Starting phenix.real_space_refine on Mon Mar 11 10:07:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dzy_8942/03_2024/6dzy_8942_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dzy_8942/03_2024/6dzy_8942.map 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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dzy_8942/03_2024/6dzy_8942.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dzy_8942/03_2024/6dzy_8942.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dzy_8942/03_2024/6dzy_8942_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dzy_8942/03_2024/6dzy_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-dev-5265/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: 4.90, per 1000 atoms: 0.62 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: 3.34 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: 1.69 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: 2.23 Time building geometry restraints manager: 3.57 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=" C VAL A 367 " pdb=" N ASN A 368 " ideal model delta sigma weight residual 1.335 1.454 -0.119 1.31e-02 5.83e+03 8.25e+01 bond pdb=" C ASN A 208 " pdb=" O ASN A 208 " ideal model delta sigma weight residual 1.235 1.137 0.098 1.26e-02 6.30e+03 6.07e+01 bond pdb=" C PRO A 571 " pdb=" N TYR A 572 " ideal model delta sigma weight residual 1.333 1.221 0.112 1.45e-02 4.76e+03 5.92e+01 bond pdb=" C ASN A 368 " pdb=" N CYS A 369 " ideal model delta sigma weight residual 1.334 1.437 -0.103 1.43e-02 4.89e+03 5.21e+01 bond pdb=" C1 HJM A 701 " pdb=" N1 HJM A 701 " ideal model delta sigma weight residual 1.463 1.568 -0.105 2.00e-02 2.50e+03 2.78e+01 ... (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 - 22.45: 4586 22.45 - 44.90: 89 44.90 - 67.35: 19 67.35 - 89.79: 9 89.79 - 112.24: 13 Dihedral angle restraints: 4716 sinusoidal: 1870 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 4713 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.211: 1206 0.211 - 0.422: 6 0.422 - 0.633: 2 0.633 - 0.844: 0 0.844 - 1.055: 1 Chirality restraints: 1215 Sorted by residual: 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 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 1.76 2.30 -0.55 2.00e-01 2.50e+01 7.43e+00 ... (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: 1.940 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: 6.270 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 25.940 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.590 ------------------------------------------------------------------------------- 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 : 0.006 0.119 8069 Z= 0.364 Angle : 0.878 26.534 10984 Z= 0.529 Chirality : 0.064 1.055 1215 Planarity : 0.013 0.298 1354 Dihedral : 12.392 112.243 2897 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 : 0.823 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 REVERT: A 81 THR cc_start: 0.8792 (p) cc_final: 0.8538 (t) REVERT: A 82 TRP cc_start: 0.5796 (m-10) cc_final: 0.5371 (m-10) REVERT: A 121 TYR cc_start: 0.9167 (t80) cc_final: 0.8563 (t80) REVERT: A 158 PHE cc_start: 0.7206 (m-80) cc_final: 0.6870 (m-80) REVERT: A 184 LEU cc_start: 0.9093 (tp) cc_final: 0.8627 (tp) REVERT: A 189 SER cc_start: 0.9611 (m) cc_final: 0.9332 (p) REVERT: A 195 LEU cc_start: 0.8511 (mt) cc_final: 0.8095 (mt) REVERT: A 197 TRP cc_start: 0.8024 (m-10) cc_final: 0.7629 (m-10) REVERT: A 268 PHE cc_start: 0.8591 (m-80) cc_final: 0.8385 (m-80) REVERT: A 326 TRP cc_start: 0.8560 (m100) cc_final: 0.8295 (m-10) REVERT: A 333 ILE cc_start: 0.9162 (pt) cc_final: 0.8877 (pt) REVERT: A 369 CYS cc_start: 0.9027 (m) cc_final: 0.8764 (m) REVERT: A 386 MET cc_start: 0.7877 (mmm) cc_final: 0.7651 (mmm) REVERT: A 390 ARG cc_start: 0.8441 (mtt180) cc_final: 0.7481 (mtt180) REVERT: A 410 TYR cc_start: 0.8215 (t80) cc_final: 0.7887 (t80) REVERT: A 417 MET cc_start: 0.8004 (mtm) cc_final: 0.7641 (mtm) REVERT: A 422 PHE cc_start: 0.7805 (t80) cc_final: 0.7379 (t80) REVERT: A 460 LYS cc_start: 0.7541 (mmtt) cc_final: 0.7340 (ttpt) REVERT: A 464 ARG cc_start: 0.8400 (mtt90) cc_final: 0.7874 (ttm110) REVERT: A 478 LEU cc_start: 0.8702 (tp) cc_final: 0.8410 (tp) REVERT: A 538 ARG cc_start: 0.8122 (mtm180) cc_final: 0.7504 (ttt-90) REVERT: A 549 LEU cc_start: 0.9293 (mp) cc_final: 0.8952 (pp) REVERT: A 555 SER cc_start: 0.8248 (p) cc_final: 0.8005 (p) REVERT: A 570 TYR cc_start: 0.6643 (m-10) cc_final: 0.6019 (m-80) REVERT: A 592 TYR cc_start: 0.7948 (t80) cc_final: 0.7717 (t80) REVERT: A 593 ILE cc_start: 0.8339 (mt) cc_final: 0.8070 (mt) REVERT: A 597 LEU cc_start: 0.8210 (mt) cc_final: 0.7917 (tt) REVERT: H 21 VAL cc_start: 0.8059 (t) cc_final: 0.7641 (t) REVERT: L 71 LEU cc_start: 0.8324 (mt) cc_final: 0.8110 (mt) REVERT: L 72 ILE cc_start: 0.8701 (mm) cc_final: 0.8054 (tp) REVERT: L 83 PRO cc_start: 0.8309 (Cg_exo) cc_final: 0.8060 (Cg_endo) REVERT: L 121 THR cc_start: 0.7359 (p) cc_final: 0.6575 (m) REVERT: V 43 THR cc_start: 0.8404 (m) cc_final: 0.8075 (t) REVERT: V 47 TYR cc_start: 0.4447 (p90) cc_final: 0.2915 (p90) REVERT: V 56 HIS cc_start: 0.6481 (t70) cc_final: 0.6070 (p-80) REVERT: V 93 THR cc_start: 0.8861 (m) cc_final: 0.8499 (p) REVERT: V 195 LEU cc_start: 0.8989 (tp) cc_final: 0.8503 (tp) REVERT: V 236 TYR cc_start: 0.7410 (m-80) cc_final: 0.7187 (m-80) REVERT: V 241 TYR cc_start: 0.8559 (t80) cc_final: 0.7786 (t80) outliers start: 11 outliers final: 8 residues processed: 478 average time/residue: 0.1985 time to fit residues: 125.8532 Evaluate side-chains 353 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 345 time to evaluate : 0.830 ------------------------------------------------------------------------------- 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: 0.4980 chunk 73 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 76 optimal weight: 0.7980 chunk 29 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 56 optimal weight: 0.1980 chunk 88 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 H 58 GLN L 51 ASN L 61 GLN V 239 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6528 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 8069 Z= 0.218 Angle : 0.668 10.365 10984 Z= 0.341 Chirality : 0.047 0.255 1215 Planarity : 0.005 0.101 1354 Dihedral : 9.957 72.892 1202 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.50 % Favored : 95.40 % Rotamer: Outliers : 0.24 % Allowed : 2.17 % Favored : 97.59 % 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: -1.82 (0.25), residues: 978 helix: -0.92 (0.23), residues: 379 sheet: -1.00 (0.37), residues: 165 loop : -1.43 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP V 62 HIS 0.005 0.001 HIS A 240 PHE 0.032 0.002 PHE V 220 TYR 0.028 0.002 TYR A 176 ARG 0.003 0.000 ARG A 462 *********************** 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 413 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 411 time to evaluate : 1.068 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: A 81 THR cc_start: 0.8944 (p) cc_final: 0.8561 (t) REVERT: A 82 TRP cc_start: 0.5802 (m-10) cc_final: 0.5437 (m-10) REVERT: A 121 TYR cc_start: 0.9301 (t80) cc_final: 0.8845 (t80) REVERT: A 148 ILE cc_start: 0.8094 (mt) cc_final: 0.7818 (mt) REVERT: A 189 SER cc_start: 0.9674 (m) cc_final: 0.9439 (p) REVERT: A 195 LEU cc_start: 0.8693 (mt) cc_final: 0.8230 (mt) REVERT: A 197 TRP cc_start: 0.8265 (m-10) cc_final: 0.7982 (m-10) REVERT: A 298 ARG cc_start: 0.8221 (tpm170) cc_final: 0.8018 (tpp-160) REVERT: A 316 ASN cc_start: 0.7952 (t0) cc_final: 0.7682 (t0) REVERT: A 385 TYR cc_start: 0.7319 (t80) cc_final: 0.7051 (t80) REVERT: A 390 ARG cc_start: 0.8612 (mtt180) cc_final: 0.8324 (mtt180) REVERT: A 391 ASN cc_start: 0.9506 (m-40) cc_final: 0.9252 (m110) REVERT: A 393 ASP cc_start: 0.8660 (t70) cc_final: 0.8429 (t70) REVERT: A 417 MET cc_start: 0.7934 (mtm) cc_final: 0.7499 (mtm) REVERT: A 425 ILE cc_start: 0.9106 (mm) cc_final: 0.8816 (mm) REVERT: A 447 ILE cc_start: 0.9613 (mt) cc_final: 0.9406 (mt) REVERT: A 453 GLU cc_start: 0.8804 (mm-30) cc_final: 0.8465 (mm-30) REVERT: A 460 LYS cc_start: 0.7670 (mmtt) cc_final: 0.7445 (ttpt) REVERT: A 538 ARG cc_start: 0.8045 (mtm180) cc_final: 0.7508 (ttt180) REVERT: A 567 GLN cc_start: 0.9099 (pm20) cc_final: 0.8832 (pm20) REVERT: A 592 TYR cc_start: 0.8165 (t80) cc_final: 0.7393 (t80) REVERT: A 593 ILE cc_start: 0.8509 (mt) cc_final: 0.8256 (mt) REVERT: H 22 GLN cc_start: 0.6393 (mp10) cc_final: 0.6186 (mp10) REVERT: H 50 TYR cc_start: 0.7441 (m-80) cc_final: 0.7174 (m-80) REVERT: L 71 LEU cc_start: 0.8595 (mt) cc_final: 0.8307 (mt) REVERT: L 72 ILE cc_start: 0.8747 (mm) cc_final: 0.8111 (tp) REVERT: L 78 GLN cc_start: 0.7889 (pp30) cc_final: 0.7389 (pp30) REVERT: L 83 PRO cc_start: 0.8403 (Cg_exo) cc_final: 0.8011 (Cg_endo) REVERT: V 37 CYS cc_start: 0.2840 (p) cc_final: 0.2488 (p) REVERT: V 47 TYR cc_start: 0.4056 (p90) cc_final: 0.2824 (p90) REVERT: V 62 TRP cc_start: 0.8846 (t60) cc_final: 0.8625 (t60) REVERT: V 93 THR cc_start: 0.8624 (m) cc_final: 0.8221 (p) REVERT: V 195 LEU cc_start: 0.8999 (tp) cc_final: 0.8657 (tp) outliers start: 2 outliers final: 0 residues processed: 411 average time/residue: 0.1930 time to fit residues: 111.7682 Evaluate side-chains 330 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 330 time to evaluate : 1.026 ------------------------------------------------------------------------------- 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: 0.8980 chunk 27 optimal weight: 10.0000 chunk 73 optimal weight: 0.0980 chunk 59 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 88 optimal weight: 6.9990 chunk 95 optimal weight: 7.9990 chunk 78 optimal weight: 5.9990 chunk 87 optimal weight: 6.9990 chunk 30 optimal weight: 8.9990 chunk 70 optimal weight: 0.8980 overall best weight: 2.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 ASN ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 54 GLN V 69 ASN V 176 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: 0.6836 moved from start: 0.4796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 8069 Z= 0.298 Angle : 0.713 10.854 10984 Z= 0.367 Chirality : 0.046 0.295 1215 Planarity : 0.005 0.095 1354 Dihedral : 8.010 65.731 1202 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.09 % Favored : 95.81 % Rotamer: Outliers : 0.12 % Allowed : 2.29 % Favored : 97.59 % 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: -1.32 (0.26), residues: 978 helix: -0.39 (0.24), residues: 372 sheet: -0.79 (0.35), residues: 184 loop : -1.22 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 541 HIS 0.014 0.002 HIS V 240 PHE 0.039 0.003 PHE A 440 TYR 0.020 0.002 TYR A 176 ARG 0.003 0.000 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 377 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 376 time to evaluate : 0.924 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: A 84 LYS cc_start: 0.8628 (mptt) cc_final: 0.7830 (tptm) REVERT: A 121 TYR cc_start: 0.9443 (t80) cc_final: 0.8996 (t80) REVERT: A 142 TYR cc_start: 0.8434 (t80) cc_final: 0.8233 (t80) REVERT: A 189 SER cc_start: 0.9667 (m) cc_final: 0.9412 (p) REVERT: A 195 LEU cc_start: 0.8915 (mt) cc_final: 0.8689 (mp) REVERT: A 197 TRP cc_start: 0.8942 (m-10) cc_final: 0.8597 (m-10) REVERT: A 229 GLU cc_start: 0.8408 (tt0) cc_final: 0.8176 (tt0) REVERT: A 238 GLN cc_start: 0.8626 (mp10) cc_final: 0.7626 (mt0) REVERT: A 245 LEU cc_start: 0.8364 (mm) cc_final: 0.8079 (mm) REVERT: A 302 LEU cc_start: 0.8831 (mt) cc_final: 0.8486 (mt) REVERT: A 316 ASN cc_start: 0.8492 (t0) cc_final: 0.8190 (t0) REVERT: A 385 TYR cc_start: 0.7930 (t80) cc_final: 0.7604 (t80) REVERT: A 410 TYR cc_start: 0.7978 (t80) cc_final: 0.7602 (t80) REVERT: A 417 MET cc_start: 0.7893 (mtm) cc_final: 0.7573 (mtm) REVERT: A 425 ILE cc_start: 0.9193 (mm) cc_final: 0.8936 (mm) REVERT: A 447 ILE cc_start: 0.9596 (mt) cc_final: 0.9374 (mt) REVERT: A 538 ARG cc_start: 0.7868 (mtm180) cc_final: 0.7389 (ttt-90) REVERT: A 565 LEU cc_start: 0.6794 (tp) cc_final: 0.6398 (tt) REVERT: A 567 GLN cc_start: 0.9146 (pm20) cc_final: 0.8832 (pm20) REVERT: A 570 TYR cc_start: 0.7407 (m-10) cc_final: 0.6998 (m-80) REVERT: A 592 TYR cc_start: 0.8221 (t80) cc_final: 0.6999 (t80) REVERT: A 596 ARG cc_start: 0.7995 (mmm160) cc_final: 0.7573 (mmm160) REVERT: A 606 GLU cc_start: 0.8166 (tp30) cc_final: 0.7920 (tp30) REVERT: H 22 GLN cc_start: 0.6569 (mp10) cc_final: 0.6364 (mp10) REVERT: H 50 TYR cc_start: 0.8026 (m-80) cc_final: 0.6891 (m-80) REVERT: H 120 TYR cc_start: 0.7603 (m-80) cc_final: 0.7081 (m-80) REVERT: H 128 ASP cc_start: 0.8662 (t70) cc_final: 0.7798 (t70) REVERT: L 78 GLN cc_start: 0.8013 (pp30) cc_final: 0.7521 (pp30) REVERT: V 20 GLN cc_start: 0.7931 (mm110) cc_final: 0.7671 (mm-40) REVERT: V 38 LYS cc_start: 0.7964 (tttt) cc_final: 0.7442 (mttt) REVERT: V 43 THR cc_start: 0.8659 (m) cc_final: 0.8374 (p) REVERT: V 62 TRP cc_start: 0.9035 (t60) cc_final: 0.8769 (t60) REVERT: V 93 THR cc_start: 0.8606 (m) cc_final: 0.8278 (p) REVERT: V 105 ASP cc_start: 0.8603 (m-30) cc_final: 0.8215 (m-30) REVERT: V 151 ILE cc_start: 0.8498 (mt) cc_final: 0.8124 (mt) REVERT: V 173 LYS cc_start: 0.7868 (mmtm) cc_final: 0.7408 (tppt) REVERT: V 239 GLN cc_start: 0.8296 (tm-30) cc_final: 0.8033 (tm-30) outliers start: 1 outliers final: 1 residues processed: 376 average time/residue: 0.1741 time to fit residues: 89.8717 Evaluate side-chains 309 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 308 time to evaluate : 0.888 ------------------------------------------------------------------------------- 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: 9.9990 chunk 66 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 42 optimal weight: 0.7980 chunk 59 optimal weight: 9.9990 chunk 88 optimal weight: 6.9990 chunk 93 optimal weight: 0.7980 chunk 46 optimal weight: 6.9990 chunk 83 optimal weight: 9.9990 chunk 25 optimal weight: 0.9980 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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** ** V 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 65 ASN ** V 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6831 moved from start: 0.5290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8069 Z= 0.204 Angle : 0.647 12.045 10984 Z= 0.330 Chirality : 0.044 0.349 1215 Planarity : 0.005 0.080 1354 Dihedral : 6.876 59.637 1202 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.09 % Favored : 95.81 % Rotamer: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % 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: -0.93 (0.26), residues: 978 helix: -0.01 (0.26), residues: 374 sheet: -0.44 (0.36), residues: 183 loop : -1.16 (0.31), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP V 184 HIS 0.006 0.001 HIS A 223 PHE 0.041 0.002 PHE A 440 TYR 0.017 0.002 TYR A 495 ARG 0.003 0.000 ARG H 117 *********************** 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 374 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 374 time to evaluate : 0.888 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: A 84 LYS cc_start: 0.8626 (mptt) cc_final: 0.7918 (tptm) REVERT: A 121 TYR cc_start: 0.9389 (t80) cc_final: 0.8908 (t80) REVERT: A 189 SER cc_start: 0.9674 (m) cc_final: 0.9384 (p) REVERT: A 195 LEU cc_start: 0.8914 (mt) cc_final: 0.8608 (mt) REVERT: A 197 TRP cc_start: 0.9002 (m-10) cc_final: 0.8532 (m-10) REVERT: A 229 GLU cc_start: 0.8508 (tt0) cc_final: 0.8149 (tt0) REVERT: A 245 LEU cc_start: 0.8410 (mm) cc_final: 0.7862 (mm) REVERT: A 266 ILE cc_start: 0.9161 (mt) cc_final: 0.8941 (tp) REVERT: A 302 LEU cc_start: 0.8862 (mt) cc_final: 0.8515 (mt) REVERT: A 316 ASN cc_start: 0.8551 (t0) cc_final: 0.8255 (t0) REVERT: A 333 ILE cc_start: 0.9291 (pt) cc_final: 0.9090 (pt) REVERT: A 385 TYR cc_start: 0.7978 (t80) cc_final: 0.7728 (t80) REVERT: A 410 TYR cc_start: 0.8164 (t80) cc_final: 0.7796 (t80) REVERT: A 417 MET cc_start: 0.7967 (mtm) cc_final: 0.7656 (mtm) REVERT: A 425 ILE cc_start: 0.9108 (mm) cc_final: 0.8861 (mm) REVERT: A 447 ILE cc_start: 0.9570 (mt) cc_final: 0.9313 (mt) REVERT: A 538 ARG cc_start: 0.7921 (mtm180) cc_final: 0.7417 (ttt-90) REVERT: A 567 GLN cc_start: 0.9171 (pm20) cc_final: 0.8858 (pm20) REVERT: A 570 TYR cc_start: 0.7513 (m-10) cc_final: 0.6230 (m-80) REVERT: A 592 TYR cc_start: 0.8228 (t80) cc_final: 0.6730 (t80) REVERT: A 596 ARG cc_start: 0.7967 (mmm160) cc_final: 0.7267 (mmm160) REVERT: H 22 GLN cc_start: 0.6461 (mp10) cc_final: 0.6217 (mp10) REVERT: H 50 TYR cc_start: 0.7953 (m-80) cc_final: 0.6800 (m-80) REVERT: H 84 LYS cc_start: 0.8046 (mmmm) cc_final: 0.7830 (tppt) REVERT: H 120 TYR cc_start: 0.7675 (m-80) cc_final: 0.7138 (m-80) REVERT: L 60 PHE cc_start: 0.8051 (m-10) cc_final: 0.7849 (m-10) REVERT: L 78 GLN cc_start: 0.7972 (pp30) cc_final: 0.7407 (pp30) REVERT: L 105 ASP cc_start: 0.8447 (m-30) cc_final: 0.8219 (m-30) REVERT: V 18 GLN cc_start: 0.8547 (mm110) cc_final: 0.8065 (mp10) REVERT: V 38 LYS cc_start: 0.7720 (tttt) cc_final: 0.7245 (mttt) REVERT: V 43 THR cc_start: 0.8679 (m) cc_final: 0.8011 (p) REVERT: V 76 ASN cc_start: 0.8051 (t0) cc_final: 0.7805 (p0) REVERT: V 79 PHE cc_start: 0.6720 (m-10) cc_final: 0.6093 (m-10) REVERT: V 105 ASP cc_start: 0.8536 (m-30) cc_final: 0.8157 (m-30) REVERT: V 124 TRP cc_start: 0.8836 (m100) cc_final: 0.8627 (m-10) REVERT: V 151 ILE cc_start: 0.8462 (mt) cc_final: 0.8075 (mt) REVERT: V 195 LEU cc_start: 0.9281 (tp) cc_final: 0.9043 (tp) REVERT: V 251 THR cc_start: 0.7506 (m) cc_final: 0.7216 (m) outliers start: 0 outliers final: 0 residues processed: 374 average time/residue: 0.1765 time to fit residues: 91.0591 Evaluate side-chains 305 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 305 time to evaluate : 1.107 ------------------------------------------------------------------------------- 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: 4.9990 chunk 53 optimal weight: 0.7980 chunk 1 optimal weight: 7.9990 chunk 69 optimal weight: 0.9990 chunk 38 optimal weight: 9.9990 chunk 80 optimal weight: 10.0000 chunk 64 optimal weight: 0.0980 chunk 0 optimal weight: 9.9990 chunk 47 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- 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** A 391 ASN V 65 ASN V 186 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6815 moved from start: 0.5616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8069 Z= 0.168 Angle : 0.626 11.942 10984 Z= 0.314 Chirality : 0.043 0.312 1215 Planarity : 0.004 0.068 1354 Dihedral : 6.331 57.399 1202 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.40 % Favored : 95.50 % Rotamer: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % 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: -0.60 (0.27), residues: 978 helix: 0.27 (0.27), residues: 373 sheet: -0.30 (0.37), residues: 183 loop : -0.95 (0.32), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP V 184 HIS 0.005 0.001 HIS A 223 PHE 0.037 0.002 PHE A 440 TYR 0.022 0.002 TYR V 48 ARG 0.003 0.000 ARG H 117 *********************** 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 375 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 375 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 revert: symmetry clash revert: symmetry clash REVERT: A 84 LYS cc_start: 0.8632 (mptt) cc_final: 0.8001 (tptm) REVERT: A 121 TYR cc_start: 0.9347 (t80) cc_final: 0.8899 (t80) REVERT: A 180 MET cc_start: 0.9003 (mtp) cc_final: 0.8733 (mtp) REVERT: A 189 SER cc_start: 0.9676 (m) cc_final: 0.9386 (p) REVERT: A 195 LEU cc_start: 0.8940 (mt) cc_final: 0.8686 (mt) REVERT: A 197 TRP cc_start: 0.8990 (m-10) cc_final: 0.8550 (m-10) REVERT: A 209 CYS cc_start: 0.6372 (t) cc_final: 0.6063 (t) REVERT: A 245 LEU cc_start: 0.8342 (mm) cc_final: 0.7784 (mm) REVERT: A 266 ILE cc_start: 0.9098 (mt) cc_final: 0.8876 (tp) REVERT: A 302 LEU cc_start: 0.8905 (mt) cc_final: 0.8547 (mt) REVERT: A 316 ASN cc_start: 0.8599 (t0) cc_final: 0.8101 (t0) REVERT: A 333 ILE cc_start: 0.9283 (pt) cc_final: 0.9059 (pt) REVERT: A 410 TYR cc_start: 0.8145 (t80) cc_final: 0.7820 (t80) REVERT: A 417 MET cc_start: 0.7942 (mtm) cc_final: 0.7653 (mtm) REVERT: A 425 ILE cc_start: 0.9061 (mm) cc_final: 0.8813 (mm) REVERT: A 447 ILE cc_start: 0.9554 (mt) cc_final: 0.9289 (mt) REVERT: A 453 GLU cc_start: 0.9080 (mm-30) cc_final: 0.8869 (mm-30) REVERT: A 538 ARG cc_start: 0.7873 (mtm180) cc_final: 0.7361 (ttt-90) REVERT: A 567 GLN cc_start: 0.9159 (pm20) cc_final: 0.8827 (pm20) REVERT: A 570 TYR cc_start: 0.7493 (m-10) cc_final: 0.6467 (m-80) REVERT: A 592 TYR cc_start: 0.8145 (t80) cc_final: 0.6750 (t80) REVERT: A 596 ARG cc_start: 0.7926 (mmm160) cc_final: 0.7248 (mmm160) REVERT: H 22 GLN cc_start: 0.6516 (mp10) cc_final: 0.6251 (mp10) REVERT: H 50 TYR cc_start: 0.7968 (m-80) cc_final: 0.6671 (m-80) REVERT: H 69 ARG cc_start: 0.7983 (ttp-110) cc_final: 0.6659 (ptm-80) REVERT: H 76 ASP cc_start: 0.8552 (t0) cc_final: 0.8239 (t0) REVERT: H 120 TYR cc_start: 0.7700 (m-80) cc_final: 0.7200 (m-80) REVERT: L 60 PHE cc_start: 0.7841 (m-10) cc_final: 0.7608 (m-10) REVERT: L 78 GLN cc_start: 0.7901 (pp30) cc_final: 0.7308 (pp30) REVERT: L 105 ASP cc_start: 0.8478 (m-30) cc_final: 0.8231 (m-30) REVERT: V 18 GLN cc_start: 0.8464 (mm110) cc_final: 0.8243 (mm110) REVERT: V 38 LYS cc_start: 0.7744 (tttt) cc_final: 0.7299 (mttt) REVERT: V 43 THR cc_start: 0.8650 (m) cc_final: 0.8409 (p) REVERT: V 47 TYR cc_start: 0.3632 (p90) cc_final: 0.2531 (p90) REVERT: V 65 ASN cc_start: 0.8651 (m110) cc_final: 0.7796 (t0) REVERT: V 66 ILE cc_start: 0.8178 (tt) cc_final: 0.7475 (tt) REVERT: V 93 THR cc_start: 0.8652 (m) cc_final: 0.8292 (p) REVERT: V 105 ASP cc_start: 0.8479 (m-30) cc_final: 0.8108 (m-30) REVERT: V 151 ILE cc_start: 0.8566 (mt) cc_final: 0.8294 (mt) REVERT: V 184 TRP cc_start: 0.8675 (m100) cc_final: 0.8149 (m100) REVERT: V 195 LEU cc_start: 0.9254 (tp) cc_final: 0.9033 (tp) REVERT: V 204 TYR cc_start: 0.7711 (t80) cc_final: 0.7455 (t80) outliers start: 0 outliers final: 0 residues processed: 375 average time/residue: 0.1798 time to fit residues: 94.8862 Evaluate side-chains 306 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 306 time to evaluate : 0.907 ------------------------------------------------------------------------------- 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: 10.0000 chunk 84 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 93 optimal weight: 9.9990 chunk 77 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 49 optimal weight: 7.9990 chunk 90 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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** A 391 ASN V 54 GLN V 187 GLN V 238 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6932 moved from start: 0.6148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 8069 Z= 0.227 Angle : 0.663 11.994 10984 Z= 0.339 Chirality : 0.045 0.287 1215 Planarity : 0.005 0.063 1354 Dihedral : 6.061 53.472 1202 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 16.73 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.11 % Favored : 94.79 % Rotamer: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % 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: -0.54 (0.27), residues: 978 helix: 0.35 (0.26), residues: 373 sheet: -0.15 (0.38), residues: 179 loop : -1.01 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP V 124 HIS 0.005 0.001 HIS A 235 PHE 0.029 0.002 PHE V 220 TYR 0.022 0.002 TYR A 171 ARG 0.004 0.001 ARG V 117 *********************** 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 373 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 373 time to evaluate : 0.944 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: A 84 LYS cc_start: 0.8801 (mptt) cc_final: 0.8176 (tptm) REVERT: A 121 TYR cc_start: 0.9426 (t80) cc_final: 0.8886 (t80) REVERT: A 180 MET cc_start: 0.9140 (mtp) cc_final: 0.8868 (mtp) REVERT: A 189 SER cc_start: 0.9691 (m) cc_final: 0.9413 (p) REVERT: A 193 ASP cc_start: 0.8267 (p0) cc_final: 0.7611 (m-30) REVERT: A 195 LEU cc_start: 0.9057 (mt) cc_final: 0.8761 (mt) REVERT: A 197 TRP cc_start: 0.9146 (m-10) cc_final: 0.8744 (m-10) REVERT: A 245 LEU cc_start: 0.8450 (mm) cc_final: 0.7980 (mm) REVERT: A 302 LEU cc_start: 0.8869 (mt) cc_final: 0.8662 (mt) REVERT: A 310 LEU cc_start: 0.8318 (tt) cc_final: 0.8103 (mt) REVERT: A 316 ASN cc_start: 0.8575 (t0) cc_final: 0.8173 (t0) REVERT: A 333 ILE cc_start: 0.9294 (pt) cc_final: 0.9039 (pt) REVERT: A 337 LEU cc_start: 0.9359 (mt) cc_final: 0.9158 (mt) REVERT: A 410 TYR cc_start: 0.8144 (t80) cc_final: 0.7669 (t80) REVERT: A 417 MET cc_start: 0.7985 (mtm) cc_final: 0.7678 (mtm) REVERT: A 425 ILE cc_start: 0.9156 (mm) cc_final: 0.8946 (mm) REVERT: A 447 ILE cc_start: 0.9564 (mt) cc_final: 0.9302 (mt) REVERT: A 538 ARG cc_start: 0.7880 (mtm180) cc_final: 0.7342 (ttt-90) REVERT: A 567 GLN cc_start: 0.9155 (pm20) cc_final: 0.8802 (pm20) REVERT: A 570 TYR cc_start: 0.7739 (m-10) cc_final: 0.6785 (m-80) REVERT: A 592 TYR cc_start: 0.8152 (t80) cc_final: 0.7186 (t80) REVERT: H 21 VAL cc_start: 0.8638 (t) cc_final: 0.8413 (t) REVERT: H 49 SER cc_start: 0.8933 (p) cc_final: 0.8594 (p) REVERT: H 76 ASP cc_start: 0.8665 (t0) cc_final: 0.8364 (t0) REVERT: H 120 TYR cc_start: 0.7925 (m-80) cc_final: 0.7284 (m-80) REVERT: L 60 PHE cc_start: 0.7883 (m-10) cc_final: 0.7379 (m-10) REVERT: L 78 GLN cc_start: 0.7858 (pp30) cc_final: 0.7291 (pp30) REVERT: L 95 PHE cc_start: 0.7869 (m-80) cc_final: 0.7474 (m-10) REVERT: V 18 GLN cc_start: 0.8486 (mm110) cc_final: 0.8216 (mm110) REVERT: V 38 LYS cc_start: 0.7841 (tttt) cc_final: 0.7407 (mttt) REVERT: V 43 THR cc_start: 0.8518 (m) cc_final: 0.7597 (p) REVERT: V 63 ILE cc_start: 0.8998 (mm) cc_final: 0.8697 (mm) REVERT: V 93 THR cc_start: 0.8657 (m) cc_final: 0.8289 (p) REVERT: V 105 ASP cc_start: 0.8552 (m-30) cc_final: 0.8208 (m-30) REVERT: V 110 TYR cc_start: 0.7517 (m-80) cc_final: 0.7115 (m-80) REVERT: V 124 TRP cc_start: 0.8997 (m-10) cc_final: 0.8738 (m-10) REVERT: V 151 ILE cc_start: 0.8691 (mt) cc_final: 0.8333 (mt) REVERT: V 184 TRP cc_start: 0.8717 (m100) cc_final: 0.8329 (m100) outliers start: 0 outliers final: 0 residues processed: 373 average time/residue: 0.1670 time to fit residues: 86.6838 Evaluate side-chains 314 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 314 time to evaluate : 0.900 ------------------------------------------------------------------------------- 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: 1.9990 chunk 53 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 79 optimal weight: 8.9990 chunk 52 optimal weight: 0.9990 chunk 93 optimal weight: 8.9990 chunk 58 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 43 optimal weight: 10.0000 chunk 57 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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** 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: 0.6925 moved from start: 0.6435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8069 Z= 0.186 Angle : 0.634 11.785 10984 Z= 0.324 Chirality : 0.043 0.246 1215 Planarity : 0.004 0.055 1354 Dihedral : 5.840 53.339 1202 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.91 % Favored : 94.99 % Rotamer: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % 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: -0.37 (0.27), residues: 978 helix: 0.54 (0.27), residues: 367 sheet: -0.08 (0.38), residues: 179 loop : -0.94 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP V 184 HIS 0.003 0.001 HIS A 223 PHE 0.026 0.002 PHE A 440 TYR 0.022 0.002 TYR V 123 ARG 0.002 0.000 ARG H 59 *********************** 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 368 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 368 time to evaluate : 0.950 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: A 84 LYS cc_start: 0.8811 (mptt) cc_final: 0.8281 (tptm) REVERT: A 121 TYR cc_start: 0.9408 (t80) cc_final: 0.8843 (t80) REVERT: A 180 MET cc_start: 0.9110 (mtp) cc_final: 0.8854 (mtt) REVERT: A 184 LEU cc_start: 0.9286 (tp) cc_final: 0.8845 (tp) REVERT: A 189 SER cc_start: 0.9657 (m) cc_final: 0.9399 (p) REVERT: A 193 ASP cc_start: 0.8274 (p0) cc_final: 0.7683 (m-30) REVERT: A 195 LEU cc_start: 0.9073 (mt) cc_final: 0.8795 (mt) REVERT: A 197 TRP cc_start: 0.9058 (m-10) cc_final: 0.8630 (m-10) REVERT: A 245 LEU cc_start: 0.8449 (mm) cc_final: 0.8062 (mm) REVERT: A 316 ASN cc_start: 0.8679 (t0) cc_final: 0.8292 (t0) REVERT: A 333 ILE cc_start: 0.9271 (pt) cc_final: 0.9019 (pt) REVERT: A 410 TYR cc_start: 0.8127 (t80) cc_final: 0.7811 (t80) REVERT: A 417 MET cc_start: 0.7972 (mtm) cc_final: 0.7633 (mtm) REVERT: A 447 ILE cc_start: 0.9574 (mt) cc_final: 0.9318 (mt) REVERT: A 538 ARG cc_start: 0.7831 (mtm180) cc_final: 0.7345 (ttt-90) REVERT: A 570 TYR cc_start: 0.7809 (m-10) cc_final: 0.6975 (m-80) REVERT: A 592 TYR cc_start: 0.8056 (t80) cc_final: 0.7195 (t80) REVERT: H 50 TYR cc_start: 0.8039 (m-10) cc_final: 0.7737 (m-80) REVERT: L 60 PHE cc_start: 0.7609 (m-10) cc_final: 0.7129 (m-10) REVERT: L 77 ASN cc_start: 0.8764 (t0) cc_final: 0.8436 (t0) REVERT: L 78 GLN cc_start: 0.7870 (pp30) cc_final: 0.7107 (pp30) REVERT: L 95 PHE cc_start: 0.7833 (m-80) cc_final: 0.7531 (m-10) REVERT: V 18 GLN cc_start: 0.8462 (mm110) cc_final: 0.8209 (mm110) REVERT: V 38 LYS cc_start: 0.7784 (tttt) cc_final: 0.7404 (mttt) REVERT: V 43 THR cc_start: 0.8497 (m) cc_final: 0.7550 (p) REVERT: V 63 ILE cc_start: 0.9107 (mm) cc_final: 0.8671 (mm) REVERT: V 105 ASP cc_start: 0.8374 (m-30) cc_final: 0.8022 (m-30) REVERT: V 110 TYR cc_start: 0.7445 (m-80) cc_final: 0.7081 (m-80) REVERT: V 124 TRP cc_start: 0.9057 (m-10) cc_final: 0.8661 (m-10) REVERT: V 151 ILE cc_start: 0.8851 (mt) cc_final: 0.8480 (mt) REVERT: V 184 TRP cc_start: 0.8707 (m100) cc_final: 0.8152 (m100) outliers start: 0 outliers final: 0 residues processed: 368 average time/residue: 0.1662 time to fit residues: 85.2739 Evaluate side-chains 304 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 304 time to evaluate : 0.908 ------------------------------------------------------------------------------- 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: 6.9990 chunk 28 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 63 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 chunk 89 optimal weight: 9.9990 chunk 81 optimal weight: 5.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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** A 391 ASN H 58 GLN V 54 GLN V 187 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: 0.6996 moved from start: 0.6782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8069 Z= 0.228 Angle : 0.664 11.919 10984 Z= 0.341 Chirality : 0.044 0.235 1215 Planarity : 0.005 0.064 1354 Dihedral : 5.879 52.966 1202 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 16.35 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.83 % Favored : 94.07 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % 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: -0.40 (0.27), residues: 978 helix: 0.60 (0.27), residues: 365 sheet: -0.13 (0.37), residues: 190 loop : -1.03 (0.31), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP V 184 HIS 0.005 0.001 HIS A 235 PHE 0.021 0.002 PHE A 440 TYR 0.018 0.002 TYR A 175 ARG 0.002 0.000 ARG V 117 *********************** 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 353 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 353 time to evaluate : 0.979 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: A 84 LYS cc_start: 0.8904 (mptt) cc_final: 0.8363 (tptm) REVERT: A 121 TYR cc_start: 0.9405 (t80) cc_final: 0.8806 (t80) REVERT: A 145 ASN cc_start: 0.8064 (m-40) cc_final: 0.7619 (m-40) REVERT: A 180 MET cc_start: 0.9156 (mtp) cc_final: 0.8940 (mtt) REVERT: A 189 SER cc_start: 0.9654 (m) cc_final: 0.9380 (p) REVERT: A 193 ASP cc_start: 0.8274 (p0) cc_final: 0.7788 (m-30) REVERT: A 197 TRP cc_start: 0.9114 (m-10) cc_final: 0.8892 (m-10) REVERT: A 245 LEU cc_start: 0.8474 (mm) cc_final: 0.7828 (mm) REVERT: A 310 LEU cc_start: 0.8213 (tt) cc_final: 0.7884 (mt) REVERT: A 316 ASN cc_start: 0.8768 (t0) cc_final: 0.8342 (t0) REVERT: A 333 ILE cc_start: 0.9278 (pt) cc_final: 0.9012 (pt) REVERT: A 337 LEU cc_start: 0.9370 (mt) cc_final: 0.9129 (mt) REVERT: A 410 TYR cc_start: 0.8146 (t80) cc_final: 0.7778 (t80) REVERT: A 417 MET cc_start: 0.8008 (mtm) cc_final: 0.7614 (mtm) REVERT: A 425 ILE cc_start: 0.9065 (mm) cc_final: 0.8817 (mm) REVERT: A 447 ILE cc_start: 0.9585 (mt) cc_final: 0.9320 (mt) REVERT: A 495 TYR cc_start: 0.7932 (m-80) cc_final: 0.7669 (m-80) REVERT: A 538 ARG cc_start: 0.7861 (mtm180) cc_final: 0.7354 (ttt-90) REVERT: A 570 TYR cc_start: 0.7955 (m-10) cc_final: 0.7011 (m-80) REVERT: A 592 TYR cc_start: 0.8069 (t80) cc_final: 0.7281 (t80) REVERT: H 50 TYR cc_start: 0.8103 (m-10) cc_final: 0.7881 (m-80) REVERT: H 86 LYS cc_start: 0.7687 (ptpp) cc_final: 0.6876 (mmtt) REVERT: H 120 TYR cc_start: 0.7920 (m-80) cc_final: 0.7581 (m-80) REVERT: L 37 GLN cc_start: 0.7556 (mm-40) cc_final: 0.7322 (tp-100) REVERT: L 60 PHE cc_start: 0.7637 (m-10) cc_final: 0.7228 (m-10) REVERT: L 77 ASN cc_start: 0.8790 (t0) cc_final: 0.8455 (t0) REVERT: L 78 GLN cc_start: 0.7866 (pp30) cc_final: 0.7079 (pp30) REVERT: L 95 PHE cc_start: 0.8013 (m-80) cc_final: 0.7809 (m-80) REVERT: L 105 ASP cc_start: 0.8466 (m-30) cc_final: 0.8262 (m-30) REVERT: V 18 GLN cc_start: 0.8484 (mm110) cc_final: 0.8185 (mm110) REVERT: V 38 LYS cc_start: 0.7840 (tttt) cc_final: 0.7462 (ttmt) REVERT: V 43 THR cc_start: 0.8426 (m) cc_final: 0.7334 (p) REVERT: V 67 ASN cc_start: 0.7976 (t0) cc_final: 0.7674 (t0) REVERT: V 102 THR cc_start: 0.6484 (p) cc_final: 0.6283 (p) REVERT: V 105 ASP cc_start: 0.8305 (m-30) cc_final: 0.7896 (m-30) REVERT: V 110 TYR cc_start: 0.7509 (m-80) cc_final: 0.7168 (m-80) REVERT: V 124 TRP cc_start: 0.9078 (m-10) cc_final: 0.8543 (m-10) REVERT: V 151 ILE cc_start: 0.8729 (mt) cc_final: 0.8387 (mt) REVERT: V 184 TRP cc_start: 0.8725 (m100) cc_final: 0.8105 (m100) REVERT: V 251 THR cc_start: 0.7954 (m) cc_final: 0.7753 (m) outliers start: 0 outliers final: 0 residues processed: 353 average time/residue: 0.1633 time to fit residues: 80.9187 Evaluate side-chains 302 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 302 time to evaluate : 0.950 ------------------------------------------------------------------------------- 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: 0.4980 chunk 89 optimal weight: 10.0000 chunk 52 optimal weight: 0.0770 chunk 37 optimal weight: 0.7980 chunk 68 optimal weight: 0.0470 chunk 26 optimal weight: 10.0000 chunk 78 optimal weight: 6.9990 chunk 82 optimal weight: 7.9990 chunk 86 optimal weight: 8.9990 chunk 57 optimal weight: 0.0270 chunk 92 optimal weight: 0.1980 overall best weight: 0.1694 ------------------------------------------------------------------------------- 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** A 391 ASN V 238 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6867 moved from start: 0.6808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8069 Z= 0.164 Angle : 0.662 11.526 10984 Z= 0.332 Chirality : 0.044 0.217 1215 Planarity : 0.004 0.046 1354 Dihedral : 5.602 50.402 1202 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.09 % Favored : 95.81 % 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: -0.25 (0.27), residues: 978 helix: 0.77 (0.27), residues: 360 sheet: -0.04 (0.37), residues: 189 loop : -0.98 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP V 184 HIS 0.006 0.001 HIS V 240 PHE 0.027 0.002 PHE A 440 TYR 0.036 0.002 TYR A 175 ARG 0.006 0.000 ARG V 117 *********************** 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 361 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 361 time to evaluate : 0.896 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: A 84 LYS cc_start: 0.8771 (mptt) cc_final: 0.8304 (tptm) REVERT: A 121 TYR cc_start: 0.9345 (t80) cc_final: 0.8731 (t80) REVERT: A 180 MET cc_start: 0.9025 (mtp) cc_final: 0.8824 (mtp) REVERT: A 189 SER cc_start: 0.9656 (m) cc_final: 0.9384 (p) REVERT: A 193 ASP cc_start: 0.8352 (p0) cc_final: 0.8008 (m-30) REVERT: A 195 LEU cc_start: 0.9028 (mt) cc_final: 0.8535 (mt) REVERT: A 197 TRP cc_start: 0.8962 (m-10) cc_final: 0.8656 (m-10) REVERT: A 245 LEU cc_start: 0.8412 (mm) cc_final: 0.8179 (mm) REVERT: A 246 GLN cc_start: 0.7114 (pm20) cc_final: 0.6899 (tt0) REVERT: A 296 LEU cc_start: 0.8346 (tp) cc_final: 0.8115 (tt) REVERT: A 316 ASN cc_start: 0.8703 (t0) cc_final: 0.8311 (t0) REVERT: A 333 ILE cc_start: 0.9265 (pt) cc_final: 0.8971 (pt) REVERT: A 337 LEU cc_start: 0.9307 (mt) cc_final: 0.9101 (mt) REVERT: A 410 TYR cc_start: 0.8003 (t80) cc_final: 0.7683 (t80) REVERT: A 417 MET cc_start: 0.8005 (mtm) cc_final: 0.7591 (mtm) REVERT: A 425 ILE cc_start: 0.8956 (mm) cc_final: 0.8743 (mm) REVERT: A 431 LEU cc_start: 0.9031 (tp) cc_final: 0.8793 (tp) REVERT: A 447 ILE cc_start: 0.9571 (mt) cc_final: 0.9344 (mt) REVERT: A 450 VAL cc_start: 0.9087 (t) cc_final: 0.8886 (t) REVERT: A 495 TYR cc_start: 0.7766 (m-80) cc_final: 0.7541 (m-80) REVERT: A 538 ARG cc_start: 0.7748 (mtm180) cc_final: 0.7227 (ttt180) REVERT: A 570 TYR cc_start: 0.7996 (m-10) cc_final: 0.7180 (m-80) REVERT: A 592 TYR cc_start: 0.7905 (t80) cc_final: 0.7209 (t80) REVERT: H 50 TYR cc_start: 0.8060 (m-10) cc_final: 0.7778 (m-80) REVERT: H 86 LYS cc_start: 0.7269 (ptpp) cc_final: 0.6728 (mmtt) REVERT: L 60 PHE cc_start: 0.7428 (m-10) cc_final: 0.7112 (m-10) REVERT: L 63 LYS cc_start: 0.8964 (tppp) cc_final: 0.8727 (tppt) REVERT: L 77 ASN cc_start: 0.8813 (t0) cc_final: 0.8468 (t0) REVERT: L 78 GLN cc_start: 0.7707 (pp30) cc_final: 0.6864 (pp30) REVERT: L 100 HIS cc_start: 0.6408 (m90) cc_final: 0.6171 (m90) REVERT: V 18 GLN cc_start: 0.8328 (mm110) cc_final: 0.8096 (mm110) REVERT: V 38 LYS cc_start: 0.7747 (tttt) cc_final: 0.7349 (ttmt) REVERT: V 43 THR cc_start: 0.8327 (m) cc_final: 0.7173 (p) REVERT: V 63 ILE cc_start: 0.9126 (mm) cc_final: 0.8760 (mm) REVERT: V 105 ASP cc_start: 0.8246 (m-30) cc_final: 0.7830 (m-30) REVERT: V 124 TRP cc_start: 0.9020 (m-10) cc_final: 0.8568 (m-10) REVERT: V 151 ILE cc_start: 0.8731 (mt) cc_final: 0.8446 (mt) REVERT: V 184 TRP cc_start: 0.8510 (m100) cc_final: 0.7927 (m100) REVERT: V 195 LEU cc_start: 0.9024 (tp) cc_final: 0.8780 (tp) REVERT: V 204 TYR cc_start: 0.7905 (t80) cc_final: 0.7670 (t80) outliers start: 0 outliers final: 0 residues processed: 361 average time/residue: 0.1620 time to fit residues: 82.6430 Evaluate side-chains 294 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 294 time to evaluate : 0.826 ------------------------------------------------------------------------------- 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: 8.9990 chunk 43 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 88 optimal weight: 7.9990 chunk 76 optimal weight: 0.0570 chunk 7 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 81 optimal weight: 9.9990 overall best weight: 2.4106 ------------------------------------------------------------------------------- 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** 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: 0.6997 moved from start: 0.7143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8069 Z= 0.237 Angle : 0.704 11.704 10984 Z= 0.356 Chirality : 0.046 0.283 1215 Planarity : 0.004 0.047 1354 Dihedral : 5.731 51.405 1202 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 17.31 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.62 % Favored : 94.27 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -0.31 (0.27), residues: 978 helix: 0.70 (0.27), residues: 364 sheet: -0.10 (0.37), residues: 188 loop : -0.99 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP V 51 HIS 0.009 0.002 HIS A 456 PHE 0.037 0.002 PHE A 465 TYR 0.032 0.002 TYR A 175 ARG 0.003 0.001 ARG H 59 ********************** 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 338 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 338 time to evaluate : 0.957 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: A 84 LYS cc_start: 0.8902 (mptt) cc_final: 0.8359 (tptm) REVERT: A 126 ILE cc_start: 0.8560 (mt) cc_final: 0.8334 (mt) REVERT: A 180 MET cc_start: 0.9179 (mtp) cc_final: 0.8957 (mtt) REVERT: A 189 SER cc_start: 0.9663 (m) cc_final: 0.9389 (p) REVERT: A 193 ASP cc_start: 0.8396 (p0) cc_final: 0.8143 (m-30) REVERT: A 240 HIS cc_start: 0.8703 (p-80) cc_final: 0.8423 (p-80) REVERT: A 245 LEU cc_start: 0.8488 (mm) cc_final: 0.8043 (mm) REVERT: A 316 ASN cc_start: 0.8781 (t0) cc_final: 0.8364 (t0) REVERT: A 337 LEU cc_start: 0.9351 (mt) cc_final: 0.9100 (mt) REVERT: A 410 TYR cc_start: 0.8127 (t80) cc_final: 0.7727 (t80) REVERT: A 417 MET cc_start: 0.8002 (mtm) cc_final: 0.7619 (mtm) REVERT: A 425 ILE cc_start: 0.9032 (mm) cc_final: 0.8801 (mm) REVERT: A 447 ILE cc_start: 0.9507 (mt) cc_final: 0.9284 (mt) REVERT: A 538 ARG cc_start: 0.7793 (mtm180) cc_final: 0.7274 (ttt-90) REVERT: A 570 TYR cc_start: 0.8068 (m-10) cc_final: 0.7692 (m-80) REVERT: A 592 TYR cc_start: 0.7962 (t80) cc_final: 0.7360 (t80) REVERT: H 50 TYR cc_start: 0.8121 (m-10) cc_final: 0.7910 (m-80) REVERT: H 86 LYS cc_start: 0.7596 (ptpp) cc_final: 0.6854 (mmtt) REVERT: H 120 TYR cc_start: 0.7619 (m-80) cc_final: 0.7136 (m-80) REVERT: L 37 GLN cc_start: 0.7708 (mm-40) cc_final: 0.7468 (tp-100) REVERT: L 60 PHE cc_start: 0.7537 (m-10) cc_final: 0.7059 (m-10) REVERT: L 63 LYS cc_start: 0.8951 (tppp) cc_final: 0.8736 (tppt) REVERT: L 77 ASN cc_start: 0.8843 (t0) cc_final: 0.8477 (t0) REVERT: L 78 GLN cc_start: 0.7800 (pp30) cc_final: 0.6983 (pp30) REVERT: V 18 GLN cc_start: 0.8327 (mm110) cc_final: 0.8096 (mm110) REVERT: V 38 LYS cc_start: 0.7850 (tttt) cc_final: 0.7411 (ttmt) REVERT: V 43 THR cc_start: 0.8301 (m) cc_final: 0.7257 (m) REVERT: V 67 ASN cc_start: 0.8035 (t0) cc_final: 0.7716 (t0) REVERT: V 102 THR cc_start: 0.6608 (p) cc_final: 0.6304 (p) REVERT: V 105 ASP cc_start: 0.8325 (m-30) cc_final: 0.7832 (m-30) REVERT: V 151 ILE cc_start: 0.8646 (mt) cc_final: 0.8309 (mt) REVERT: V 184 TRP cc_start: 0.8541 (m100) cc_final: 0.8024 (m100) outliers start: 0 outliers final: 0 residues processed: 338 average time/residue: 0.1712 time to fit residues: 81.0632 Evaluate side-chains 299 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 299 time to evaluate : 1.063 ------------------------------------------------------------------------------- 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: 0.5980 chunk 70 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 21 optimal weight: 0.6980 chunk 77 optimal weight: 7.9990 chunk 32 optimal weight: 0.7980 chunk 79 optimal weight: 5.9990 chunk 9 optimal weight: 0.5980 chunk 14 optimal weight: 0.8980 chunk 67 optimal weight: 0.0370 chunk 4 optimal weight: 6.9990 overall best weight: 0.5458 ------------------------------------------------------------------------------- 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 A 223 HIS ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 391 ASN V 54 GLN V 187 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.160586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.138484 restraints weight = 15056.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.144009 restraints weight = 8344.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.147880 restraints weight = 5214.782| |-----------------------------------------------------------------------------| r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6725 moved from start: 0.7197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8069 Z= 0.175 Angle : 0.682 11.561 10984 Z= 0.340 Chirality : 0.044 0.203 1215 Planarity : 0.004 0.043 1354 Dihedral : 5.667 50.049 1202 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.60 % Favored : 95.30 % 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: -0.31 (0.27), residues: 978 helix: 0.81 (0.28), residues: 355 sheet: -0.01 (0.37), residues: 190 loop : -1.12 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP V 184 HIS 0.006 0.002 HIS V 240 PHE 0.020 0.002 PHE A 440 TYR 0.041 0.002 TYR A 175 ARG 0.003 0.000 ARG H 59 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2406.19 seconds wall clock time: 43 minutes 53.10 seconds (2633.10 seconds total)