: -0.26 (0.25), residues: 369 sheet: -0.81 (0.35), residues: 185 loop : -1.29 (0.32), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP A 541 HIS 0.005 0.002 HIS A 240 PHE 0.039 0.002 PHE A 440 TYR 0.019 0.002 TYR A 312 ARG 0.009 0.001 ARG V 117 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 375 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 375 average time/residue: 0.1751 time to fit residues: 91.6564 Evaluate side-chains 317 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 316 time to evaluate : 0.941 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0791 time to fit residues: 1.3745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 87 optimal weight: 7.9990 chunk 66 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 42 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 88 optimal weight: 10.0000 chunk 93 optimal weight: 5.9990 chunk 46 optimal weight: 7.9990 chunk 83 optimal weight: 9.9990 chunk 25 optimal weight: 3.9990 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 58 GLN ** H 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 20 GLN ** V 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7039 moved from start: 0.6337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 8069 Z= 0.310 Angle : 0.733 10.305 10984 Z= 0.379 Chirality : 0.047 0.375 1215 Planarity : 0.006 0.093 1354 Dihedral : 6.653 58.345 1178 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 20.15 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.11 % Favored : 94.79 % Rotamer: Outliers : 0.12 % Allowed : 2.05 % Favored : 97.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.32 % 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: -1.09 (0.26), residues: 978 helix: 0.04 (0.26), residues: 370 sheet: -0.62 (0.37), residues: 184 loop : -1.37 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP V 124 HIS 0.006 0.002 HIS L 100 PHE 0.042 0.003 PHE A 440 TYR 0.019 0.002 TYR A 171 ARG 0.005 0.001 ARG L 85 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 378 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 378 average time/residue: 0.1707 time to fit residues: 90.1451 Evaluate side-chains 303 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 302 time to evaluate : 0.864 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0759 time to fit residues: 1.2543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 78 optimal weight: 8.9990 chunk 53 optimal weight: 7.9990 chunk 1 optimal weight: 6.9990 chunk 69 optimal weight: 0.8980 chunk 38 optimal weight: 9.9990 chunk 80 optimal weight: 9.9990 chunk 64 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 47 optimal weight: 7.9990 chunk 84 optimal weight: 8.9990 chunk 23 optimal weight: 3.9990 overall best weight: 5.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN ** A 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 ASN ** H 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 54 GLN V 187 GLN ** V 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.7441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 8069 Z= 0.437 Angle : 0.871 12.662 10984 Z= 0.455 Chirality : 0.051 0.440 1215 Planarity : 0.007 0.087 1354 Dihedral : 7.188 59.536 1178 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 26.01 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.36 % Favored : 92.54 % Rotamer: Outliers : 0.12 % Allowed : 3.97 % Favored : 95.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.32 % 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: -1.45 (0.26), residues: 978 helix: -0.27 (0.25), residues: 362 sheet: -0.89 (0.34), residues: 201 loop : -1.53 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP V 184 HIS 0.005 0.002 HIS A 143 PHE 0.030 0.003 PHE A 440 TYR 0.036 0.003 TYR A 592 ARG 0.020 0.001 ARG V 203 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 342 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 342 average time/residue: 0.1730 time to fit residues: 82.1884 Evaluate side-chains 285 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 284 time to evaluate : 0.876 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0741 time to fit residues: 1.3106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 31 optimal weight: 0.0670 chunk 84 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 93 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 49 optimal weight: 0.6980 chunk 90 optimal weight: 8.9990 overall best weight: 1.3320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN ** A 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 ASN A 391 ASN V 186 GLN ** V 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.7465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8069 Z= 0.200 Angle : 0.685 12.539 10984 Z= 0.353 Chirality : 0.045 0.408 1215 Planarity : 0.005 0.070 1354 Dihedral : 6.505 59.055 1178 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 18.48 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.42 % Favored : 94.48 % Rotamer: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.26), residues: 978 helix: 0.30 (0.27), residues: 359 sheet: -0.62 (0.35), residues: 194 loop : -1.32 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP V 184 HIS 0.007 0.002 HIS A 240 PHE 0.040 0.002 PHE A 551 TYR 0.043 0.002 TYR A 592 ARG 0.013 0.001 ARG V 203 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 367 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 367 average time/residue: 0.1737 time to fit residues: 88.4620 Evaluate side-chains 287 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 287 time to evaluate : 0.906 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 10 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 79 optimal weight: 0.0030 chunk 52 optimal weight: 8.9990 chunk 93 optimal weight: 10.0000 chunk 58 optimal weight: 8.9990 chunk 56 optimal weight: 5.9990 chunk 43 optimal weight: 0.0010 chunk 57 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 moved from start: 0.7528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8069 Z= 0.186 Angle : 0.690 12.036 10984 Z= 0.348 Chirality : 0.045 0.381 1215 Planarity : 0.004 0.055 1354 Dihedral : 6.198 56.967 1178 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 17.51 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.40 % Favored : 95.50 % Rotamer: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.32 % 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: -0.78 (0.27), residues: 978 helix: 0.49 (0.27), residues: 357 sheet: -0.46 (0.35), residues: 194 loop : -1.37 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP V 184 HIS 0.007 0.001 HIS A 240 PHE 0.027 0.002 PHE A 465 TYR 0.033 0.002 TYR A 592 ARG 0.009 0.001 ARG V 203 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 365 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 365 average time/residue: 0.1767 time to fit residues: 90.6694 Evaluate side-chains 294 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 294 time to evaluate : 0.888 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 55 optimal weight: 8.9990 chunk 28 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 73 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 chunk 89 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN ** A 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 391 ASN L 62 GLN ** V 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 moved from start: 0.7732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 8069 Z= 0.218 Angle : 0.682 11.867 10984 Z= 0.348 Chirality : 0.043 0.193 1215 Planarity : 0.005 0.100 1354 Dihedral : 6.177 56.427 1178 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 18.93 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.11 % Favored : 94.79 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.27), residues: 978 helix: 0.56 (0.28), residues: 352 sheet: -0.36 (0.36), residues: 194 loop : -1.38 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP V 184 HIS 0.006 0.001 HIS A 240 PHE 0.022 0.002 PHE A 341 TYR 0.028 0.002 TYR A 592 ARG 0.011 0.001 ARG H 38 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 359 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 359 average time/residue: 0.1647 time to fit residues: 83.3916 Evaluate side-chains 281 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 281 time to evaluate : 0.913 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 87 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 chunk 52 optimal weight: 8.9990 chunk 37 optimal weight: 3.9990 chunk 68 optimal weight: 0.4980 chunk 26 optimal weight: 0.8980 chunk 78 optimal weight: 8.9990 chunk 82 optimal weight: 0.7980 chunk 86 optimal weight: 0.2980 chunk 57 optimal weight: 0.0270 chunk 92 optimal weight: 0.7980 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 143 HIS ** A 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 355 ASN ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6958 moved from start: 0.7803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 8069 Z= 0.184 Angle : 0.675 11.774 10984 Z= 0.337 Chirality : 0.043 0.182 1215 Planarity : 0.005 0.070 1354 Dihedral : 5.946 53.560 1178 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 17.06 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.60 % Favored : 95.30 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.32 % 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 (0.27), residues: 978 helix: 0.57 (0.28), residues: 361 sheet: -0.34 (0.36), residues: 193 loop : -1.35 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP V 184 HIS 0.006 0.001 HIS A 240 PHE 0.021 0.002 PHE A 440 TYR 0.027 0.002 TYR A 592 ARG 0.006 0.001 ARG V 203 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 344 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 344 average time/residue: 0.1761 time to fit residues: 86.5403 Evaluate side-chains 282 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 282 time to evaluate : 0.898 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 56 optimal weight: 6.9990 chunk 43 optimal weight: 0.9990 chunk 64 optimal weight: 9.9990 chunk 96 optimal weight: 7.9990 chunk 88 optimal weight: 9.9990 chunk 76 optimal weight: 7.9990 chunk 7 optimal weight: 0.0670 chunk 59 optimal weight: 5.9990 chunk 47 optimal weight: 0.2980 chunk 61 optimal weight: 2.9990 chunk 81 optimal weight: 0.0050 overall best weight: 0.8736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 143 HIS ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 391 ASN ** V 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6971 moved from start: 0.7881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 8069 Z= 0.183 Angle : 0.671 11.632 10984 Z= 0.335 Chirality : 0.042 0.162 1215 Planarity : 0.004 0.043 1354 Dihedral : 5.852 49.187 1178 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 17.13 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.50 % Favored : 95.40 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.32 % 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: -0.59 (0.27), residues: 978 helix: 0.63 (0.28), residues: 360 sheet: -0.21 (0.36), residues: 188 loop : -1.34 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP V 184 HIS 0.005 0.001 HIS A 240 PHE 0.019 0.002 PHE A 170 TYR 0.020 0.001 TYR A 592 ARG 0.012 0.001 ARG L 85 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 340 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 340 average time/residue: 0.1688 time to fit residues: 81.0601 Evaluate side-chains 268 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 268 time to evaluate : 0.876 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 23 optimal weight: 2.9990 chunk 70 optimal weight: 0.0270 chunk 11 optimal weight: 0.0040 chunk 21 optimal weight: 3.9990 chunk 77 optimal weight: 10.0000 chunk 32 optimal weight: 0.5980 chunk 79 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 14 optimal weight: 6.9990 chunk 67 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 overall best weight: 0.9254 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 239 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 = 0.4024 r_free = 0.4024 target = 0.160386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.138334 restraints weight = 15535.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.143621 restraints weight = 8861.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.147426 restraints weight = 5693.558| |-----------------------------------------------------------------------------| r_work (final): 0.3856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6849 moved from start: 0.7970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 8069 Z= 0.200 Angle : 0.674 11.530 10984 Z= 0.339 Chirality : 0.043 0.209 1215 Planarity : 0.004 0.043 1354 Dihedral : 5.921 49.383 1178 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 18.03 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.81 % Favored : 95.09 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.32 % 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 (0.27), residues: 978 helix: 0.64 (0.28), residues: 358 sheet: -0.07 (0.37), residues: 187 loop : -1.38 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP V 184 HIS 0.005 0.001 HIS A 240 PHE 0.024 0.002 PHE A 465 TYR 0.020 0.002 TYR A 385 ARG 0.004 0.001 ARG V 203 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2324.20 seconds wall clock time: 42 minutes 48.61 seconds (2568.61 seconds total)