Starting phenix.real_space_refine on Tue Nov 19 03:02:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lid_0904/11_2024/6lid_0904.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lid_0904/11_2024/6lid_0904.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lid_0904/11_2024/6lid_0904.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lid_0904/11_2024/6lid_0904.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lid_0904/11_2024/6lid_0904.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lid_0904/11_2024/6lid_0904.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 P 4 5.49 5 S 90 5.16 5 C 11548 2.51 5 N 2824 2.21 5 O 3496 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 17964 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 5084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 5084 Classifications: {'peptide': 623} Link IDs: {'PTRANS': 25, 'TRANS': 597} Chain: "B" Number of atoms: 3538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3538 Classifications: {'peptide': 458} Link IDs: {'PTRANS': 26, 'TRANS': 431} Chain: "C" Number of atoms: 5084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 5084 Classifications: {'peptide': 623} Link IDs: {'PTRANS': 25, 'TRANS': 597} Chain: "D" Number of atoms: 3538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3538 Classifications: {'peptide': 458} Link IDs: {'PTRANS': 26, 'TRANS': 431} Chain: "E" 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: "F" 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: "G" 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: "H" 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: "I" 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: "J" 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: "K" 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: "L" 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: "M" 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: "N" 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 96 Unusual residues: {'3PH': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 96 Unusual residues: {'3PH': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 116 Classifications: {'water': 116} Link IDs: {None: 115} Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "C" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 116 Classifications: {'water': 116} Link IDs: {None: 115} Chain: "D" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Time building chain proxies: 15.23, per 1000 atoms: 0.85 Number of scatterers: 17964 At special positions: 0 Unit cell: (81.825, 138.557, 138.557, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 2 19.99 S 90 16.00 P 4 15.00 O 3496 8.00 N 2824 7.00 C 11548 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 114 " - pdb=" SG CYS B 144 " distance=2.86 Simple disulfide: pdb=" SG CYS A 242 " - pdb=" SG CYS A 273 " distance=2.04 Simple disulfide: pdb=" SG CYS A 571 " - pdb=" SG CYS A 666 " distance=2.03 Simple disulfide: pdb=" SG CYS C 114 " - pdb=" SG CYS D 144 " distance=2.95 Simple disulfide: pdb=" SG CYS C 242 " - pdb=" SG CYS C 273 " distance=2.04 Simple disulfide: pdb=" SG CYS C 571 " - pdb=" SG CYS C 666 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " NAG-ASN " NAG E 1 " - " ASN A 261 " " NAG F 1 " - " ASN A 332 " " NAG G 1 " - " ASN A 495 " " NAG H 1 " - " ASN A 513 " " NAG I 1 " - " ASN A 575 " " NAG J 1 " - " ASN C 261 " " NAG K 1 " - " ASN C 332 " " NAG L 1 " - " ASN C 495 " " NAG M 1 " - " ASN C 513 " " NAG N 1 " - " ASN C 575 " Time building additional restraints: 5.79 Conformation dependent library (CDL) restraints added in 2.6 seconds 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4048 Finding SS restraints... Secondary structure from input PDB file: 109 helices and 16 sheets defined 54.1% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.40 Creating SS restraints... Processing helix chain 'A' and resid 69 through 74 removed outlier: 3.606A pdb=" N PHE A 74 " --> pdb=" O LYS A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 92 removed outlier: 3.581A pdb=" N ILE A 84 " --> pdb=" O ALA A 80 " (cutoff:3.500A) Proline residue: A 85 - end of helix removed outlier: 3.841A pdb=" N LEU A 89 " --> pdb=" O PRO A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 111 removed outlier: 3.514A pdb=" N ALA A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 121 removed outlier: 4.001A pdb=" N GLY A 121 " --> pdb=" O TRP A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 131 removed outlier: 3.982A pdb=" N PHE A 131 " --> pdb=" O PRO A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 147 Processing helix chain 'A' and resid 148 through 154 Processing helix chain 'A' and resid 189 through 202 Processing helix chain 'A' and resid 220 through 227 Processing helix chain 'A' and resid 230 through 236 removed outlier: 3.980A pdb=" N THR A 234 " --> pdb=" O GLY A 231 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASP A 235 " --> pdb=" O LYS A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 306 removed outlier: 3.503A pdb=" N GLN A 293 " --> pdb=" O ASN A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 319 Processing helix chain 'A' and resid 342 through 344 No H-bonds generated for 'chain 'A' and resid 342 through 344' Processing helix chain 'A' and resid 356 through 369 Processing helix chain 'A' and resid 370 through 372 No H-bonds generated for 'chain 'A' and resid 370 through 372' Processing helix chain 'A' and resid 389 through 394 Processing helix chain 'A' and resid 395 through 398 Processing helix chain 'A' and resid 420 through 435 Processing helix chain 'A' and resid 452 through 457 Processing helix chain 'A' and resid 458 through 460 No H-bonds generated for 'chain 'A' and resid 458 through 460' Processing helix chain 'A' and resid 461 through 472 Processing helix chain 'A' and resid 502 through 506 removed outlier: 3.663A pdb=" N SER A 505 " --> pdb=" O THR A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 519 Processing helix chain 'A' and resid 537 through 542 Processing helix chain 'A' and resid 547 through 562 removed outlier: 3.531A pdb=" N LEU A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 567 Processing helix chain 'A' and resid 606 through 610 Processing helix chain 'A' and resid 655 through 659 Processing helix chain 'A' and resid 662 through 664 No H-bonds generated for 'chain 'A' and resid 662 through 664' Processing helix chain 'B' and resid 32 through 44 removed outlier: 3.837A pdb=" N ILE B 38 " --> pdb=" O SER B 34 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE B 39 " --> pdb=" O GLY B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 49 removed outlier: 4.173A pdb=" N ILE B 48 " --> pdb=" O GLY B 45 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE B 49 " --> pdb=" O SER B 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 45 through 49' Processing helix chain 'B' and resid 50 through 57 removed outlier: 4.519A pdb=" N SER B 54 " --> pdb=" O VAL B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 91 removed outlier: 3.514A pdb=" N ILE B 67 " --> pdb=" O GLY B 63 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TRP B 69 " --> pdb=" O CYS B 65 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLY B 73 " --> pdb=" O TRP B 69 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR B 88 " --> pdb=" O ALA B 84 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE B 90 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR B 91 " --> pdb=" O GLY B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 104 removed outlier: 3.649A pdb=" N GLU B 102 " --> pdb=" O PRO B 98 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA B 103 " --> pdb=" O TYR B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 119 removed outlier: 3.881A pdb=" N ALA B 109 " --> pdb=" O GLY B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 138 removed outlier: 3.806A pdb=" N TYR B 135 " --> pdb=" O SER B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 141 No H-bonds generated for 'chain 'B' and resid 139 through 141' Processing helix chain 'B' and resid 147 through 166 removed outlier: 3.678A pdb=" N VAL B 151 " --> pdb=" O PRO B 147 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA B 157 " --> pdb=" O CYS B 153 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR B 164 " --> pdb=" O LEU B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 176 removed outlier: 3.527A pdb=" N TYR B 175 " --> pdb=" O ARG B 171 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL B 176 " --> pdb=" O LEU B 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 171 through 176' Processing helix chain 'B' and resid 176 through 202 removed outlier: 3.607A pdb=" N LYS B 184 " --> pdb=" O PHE B 180 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE B 187 " --> pdb=" O ALA B 183 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE B 191 " --> pdb=" O ILE B 187 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU B 198 " --> pdb=" O SER B 194 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY B 202 " --> pdb=" O LEU B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 208 removed outlier: 3.739A pdb=" N PHE B 207 " --> pdb=" O THR B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 229 removed outlier: 3.621A pdb=" N SER B 222 " --> pdb=" O VAL B 218 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU B 223 " --> pdb=" O GLY B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 238 removed outlier: 3.659A pdb=" N GLN B 237 " --> pdb=" O GLY B 234 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU B 238 " --> pdb=" O TRP B 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 234 through 238' Processing helix chain 'B' and resid 250 through 278 Proline residue: B 261 - end of helix removed outlier: 4.168A pdb=" N VAL B 277 " --> pdb=" O SER B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 285 removed outlier: 3.709A pdb=" N LEU B 284 " --> pdb=" O ALA B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 295 removed outlier: 3.520A pdb=" N THR B 292 " --> pdb=" O ALA B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 319 removed outlier: 3.652A pdb=" N ALA B 310 " --> pdb=" O PRO B 306 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE B 314 " --> pdb=" O ALA B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 322 No H-bonds generated for 'chain 'B' and resid 320 through 322' Processing helix chain 'B' and resid 325 through 333 removed outlier: 3.507A pdb=" N VAL B 330 " --> pdb=" O ARG B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 366 Processing helix chain 'B' and resid 374 through 396 removed outlier: 3.847A pdb=" N ALA B 381 " --> pdb=" O TYR B 377 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE B 385 " --> pdb=" O ALA B 381 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE B 394 " --> pdb=" O ILE B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 432 removed outlier: 3.511A pdb=" N SER B 421 " --> pdb=" O MET B 417 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL B 422 " --> pdb=" O THR B 418 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL B 425 " --> pdb=" O SER B 421 " (cutoff:3.500A) Proline residue: B 428 - end of helix Processing helix chain 'B' and resid 435 through 440 Processing helix chain 'B' and resid 440 through 455 removed outlier: 3.726A pdb=" N GLY B 447 " --> pdb=" O PHE B 443 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU B 448 " --> pdb=" O ILE B 444 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU B 449 " --> pdb=" O LEU B 445 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE B 450 " --> pdb=" O SER B 446 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N PHE B 452 " --> pdb=" O LEU B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 478 Proline residue: B 468 - end of helix removed outlier: 3.510A pdb=" N MET B 475 " --> pdb=" O MET B 471 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N MET B 477 " --> pdb=" O LEU B 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 74 removed outlier: 3.606A pdb=" N PHE C 74 " --> pdb=" O LYS C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 92 removed outlier: 3.581A pdb=" N ILE C 84 " --> pdb=" O ALA C 80 " (cutoff:3.500A) Proline residue: C 85 - end of helix removed outlier: 3.841A pdb=" N LEU C 89 " --> pdb=" O PRO C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 111 removed outlier: 3.514A pdb=" N ALA C 106 " --> pdb=" O ALA C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 121 removed outlier: 4.001A pdb=" N GLY C 121 " --> pdb=" O TRP C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 131 removed outlier: 3.982A pdb=" N PHE C 131 " --> pdb=" O PRO C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 147 Processing helix chain 'C' and resid 148 through 154 Processing helix chain 'C' and resid 189 through 202 Processing helix chain 'C' and resid 220 through 227 Processing helix chain 'C' and resid 230 through 236 removed outlier: 3.980A pdb=" N THR C 234 " --> pdb=" O GLY C 231 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASP C 235 " --> pdb=" O LYS C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 306 removed outlier: 3.502A pdb=" N GLN C 293 " --> pdb=" O ASN C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 319 Processing helix chain 'C' and resid 342 through 344 No H-bonds generated for 'chain 'C' and resid 342 through 344' Processing helix chain 'C' and resid 356 through 369 Processing helix chain 'C' and resid 370 through 372 No H-bonds generated for 'chain 'C' and resid 370 through 372' Processing helix chain 'C' and resid 389 through 394 Processing helix chain 'C' and resid 395 through 398 Processing helix chain 'C' and resid 420 through 435 Processing helix chain 'C' and resid 452 through 457 Processing helix chain 'C' and resid 458 through 460 No H-bonds generated for 'chain 'C' and resid 458 through 460' Processing helix chain 'C' and resid 461 through 472 Processing helix chain 'C' and resid 502 through 506 removed outlier: 3.663A pdb=" N SER C 505 " --> pdb=" O THR C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 514 through 519 Processing helix chain 'C' and resid 537 through 542 Processing helix chain 'C' and resid 547 through 562 removed outlier: 3.531A pdb=" N LEU C 551 " --> pdb=" O SER C 547 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 567 Processing helix chain 'C' and resid 606 through 610 Processing helix chain 'C' and resid 655 through 659 Processing helix chain 'C' and resid 662 through 664 No H-bonds generated for 'chain 'C' and resid 662 through 664' Processing helix chain 'D' and resid 32 through 44 removed outlier: 3.837A pdb=" N ILE D 38 " --> pdb=" O SER D 34 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE D 39 " --> pdb=" O GLY D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 49 removed outlier: 4.172A pdb=" N ILE D 48 " --> pdb=" O GLY D 45 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE D 49 " --> pdb=" O SER D 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 45 through 49' Processing helix chain 'D' and resid 50 through 57 removed outlier: 4.519A pdb=" N SER D 54 " --> pdb=" O VAL D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 91 removed outlier: 3.513A pdb=" N ILE D 67 " --> pdb=" O GLY D 63 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TRP D 69 " --> pdb=" O CYS D 65 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLY D 73 " --> pdb=" O TRP D 69 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR D 88 " --> pdb=" O ALA D 84 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE D 90 " --> pdb=" O LEU D 86 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR D 91 " --> pdb=" O GLY D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 104 removed outlier: 3.649A pdb=" N GLU D 102 " --> pdb=" O PRO D 98 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA D 103 " --> pdb=" O TYR D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 119 removed outlier: 3.882A pdb=" N ALA D 109 " --> pdb=" O GLY D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 138 removed outlier: 3.806A pdb=" N TYR D 135 " --> pdb=" O SER D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 141 No H-bonds generated for 'chain 'D' and resid 139 through 141' Processing helix chain 'D' and resid 147 through 166 removed outlier: 3.678A pdb=" N VAL D 151 " --> pdb=" O PRO D 147 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA D 157 " --> pdb=" O CYS D 153 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR D 164 " --> pdb=" O LEU D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 176 removed outlier: 3.527A pdb=" N TYR D 175 " --> pdb=" O ARG D 171 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL D 176 " --> pdb=" O LEU D 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 171 through 176' Processing helix chain 'D' and resid 176 through 202 removed outlier: 3.606A pdb=" N LYS D 184 " --> pdb=" O PHE D 180 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE D 187 " --> pdb=" O ALA D 183 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE D 191 " --> pdb=" O ILE D 187 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU D 198 " --> pdb=" O SER D 194 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY D 202 " --> pdb=" O LEU D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 229 removed outlier: 3.621A pdb=" N SER D 222 " --> pdb=" O VAL D 218 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU D 223 " --> pdb=" O GLY D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 238 removed outlier: 3.659A pdb=" N GLN D 237 " --> pdb=" O GLY D 234 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU D 238 " --> pdb=" O TRP D 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 234 through 238' Processing helix chain 'D' and resid 250 through 278 Proline residue: D 261 - end of helix removed outlier: 4.168A pdb=" N VAL D 277 " --> pdb=" O SER D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 285 removed outlier: 3.709A pdb=" N LEU D 284 " --> pdb=" O ALA D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 295 removed outlier: 3.520A pdb=" N THR D 292 " --> pdb=" O ALA D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 319 removed outlier: 3.653A pdb=" N ALA D 310 " --> pdb=" O PRO D 306 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE D 314 " --> pdb=" O ALA D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 322 No H-bonds generated for 'chain 'D' and resid 320 through 322' Processing helix chain 'D' and resid 325 through 333 removed outlier: 3.507A pdb=" N VAL D 330 " --> pdb=" O ARG D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 366 Processing helix chain 'D' and resid 374 through 396 removed outlier: 3.848A pdb=" N ALA D 381 " --> pdb=" O TYR D 377 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE D 385 " --> pdb=" O ALA D 381 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE D 394 " --> pdb=" O ILE D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 432 removed outlier: 3.510A pdb=" N SER D 421 " --> pdb=" O MET D 417 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL D 422 " --> pdb=" O THR D 418 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL D 425 " --> pdb=" O SER D 421 " (cutoff:3.500A) Proline residue: D 428 - end of helix Processing helix chain 'D' and resid 435 through 440 Processing helix chain 'D' and resid 440 through 455 removed outlier: 3.727A pdb=" N GLY D 447 " --> pdb=" O PHE D 443 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU D 448 " --> pdb=" O ILE D 444 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU D 449 " --> pdb=" O LEU D 445 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE D 450 " --> pdb=" O SER D 446 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N PHE D 452 " --> pdb=" O LEU D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 478 Proline residue: D 468 - end of helix removed outlier: 3.511A pdb=" N MET D 475 " --> pdb=" O MET D 471 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N MET D 477 " --> pdb=" O LEU D 473 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 407 through 408 removed outlier: 4.077A pdb=" N PHE A 407 " --> pdb=" O MET A 381 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR A 383 " --> pdb=" O PHE A 407 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N TRP A 443 " --> pdb=" O ILE A 477 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N TYR A 479 " --> pdb=" O TRP A 443 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 166 through 168 removed outlier: 7.136A pdb=" N LYS A 167 " --> pdb=" O GLU A 178 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 239 through 240 removed outlier: 3.536A pdb=" N GLN A 272 " --> pdb=" O ASP A 267 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 329 through 330 removed outlier: 4.115A pdb=" N ILE A 329 " --> pdb=" O TYR A 347 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 632 through 634 removed outlier: 11.470A pdb=" N LYS A 617 " --> pdb=" O ASN A 651 " (cutoff:3.500A) removed outlier: 9.002A pdb=" N ASN A 651 " --> pdb=" O LYS A 617 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N ARG A 619 " --> pdb=" O GLU A 649 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLU A 649 " --> pdb=" O ARG A 619 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ILE A 647 " --> pdb=" O ARG A 621 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N SER A 623 " --> pdb=" O GLY A 645 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N GLY A 645 " --> pdb=" O SER A 623 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 603 through 605 Processing sheet with id=AA7, first strand: chain 'A' and resid 673 through 675 removed outlier: 3.522A pdb=" N ILE A 680 " --> pdb=" O SER A 675 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 344 through 345 Processing sheet with id=AA9, first strand: chain 'C' and resid 407 through 408 removed outlier: 4.077A pdb=" N PHE C 407 " --> pdb=" O MET C 381 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N THR C 383 " --> pdb=" O PHE C 407 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N TRP C 443 " --> pdb=" O ILE C 477 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N TYR C 479 " --> pdb=" O TRP C 443 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 166 through 168 removed outlier: 7.135A pdb=" N LYS C 167 " --> pdb=" O GLU C 178 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 239 through 240 removed outlier: 3.537A pdb=" N GLN C 272 " --> pdb=" O ASP C 267 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 329 through 330 removed outlier: 4.114A pdb=" N ILE C 329 " --> pdb=" O TYR C 347 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 632 through 634 removed outlier: 11.470A pdb=" N LYS C 617 " --> pdb=" O ASN C 651 " (cutoff:3.500A) removed outlier: 9.002A pdb=" N ASN C 651 " --> pdb=" O LYS C 617 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N ARG C 619 " --> pdb=" O GLU C 649 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLU C 649 " --> pdb=" O ARG C 619 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ILE C 647 " --> pdb=" O ARG C 621 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N SER C 623 " --> pdb=" O GLY C 645 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N GLY C 645 " --> pdb=" O SER C 623 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 603 through 605 Processing sheet with id=AB6, first strand: chain 'C' and resid 673 through 675 removed outlier: 3.522A pdb=" N ILE C 680 " --> pdb=" O SER C 675 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 344 through 345 735 hydrogen bonds defined for protein. 2082 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: 6.96 Time building geometry restraints manager: 6.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4702 1.33 - 1.45: 3458 1.45 - 1.57: 9862 1.57 - 1.69: 4 1.69 - 1.81: 146 Bond restraints: 18172 Sorted by residual: bond pdb=" C31 3PH B 702 " pdb=" O31 3PH B 702 " ideal model delta sigma weight residual 1.325 1.450 -0.125 2.00e-02 2.50e+03 3.92e+01 bond pdb=" C31 3PH D 702 " pdb=" O31 3PH D 702 " ideal model delta sigma weight residual 1.325 1.450 -0.125 2.00e-02 2.50e+03 3.89e+01 bond pdb=" C31 3PH B 701 " pdb=" O31 3PH B 701 " ideal model delta sigma weight residual 1.325 1.447 -0.122 2.00e-02 2.50e+03 3.74e+01 bond pdb=" C21 3PH D 701 " pdb=" O21 3PH D 701 " ideal model delta sigma weight residual 1.328 1.450 -0.122 2.00e-02 2.50e+03 3.74e+01 bond pdb=" C31 3PH D 701 " pdb=" O31 3PH D 701 " ideal model delta sigma weight residual 1.325 1.447 -0.122 2.00e-02 2.50e+03 3.71e+01 ... (remaining 18167 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 23517 1.98 - 3.96: 923 3.96 - 5.95: 164 5.95 - 7.93: 58 7.93 - 9.91: 34 Bond angle restraints: 24696 Sorted by residual: angle pdb=" N GLU D 484 " pdb=" CA GLU D 484 " pdb=" C GLU D 484 " ideal model delta sigma weight residual 108.74 118.65 -9.91 1.38e+00 5.25e-01 5.16e+01 angle pdb=" N TYR A 175 " pdb=" CA TYR A 175 " pdb=" C TYR A 175 " ideal model delta sigma weight residual 110.91 118.92 -8.01 1.17e+00 7.31e-01 4.69e+01 angle pdb=" N TYR C 175 " pdb=" CA TYR C 175 " pdb=" C TYR C 175 " ideal model delta sigma weight residual 110.91 118.88 -7.97 1.17e+00 7.31e-01 4.64e+01 angle pdb=" N ILE D 465 " pdb=" CA ILE D 465 " pdb=" C ILE D 465 " ideal model delta sigma weight residual 111.90 106.55 5.35 8.10e-01 1.52e+00 4.37e+01 angle pdb=" N ILE B 465 " pdb=" CA ILE B 465 " pdb=" C ILE B 465 " ideal model delta sigma weight residual 111.90 106.55 5.35 8.10e-01 1.52e+00 4.36e+01 ... (remaining 24691 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.96: 10328 23.96 - 47.93: 548 47.93 - 71.89: 93 71.89 - 95.85: 19 95.85 - 119.81: 2 Dihedral angle restraints: 10990 sinusoidal: 4674 harmonic: 6316 Sorted by residual: dihedral pdb=" CA TYR A 259 " pdb=" C TYR A 259 " pdb=" N GLY A 260 " pdb=" CA GLY A 260 " ideal model delta harmonic sigma weight residual 180.00 153.09 26.91 0 5.00e+00 4.00e-02 2.90e+01 dihedral pdb=" CA TYR C 259 " pdb=" C TYR C 259 " pdb=" N GLY C 260 " pdb=" CA GLY C 260 " ideal model delta harmonic sigma weight residual 180.00 153.12 26.88 0 5.00e+00 4.00e-02 2.89e+01 dihedral pdb=" CB CYS C 114 " pdb=" SG CYS C 114 " pdb=" SG CYS D 144 " pdb=" CB CYS D 144 " ideal model delta sinusoidal sigma weight residual 93.00 134.07 -41.07 1 1.00e+01 1.00e-02 2.36e+01 ... (remaining 10987 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.146: 2768 0.146 - 0.293: 36 0.293 - 0.439: 10 0.439 - 0.585: 0 0.585 - 0.732: 4 Chirality restraints: 2818 Sorted by residual: chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN A 261 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.67 -0.73 2.00e-01 2.50e+01 1.34e+01 chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN C 261 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.67 -0.73 2.00e-01 2.50e+01 1.34e+01 chirality pdb=" C1 NAG M 1 " pdb=" ND2 ASN C 513 " pdb=" C2 NAG M 1 " pdb=" O5 NAG M 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.79 -0.61 2.00e-01 2.50e+01 9.22e+00 ... (remaining 2815 not shown) Planarity restraints: 3066 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 260 " -0.054 5.00e-02 4.00e+02 8.13e-02 1.06e+01 pdb=" N PRO B 261 " 0.140 5.00e-02 4.00e+02 pdb=" CA PRO B 261 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 261 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE D 260 " 0.054 5.00e-02 4.00e+02 8.12e-02 1.05e+01 pdb=" N PRO D 261 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO D 261 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO D 261 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 427 " 0.045 5.00e-02 4.00e+02 6.70e-02 7.19e+00 pdb=" N PRO B 428 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO B 428 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 428 " 0.038 5.00e-02 4.00e+02 ... (remaining 3063 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 158 2.49 - 3.09: 11084 3.09 - 3.70: 27251 3.70 - 4.30: 43223 4.30 - 4.90: 67678 Nonbonded interactions: 149394 Sorted by model distance: nonbonded pdb=" ND1 HIS B 456 " pdb=" CE1 TYR B 457 " model vdw 1.890 3.420 nonbonded pdb=" ND1 HIS D 456 " pdb=" CE1 TYR D 457 " model vdw 1.894 3.420 nonbonded pdb=" CE1 HIS B 456 " pdb=" CE1 TYR B 457 " model vdw 2.208 3.560 nonbonded pdb=" O PRO B 482 " pdb=" N GLU B 484 " model vdw 2.238 3.120 nonbonded pdb=" CE1 HIS D 456 " pdb=" CE1 TYR D 457 " model vdw 2.238 3.560 ... (remaining 149389 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.640 Check model and map are aligned: 0.130 Set scattering table: 0.150 Process input model: 48.820 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:16.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 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 : 0.007 0.125 18172 Z= 0.457 Angle : 0.995 9.912 24696 Z= 0.528 Chirality : 0.064 0.732 2818 Planarity : 0.007 0.081 3056 Dihedral : 15.030 119.812 6924 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.83 % Favored : 95.08 % Rotamer: Outliers : 1.96 % Allowed : 3.17 % Favored : 94.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.84 (0.13), residues: 2154 helix: -4.66 (0.05), residues: 998 sheet: -0.33 (0.34), residues: 182 loop : -1.96 (0.16), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 383 HIS 0.007 0.001 HIS C 348 PHE 0.023 0.002 PHE A 407 TYR 0.022 0.002 TYR C 65 ARG 0.004 0.000 ARG B 296 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 343 time to evaluate : 2.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 357 MET cc_start: 0.8938 (tmm) cc_final: 0.8566 (tmm) REVERT: A 381 MET cc_start: 0.8748 (ttp) cc_final: 0.8385 (ttp) REVERT: A 432 MET cc_start: 0.9225 (mmm) cc_final: 0.9000 (mmp) REVERT: A 435 MET cc_start: 0.9140 (ptt) cc_final: 0.8845 (ptt) REVERT: B 116 SER cc_start: 0.7218 (OUTLIER) cc_final: 0.6721 (m) REVERT: B 468 PRO cc_start: 0.5965 (Cg_exo) cc_final: 0.5617 (Cg_endo) REVERT: C 357 MET cc_start: 0.8938 (tmm) cc_final: 0.8567 (tmm) REVERT: C 381 MET cc_start: 0.8747 (ttp) cc_final: 0.8380 (ttp) REVERT: C 432 MET cc_start: 0.9234 (mmm) cc_final: 0.9000 (mmp) REVERT: C 435 MET cc_start: 0.9146 (ptt) cc_final: 0.8850 (ptt) REVERT: D 116 SER cc_start: 0.7110 (OUTLIER) cc_final: 0.6571 (m) REVERT: D 194 SER cc_start: 0.7013 (p) cc_final: 0.6473 (m) outliers start: 37 outliers final: 4 residues processed: 368 average time/residue: 1.2060 time to fit residues: 502.3817 Evaluate side-chains 205 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 199 time to evaluate : 1.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 145 LYS Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 145 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 180 optimal weight: 0.4980 chunk 162 optimal weight: 9.9990 chunk 90 optimal weight: 6.9990 chunk 55 optimal weight: 9.9990 chunk 109 optimal weight: 2.9990 chunk 86 optimal weight: 6.9990 chunk 167 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 101 optimal weight: 9.9990 chunk 124 optimal weight: 1.9990 chunk 194 optimal weight: 5.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN A 156 ASN A 201 HIS A 220 HIS A 324 HIS A 330 GLN A 422 ASN A 442 ASN A 493 ASN A 510 GLN A 598 ASN A 609 ASN A 625 ASN B 239 ASN B 247 ASN C 125 GLN C 156 ASN C 201 HIS C 220 HIS C 324 HIS C 330 GLN C 422 ASN C 442 ASN C 493 ASN C 510 GLN C 598 ASN C 609 ASN C 625 ASN D 239 ASN D 247 ASN D 474 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 18172 Z= 0.394 Angle : 0.835 10.188 24696 Z= 0.422 Chirality : 0.057 0.490 2818 Planarity : 0.007 0.047 3056 Dihedral : 11.806 111.825 2962 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.90 % Favored : 96.01 % Rotamer: Outliers : 3.12 % Allowed : 10.41 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.16), residues: 2154 helix: -2.15 (0.13), residues: 1006 sheet: 0.09 (0.35), residues: 180 loop : -1.36 (0.18), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 239 HIS 0.010 0.002 HIS C 348 PHE 0.026 0.002 PHE C 407 TYR 0.019 0.002 TYR D 97 ARG 0.011 0.001 ARG D 296 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 214 time to evaluate : 2.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 271 ASN cc_start: 0.8756 (OUTLIER) cc_final: 0.8197 (t0) REVERT: A 280 LYS cc_start: 0.8692 (pttp) cc_final: 0.8421 (ptpt) REVERT: A 432 MET cc_start: 0.9057 (mmm) cc_final: 0.8846 (mmp) REVERT: A 465 MET cc_start: 0.8977 (mmm) cc_final: 0.8753 (mmm) REVERT: A 523 SER cc_start: 0.8724 (m) cc_final: 0.8517 (t) REVERT: A 542 LYS cc_start: 0.8882 (mtpt) cc_final: 0.8588 (mtpt) REVERT: B 134 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.7219 (mp0) REVERT: B 181 THR cc_start: 0.7026 (OUTLIER) cc_final: 0.6688 (p) REVERT: B 194 SER cc_start: 0.7230 (p) cc_final: 0.6848 (m) REVERT: B 239 ASN cc_start: 0.5592 (OUTLIER) cc_final: 0.5364 (t0) REVERT: B 254 LEU cc_start: 0.6202 (OUTLIER) cc_final: 0.4822 (tp) REVERT: B 337 MET cc_start: 0.5874 (OUTLIER) cc_final: 0.5590 (tpt) REVERT: B 453 LEU cc_start: 0.5541 (OUTLIER) cc_final: 0.5004 (tp) REVERT: C 271 ASN cc_start: 0.8753 (OUTLIER) cc_final: 0.8196 (t0) REVERT: C 280 LYS cc_start: 0.8694 (pttp) cc_final: 0.8422 (ptpt) REVERT: C 432 MET cc_start: 0.9068 (mmm) cc_final: 0.8848 (mmp) REVERT: C 465 MET cc_start: 0.8974 (mmm) cc_final: 0.8752 (mmm) REVERT: C 523 SER cc_start: 0.8720 (m) cc_final: 0.8519 (t) REVERT: C 542 LYS cc_start: 0.8877 (mtpt) cc_final: 0.8589 (mtpt) REVERT: C 610 MET cc_start: 0.8484 (OUTLIER) cc_final: 0.8041 (mmt) REVERT: D 134 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.7226 (mp0) REVERT: D 180 PHE cc_start: 0.5453 (m-10) cc_final: 0.5140 (m-10) REVERT: D 181 THR cc_start: 0.6915 (OUTLIER) cc_final: 0.6422 (p) REVERT: D 194 SER cc_start: 0.6966 (p) cc_final: 0.6530 (m) REVERT: D 239 ASN cc_start: 0.5746 (OUTLIER) cc_final: 0.5486 (t0) REVERT: D 464 LYS cc_start: 0.4282 (OUTLIER) cc_final: 0.3489 (mmtm) outliers start: 59 outliers final: 15 residues processed: 256 average time/residue: 1.2922 time to fit residues: 372.5635 Evaluate side-chains 205 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 177 time to evaluate : 2.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 337 MET Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 440 CYS Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain C residue 271 ASN Chi-restraints excluded: chain C residue 338 ASP Chi-restraints excluded: chain C residue 610 MET Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 239 ASN Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 464 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 108 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 161 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 194 optimal weight: 0.5980 chunk 210 optimal weight: 5.9990 chunk 173 optimal weight: 1.9990 chunk 193 optimal weight: 0.7980 chunk 66 optimal weight: 8.9990 chunk 156 optimal weight: 2.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 609 ASN A 679 ASN B 239 ASN C 609 ASN C 679 ASN D 239 ASN D 474 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 18172 Z= 0.222 Angle : 0.713 9.815 24696 Z= 0.351 Chirality : 0.050 0.397 2818 Planarity : 0.005 0.041 3056 Dihedral : 11.345 112.124 2952 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.70 % Allowed : 12.68 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.17), residues: 2154 helix: -0.73 (0.16), residues: 1000 sheet: 0.20 (0.36), residues: 178 loop : -1.14 (0.19), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 239 HIS 0.006 0.001 HIS C 348 PHE 0.017 0.001 PHE A 407 TYR 0.017 0.001 TYR A 259 ARG 0.007 0.000 ARG D 296 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 209 time to evaluate : 2.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 271 ASN cc_start: 0.8701 (OUTLIER) cc_final: 0.8251 (t0) REVERT: A 280 LYS cc_start: 0.8618 (pttp) cc_final: 0.8353 (ptpt) REVERT: A 512 ASP cc_start: 0.7368 (p0) cc_final: 0.6962 (p0) REVERT: A 542 LYS cc_start: 0.8851 (mtpt) cc_final: 0.8536 (mtpt) REVERT: A 663 ARG cc_start: 0.7245 (tpt90) cc_final: 0.6969 (tpt90) REVERT: B 194 SER cc_start: 0.7053 (p) cc_final: 0.6738 (m) REVERT: B 254 LEU cc_start: 0.6186 (OUTLIER) cc_final: 0.4835 (tp) REVERT: B 402 GLU cc_start: 0.5695 (mp0) cc_final: 0.4187 (tp30) REVERT: C 271 ASN cc_start: 0.8722 (OUTLIER) cc_final: 0.8253 (t0) REVERT: C 280 LYS cc_start: 0.8618 (pttp) cc_final: 0.8355 (ptpt) REVERT: C 512 ASP cc_start: 0.7400 (p0) cc_final: 0.6969 (p0) REVERT: C 542 LYS cc_start: 0.8862 (mtpt) cc_final: 0.8555 (mtpt) REVERT: C 610 MET cc_start: 0.8388 (OUTLIER) cc_final: 0.7997 (mmt) REVERT: C 663 ARG cc_start: 0.7249 (tpt90) cc_final: 0.6970 (tpt90) REVERT: D 101 MET cc_start: 0.6551 (ppp) cc_final: 0.6348 (pp-130) REVERT: D 107 ILE cc_start: 0.5855 (mt) cc_final: 0.5581 (pp) REVERT: D 134 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.7107 (mp0) REVERT: D 180 PHE cc_start: 0.5336 (m-10) cc_final: 0.5109 (m-10) REVERT: D 194 SER cc_start: 0.6818 (p) cc_final: 0.6500 (m) REVERT: D 263 VAL cc_start: 0.6235 (p) cc_final: 0.5744 (p) REVERT: D 360 ILE cc_start: 0.8475 (OUTLIER) cc_final: 0.8162 (mp) REVERT: D 442 LEU cc_start: 0.6829 (OUTLIER) cc_final: 0.6374 (mt) outliers start: 51 outliers final: 12 residues processed: 246 average time/residue: 1.3948 time to fit residues: 384.8202 Evaluate side-chains 213 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 194 time to evaluate : 2.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 440 CYS Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 271 ASN Chi-restraints excluded: chain C residue 437 GLU Chi-restraints excluded: chain C residue 610 MET Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 442 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 192 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 chunk 101 optimal weight: 8.9990 chunk 21 optimal weight: 3.9990 chunk 92 optimal weight: 7.9990 chunk 130 optimal weight: 1.9990 chunk 195 optimal weight: 0.6980 chunk 206 optimal weight: 6.9990 chunk 102 optimal weight: 6.9990 chunk 185 optimal weight: 0.9980 chunk 55 optimal weight: 0.0000 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 609 ASN A 679 ASN B 474 GLN C 609 ASN C 679 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18172 Z= 0.204 Angle : 0.675 9.812 24696 Z= 0.329 Chirality : 0.049 0.369 2818 Planarity : 0.004 0.041 3056 Dihedral : 10.841 113.323 2948 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.64 % Allowed : 13.27 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.18), residues: 2154 helix: -0.04 (0.16), residues: 1000 sheet: 0.36 (0.37), residues: 180 loop : -0.92 (0.19), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 239 HIS 0.006 0.001 HIS A 348 PHE 0.016 0.001 PHE A 407 TYR 0.018 0.001 TYR D 377 ARG 0.005 0.000 ARG C 663 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 216 time to evaluate : 1.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 271 ASN cc_start: 0.8668 (OUTLIER) cc_final: 0.8285 (t0) REVERT: A 512 ASP cc_start: 0.7318 (p0) cc_final: 0.6933 (p0) REVERT: A 542 LYS cc_start: 0.8818 (mtpt) cc_final: 0.8497 (mtpt) REVERT: A 610 MET cc_start: 0.8297 (mtp) cc_final: 0.8017 (mmt) REVERT: B 134 GLU cc_start: 0.7139 (OUTLIER) cc_final: 0.6931 (mp0) REVERT: B 194 SER cc_start: 0.6978 (p) cc_final: 0.6759 (m) REVERT: B 254 LEU cc_start: 0.6174 (OUTLIER) cc_final: 0.4849 (tp) REVERT: B 276 THR cc_start: 0.7778 (m) cc_final: 0.7439 (t) REVERT: B 284 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.8057 (mt) REVERT: B 365 TYR cc_start: 0.8032 (OUTLIER) cc_final: 0.7342 (m-10) REVERT: B 402 GLU cc_start: 0.5706 (mp0) cc_final: 0.4233 (tp30) REVERT: B 453 LEU cc_start: 0.5694 (OUTLIER) cc_final: 0.5203 (tp) REVERT: C 271 ASN cc_start: 0.8668 (OUTLIER) cc_final: 0.8287 (t0) REVERT: C 512 ASP cc_start: 0.7316 (p0) cc_final: 0.6915 (p0) REVERT: C 542 LYS cc_start: 0.8817 (mtpt) cc_final: 0.8486 (mtpt) REVERT: C 610 MET cc_start: 0.8364 (OUTLIER) cc_final: 0.8079 (mmt) REVERT: C 653 LYS cc_start: 0.8705 (OUTLIER) cc_final: 0.7971 (mtpt) REVERT: D 107 ILE cc_start: 0.5830 (mt) cc_final: 0.5526 (pp) REVERT: D 134 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.7170 (mp0) REVERT: D 194 SER cc_start: 0.6935 (p) cc_final: 0.6651 (m) REVERT: D 263 VAL cc_start: 0.6136 (OUTLIER) cc_final: 0.5680 (p) REVERT: D 276 THR cc_start: 0.7737 (OUTLIER) cc_final: 0.7434 (t) REVERT: D 360 ILE cc_start: 0.8452 (OUTLIER) cc_final: 0.8090 (mp) REVERT: D 442 LEU cc_start: 0.6814 (OUTLIER) cc_final: 0.6339 (mt) REVERT: D 464 LYS cc_start: 0.4278 (OUTLIER) cc_final: 0.3556 (mmtt) outliers start: 50 outliers final: 19 residues processed: 248 average time/residue: 1.3028 time to fit residues: 363.5731 Evaluate side-chains 231 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 197 time to evaluate : 1.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 365 TYR Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 440 CYS Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 271 ASN Chi-restraints excluded: chain C residue 338 ASP Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 437 GLU Chi-restraints excluded: chain C residue 610 MET Chi-restraints excluded: chain C residue 653 LYS Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 205 LYS Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 464 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 172 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 chunk 154 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 176 optimal weight: 0.8980 chunk 142 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 105 optimal weight: 0.0870 chunk 185 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 459 ASN A 609 ASN A 679 ASN B 237 GLN B 474 GLN C 459 ASN C 609 ASN C 679 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18172 Z= 0.176 Angle : 0.656 9.855 24696 Z= 0.318 Chirality : 0.048 0.362 2818 Planarity : 0.004 0.043 3056 Dihedral : 10.515 111.531 2948 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.80 % Allowed : 13.85 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.18), residues: 2154 helix: 0.38 (0.17), residues: 1002 sheet: 0.47 (0.37), residues: 180 loop : -0.82 (0.19), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 383 HIS 0.005 0.001 HIS A 348 PHE 0.016 0.001 PHE A 407 TYR 0.017 0.001 TYR D 377 ARG 0.003 0.000 ARG C 663 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 200 time to evaluate : 1.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 271 ASN cc_start: 0.8665 (OUTLIER) cc_final: 0.8279 (t0) REVERT: A 512 ASP cc_start: 0.7259 (p0) cc_final: 0.6843 (p0) REVERT: A 610 MET cc_start: 0.8300 (OUTLIER) cc_final: 0.8024 (mmt) REVERT: B 180 PHE cc_start: 0.5637 (m-10) cc_final: 0.5430 (m-10) REVERT: B 194 SER cc_start: 0.6958 (p) cc_final: 0.6714 (m) REVERT: B 254 LEU cc_start: 0.6143 (OUTLIER) cc_final: 0.4854 (tp) REVERT: B 276 THR cc_start: 0.7725 (m) cc_final: 0.7484 (t) REVERT: B 337 MET cc_start: 0.6072 (ttm) cc_final: 0.5651 (tpp) REVERT: B 365 TYR cc_start: 0.8033 (OUTLIER) cc_final: 0.7399 (m-10) REVERT: B 402 GLU cc_start: 0.5732 (mp0) cc_final: 0.4309 (tp30) REVERT: C 271 ASN cc_start: 0.8666 (OUTLIER) cc_final: 0.8280 (t0) REVERT: C 512 ASP cc_start: 0.7260 (p0) cc_final: 0.6843 (p0) REVERT: C 653 LYS cc_start: 0.8698 (OUTLIER) cc_final: 0.7920 (mtpt) REVERT: D 180 PHE cc_start: 0.5473 (m-10) cc_final: 0.5245 (m-10) REVERT: D 194 SER cc_start: 0.6861 (p) cc_final: 0.6614 (m) REVERT: D 263 VAL cc_start: 0.6193 (OUTLIER) cc_final: 0.5682 (p) REVERT: D 276 THR cc_start: 0.7729 (m) cc_final: 0.7512 (t) REVERT: D 360 ILE cc_start: 0.8496 (OUTLIER) cc_final: 0.8124 (mp) REVERT: D 442 LEU cc_start: 0.6828 (OUTLIER) cc_final: 0.6363 (mt) REVERT: D 464 LYS cc_start: 0.4138 (OUTLIER) cc_final: 0.3789 (mmtp) outliers start: 53 outliers final: 20 residues processed: 238 average time/residue: 1.3143 time to fit residues: 353.7352 Evaluate side-chains 215 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 185 time to evaluate : 1.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 365 TYR Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 440 CYS Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 271 ASN Chi-restraints excluded: chain C residue 338 ASP Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 437 GLU Chi-restraints excluded: chain C residue 653 LYS Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 205 LYS Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 464 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 69 optimal weight: 0.9990 chunk 186 optimal weight: 4.9990 chunk 40 optimal weight: 0.7980 chunk 121 optimal weight: 0.9980 chunk 51 optimal weight: 0.4980 chunk 207 optimal weight: 8.9990 chunk 171 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 108 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 459 ASN A 609 ASN A 679 ASN B 474 GLN C 459 ASN C 609 ASN C 679 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18172 Z= 0.175 Angle : 0.650 9.855 24696 Z= 0.315 Chirality : 0.048 0.358 2818 Planarity : 0.004 0.047 3056 Dihedral : 10.280 110.396 2948 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.59 % Allowed : 14.64 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.18), residues: 2154 helix: 0.59 (0.17), residues: 1010 sheet: 0.48 (0.37), residues: 180 loop : -0.68 (0.20), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 569 HIS 0.005 0.001 HIS C 348 PHE 0.016 0.001 PHE C 407 TYR 0.016 0.001 TYR D 377 ARG 0.002 0.000 ARG D 405 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 197 time to evaluate : 2.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 271 ASN cc_start: 0.8661 (OUTLIER) cc_final: 0.8270 (t0) REVERT: A 512 ASP cc_start: 0.7238 (p0) cc_final: 0.6795 (p0) REVERT: A 610 MET cc_start: 0.8340 (OUTLIER) cc_final: 0.8058 (mmt) REVERT: A 653 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.7898 (mtpt) REVERT: B 180 PHE cc_start: 0.5563 (m-10) cc_final: 0.5347 (m-10) REVERT: B 193 ILE cc_start: 0.4565 (pp) cc_final: 0.4301 (pp) REVERT: B 254 LEU cc_start: 0.6183 (OUTLIER) cc_final: 0.4923 (tp) REVERT: B 365 TYR cc_start: 0.8028 (OUTLIER) cc_final: 0.7388 (m-10) REVERT: B 402 GLU cc_start: 0.5801 (mp0) cc_final: 0.4285 (tp30) REVERT: C 271 ASN cc_start: 0.8661 (OUTLIER) cc_final: 0.8270 (t0) REVERT: C 512 ASP cc_start: 0.7258 (p0) cc_final: 0.6818 (p0) REVERT: C 610 MET cc_start: 0.8337 (OUTLIER) cc_final: 0.8045 (mmt) REVERT: C 653 LYS cc_start: 0.8695 (OUTLIER) cc_final: 0.7909 (mtpt) REVERT: D 180 PHE cc_start: 0.5421 (m-10) cc_final: 0.5100 (m-10) REVERT: D 194 SER cc_start: 0.6865 (p) cc_final: 0.6618 (m) REVERT: D 263 VAL cc_start: 0.6234 (OUTLIER) cc_final: 0.5724 (p) REVERT: D 360 ILE cc_start: 0.8457 (OUTLIER) cc_final: 0.8081 (mp) REVERT: D 442 LEU cc_start: 0.6869 (OUTLIER) cc_final: 0.6405 (mt) REVERT: D 464 LYS cc_start: 0.4134 (OUTLIER) cc_final: 0.3805 (mmtp) outliers start: 49 outliers final: 17 residues processed: 233 average time/residue: 1.3280 time to fit residues: 349.8066 Evaluate side-chains 217 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 188 time to evaluate : 1.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 653 LYS Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 365 TYR Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 440 CYS Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 271 ASN Chi-restraints excluded: chain C residue 338 ASP Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 610 MET Chi-restraints excluded: chain C residue 653 LYS Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 205 LYS Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 464 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 199 optimal weight: 8.9990 chunk 23 optimal weight: 1.9990 chunk 117 optimal weight: 4.9990 chunk 151 optimal weight: 5.9990 chunk 174 optimal weight: 1.9990 chunk 115 optimal weight: 0.1980 chunk 206 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 125 optimal weight: 4.9990 chunk 95 optimal weight: 0.9980 chunk 127 optimal weight: 2.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 459 ASN A 609 ASN A 679 ASN C 459 ASN C 609 ASN C 679 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 18172 Z= 0.255 Angle : 0.694 10.001 24696 Z= 0.341 Chirality : 0.051 0.394 2818 Planarity : 0.005 0.054 3056 Dihedral : 10.435 111.902 2948 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.59 % Allowed : 15.38 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.18), residues: 2154 helix: 0.60 (0.17), residues: 1008 sheet: 0.42 (0.38), residues: 180 loop : -0.73 (0.20), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 239 HIS 0.009 0.001 HIS A 244 PHE 0.021 0.002 PHE C 407 TYR 0.019 0.002 TYR A 259 ARG 0.003 0.000 ARG C 379 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 198 time to evaluate : 2.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 271 ASN cc_start: 0.8702 (OUTLIER) cc_final: 0.8352 (t0) REVERT: A 512 ASP cc_start: 0.7372 (p0) cc_final: 0.6902 (p0) REVERT: A 610 MET cc_start: 0.8335 (OUTLIER) cc_final: 0.8091 (mmt) REVERT: A 653 LYS cc_start: 0.8734 (OUTLIER) cc_final: 0.7937 (mtpt) REVERT: B 134 GLU cc_start: 0.7106 (OUTLIER) cc_final: 0.6774 (mp0) REVERT: B 193 ILE cc_start: 0.4936 (pp) cc_final: 0.4689 (pp) REVERT: B 254 LEU cc_start: 0.6187 (OUTLIER) cc_final: 0.4860 (tp) REVERT: B 323 THR cc_start: 0.5753 (OUTLIER) cc_final: 0.5436 (p) REVERT: B 365 TYR cc_start: 0.8048 (OUTLIER) cc_final: 0.7217 (m-10) REVERT: B 402 GLU cc_start: 0.5690 (mp0) cc_final: 0.4174 (tp30) REVERT: B 442 LEU cc_start: 0.6553 (OUTLIER) cc_final: 0.6222 (mt) REVERT: C 271 ASN cc_start: 0.8702 (OUTLIER) cc_final: 0.8349 (t0) REVERT: C 512 ASP cc_start: 0.7372 (p0) cc_final: 0.6900 (p0) REVERT: C 610 MET cc_start: 0.8370 (OUTLIER) cc_final: 0.8038 (mmt) REVERT: C 653 LYS cc_start: 0.8736 (OUTLIER) cc_final: 0.7967 (mtpt) REVERT: D 180 PHE cc_start: 0.5406 (m-10) cc_final: 0.4932 (m-10) REVERT: D 194 SER cc_start: 0.6939 (p) cc_final: 0.6681 (m) REVERT: D 263 VAL cc_start: 0.6358 (OUTLIER) cc_final: 0.5834 (p) REVERT: D 323 THR cc_start: 0.5828 (OUTLIER) cc_final: 0.5509 (p) REVERT: D 360 ILE cc_start: 0.8554 (OUTLIER) cc_final: 0.8184 (mp) REVERT: D 442 LEU cc_start: 0.6757 (OUTLIER) cc_final: 0.6292 (mt) REVERT: D 464 LYS cc_start: 0.4024 (OUTLIER) cc_final: 0.3773 (ptpt) outliers start: 49 outliers final: 19 residues processed: 233 average time/residue: 1.2847 time to fit residues: 338.9257 Evaluate side-chains 223 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 188 time to evaluate : 2.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 653 LYS Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 365 TYR Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 440 CYS Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 271 ASN Chi-restraints excluded: chain C residue 338 ASP Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 610 MET Chi-restraints excluded: chain C residue 653 LYS Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 205 LYS Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 464 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 82 optimal weight: 8.9990 chunk 123 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 40 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 131 optimal weight: 0.6980 chunk 140 optimal weight: 0.7980 chunk 101 optimal weight: 7.9990 chunk 19 optimal weight: 0.0170 chunk 162 optimal weight: 0.0170 chunk 187 optimal weight: 9.9990 overall best weight: 0.4456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 459 ASN A 609 ASN A 679 ASN C 459 ASN C 609 ASN C 679 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.3541 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: