Starting phenix.real_space_refine on Fri Jul 19 15:16:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w6g_37322/07_2024/8w6g_37322.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w6g_37322/07_2024/8w6g_37322.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w6g_37322/07_2024/8w6g_37322.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w6g_37322/07_2024/8w6g_37322.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w6g_37322/07_2024/8w6g_37322.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w6g_37322/07_2024/8w6g_37322.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 58 5.16 5 C 5582 2.51 5 N 1280 2.21 5 O 1392 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 12": "NH1" <-> "NH2" Residue "A PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 302": "OE1" <-> "OE2" Residue "A ARG 320": "NH1" <-> "NH2" Residue "A GLU 396": "OE1" <-> "OE2" Residue "A ARG 437": "NH1" <-> "NH2" Residue "A TYR 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 12": "NH1" <-> "NH2" Residue "B PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 302": "OE1" <-> "OE2" Residue "B ARG 320": "NH1" <-> "NH2" Residue "B GLU 396": "OE1" <-> "OE2" Residue "B ARG 437": "NH1" <-> "NH2" Residue "B TYR 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 8314 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4049 Classifications: {'peptide': 527} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 33, 'TRANS': 493} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 4049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4049 Classifications: {'peptide': 527} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 33, 'TRANS': 493} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 108 Unusual residues: {'3PH': 1, 'VIJ': 1, 'Y01': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 108 Unusual residues: {'3PH': 1, 'VIJ': 1, 'Y01': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 5.66, per 1000 atoms: 0.68 Number of scatterers: 8314 At special positions: 0 Unit cell: (98.917, 107.613, 90.221, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 58 16.00 P 2 15.00 O 1392 8.00 N 1280 7.00 C 5582 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.19 Conformation dependent library (CDL) restraints added in 1.7 seconds 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1976 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 2 sheets defined 71.9% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 3 through 11 removed outlier: 4.022A pdb=" N TRP A 9 " --> pdb=" O TRP A 5 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA A 10 " --> pdb=" O GLN A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 11 through 24 removed outlier: 3.658A pdb=" N ILE A 16 " --> pdb=" O ARG A 12 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N VAL A 17 " --> pdb=" O SER A 13 " (cutoff:3.500A) Proline residue: A 21 - end of helix Processing helix chain 'A' and resid 25 through 31 removed outlier: 3.619A pdb=" N VAL A 31 " --> pdb=" O LEU A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 51 removed outlier: 3.568A pdb=" N CYS A 38 " --> pdb=" O LYS A 34 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA A 41 " --> pdb=" O TYR A 37 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N CYS A 50 " --> pdb=" O ALA A 46 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR A 51 " --> pdb=" O LEU A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 60 removed outlier: 3.535A pdb=" N ALA A 60 " --> pdb=" O LEU A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 65 Processing helix chain 'A' and resid 74 through 80 removed outlier: 3.899A pdb=" N VAL A 80 " --> pdb=" O SER A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 103 removed outlier: 3.710A pdb=" N LEU A 88 " --> pdb=" O LYS A 84 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL A 96 " --> pdb=" O GLY A 92 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TRP A 103 " --> pdb=" O ALA A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 117 removed outlier: 3.568A pdb=" N LEU A 111 " --> pdb=" O LYS A 107 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU A 114 " --> pdb=" O ALA A 110 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE A 116 " --> pdb=" O ARG A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 136 removed outlier: 3.565A pdb=" N LEU A 124 " --> pdb=" O ARG A 120 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL A 131 " --> pdb=" O GLY A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 162 Proline residue: A 150 - end of helix removed outlier: 3.564A pdb=" N LEU A 156 " --> pdb=" O ALA A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 232 removed outlier: 3.721A pdb=" N SER A 222 " --> pdb=" O THR A 218 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL A 225 " --> pdb=" O MET A 221 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N CYS A 226 " --> pdb=" O SER A 222 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER A 230 " --> pdb=" O CYS A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 235 No H-bonds generated for 'chain 'A' and resid 233 through 235' Processing helix chain 'A' and resid 241 through 254 removed outlier: 3.695A pdb=" N VAL A 245 " --> pdb=" O ALA A 241 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU A 246 " --> pdb=" O PRO A 242 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN A 247 " --> pdb=" O ASN A 243 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN A 251 " --> pdb=" O GLN A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 290 removed outlier: 3.755A pdb=" N SER A 268 " --> pdb=" O ALA A 264 " (cutoff:3.500A) Proline residue: A 272 - end of helix Processing helix chain 'A' and resid 304 through 321 removed outlier: 4.087A pdb=" N VAL A 314 " --> pdb=" O ALA A 310 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE A 315 " --> pdb=" O ALA A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 345 removed outlier: 3.627A pdb=" N ILE A 334 " --> pdb=" O LYS A 330 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR A 345 " --> pdb=" O LEU A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 358 Processing helix chain 'A' and resid 369 through 381 removed outlier: 3.630A pdb=" N VAL A 373 " --> pdb=" O SER A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 417 removed outlier: 3.663A pdb=" N GLN A 415 " --> pdb=" O LYS A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 438 removed outlier: 3.865A pdb=" N VAL A 422 " --> pdb=" O PRO A 418 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU A 423 " --> pdb=" O TRP A 419 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY A 428 " --> pdb=" O LEU A 424 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR A 429 " --> pdb=" O LEU A 425 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER A 435 " --> pdb=" O LEU A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 446 Processing helix chain 'A' and resid 447 through 453 Proline residue: A 450 - end of helix removed outlier: 4.309A pdb=" N SER A 453 " --> pdb=" O PRO A 450 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 447 through 453' Processing helix chain 'A' and resid 455 through 457 No H-bonds generated for 'chain 'A' and resid 455 through 457' Processing helix chain 'A' and resid 458 through 471 Processing helix chain 'A' and resid 475 through 492 removed outlier: 3.569A pdb=" N ILE A 482 " --> pdb=" O ALA A 478 " (cutoff:3.500A) Proline residue: A 485 - end of helix Processing helix chain 'A' and resid 502 through 508 Processing helix chain 'A' and resid 509 through 511 No H-bonds generated for 'chain 'A' and resid 509 through 511' Processing helix chain 'A' and resid 520 through 525 removed outlier: 3.623A pdb=" N ILE A 524 " --> pdb=" O PRO A 520 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL A 525 " --> pdb=" O PRO A 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 520 through 525' Processing helix chain 'A' and resid 532 through 555 removed outlier: 3.642A pdb=" N PHE A 541 " --> pdb=" O ALA A 537 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N LEU A 542 " --> pdb=" O ARG A 538 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU A 543 " --> pdb=" O ALA A 539 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE A 545 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A 553 " --> pdb=" O LEU A 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 11 removed outlier: 4.021A pdb=" N TRP B 9 " --> pdb=" O TRP B 5 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 24 removed outlier: 3.657A pdb=" N ILE B 16 " --> pdb=" O ARG B 12 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N VAL B 17 " --> pdb=" O SER B 13 " (cutoff:3.500A) Proline residue: B 21 - end of helix Processing helix chain 'B' and resid 25 through 31 removed outlier: 3.618A pdb=" N VAL B 31 " --> pdb=" O LEU B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 51 removed outlier: 3.567A pdb=" N CYS B 38 " --> pdb=" O LYS B 34 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA B 41 " --> pdb=" O TYR B 37 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N CYS B 50 " --> pdb=" O ALA B 46 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR B 51 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 60 removed outlier: 3.535A pdb=" N ALA B 60 " --> pdb=" O LEU B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 65 Processing helix chain 'B' and resid 74 through 80 removed outlier: 3.899A pdb=" N VAL B 80 " --> pdb=" O SER B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 103 removed outlier: 3.709A pdb=" N LEU B 88 " --> pdb=" O LYS B 84 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL B 96 " --> pdb=" O GLY B 92 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA B 99 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TRP B 103 " --> pdb=" O ALA B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 117 removed outlier: 3.569A pdb=" N LEU B 111 " --> pdb=" O LYS B 107 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE B 116 " --> pdb=" O ARG B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 136 removed outlier: 3.564A pdb=" N LEU B 124 " --> pdb=" O ARG B 120 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL B 131 " --> pdb=" O GLY B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 162 Proline residue: B 150 - end of helix removed outlier: 3.563A pdb=" N LEU B 156 " --> pdb=" O ALA B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 232 removed outlier: 3.722A pdb=" N SER B 222 " --> pdb=" O THR B 218 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL B 225 " --> pdb=" O MET B 221 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N CYS B 226 " --> pdb=" O SER B 222 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER B 230 " --> pdb=" O CYS B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 235 No H-bonds generated for 'chain 'B' and resid 233 through 235' Processing helix chain 'B' and resid 241 through 254 removed outlier: 3.694A pdb=" N VAL B 245 " --> pdb=" O ALA B 241 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU B 246 " --> pdb=" O PRO B 242 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN B 247 " --> pdb=" O ASN B 243 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN B 251 " --> pdb=" O GLN B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 290 removed outlier: 3.755A pdb=" N SER B 268 " --> pdb=" O ALA B 264 " (cutoff:3.500A) Proline residue: B 272 - end of helix Processing helix chain 'B' and resid 304 through 321 removed outlier: 4.087A pdb=" N VAL B 314 " --> pdb=" O ALA B 310 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE B 315 " --> pdb=" O ALA B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 345 removed outlier: 3.628A pdb=" N ILE B 334 " --> pdb=" O LYS B 330 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR B 345 " --> pdb=" O LEU B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 358 Processing helix chain 'B' and resid 369 through 381 removed outlier: 3.629A pdb=" N VAL B 373 " --> pdb=" O SER B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 417 removed outlier: 3.662A pdb=" N GLN B 415 " --> pdb=" O LYS B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 438 removed outlier: 3.865A pdb=" N VAL B 422 " --> pdb=" O PRO B 418 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU B 423 " --> pdb=" O TRP B 419 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY B 428 " --> pdb=" O LEU B 424 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR B 429 " --> pdb=" O LEU B 425 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER B 435 " --> pdb=" O LEU B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 446 Processing helix chain 'B' and resid 447 through 453 Proline residue: B 450 - end of helix removed outlier: 4.309A pdb=" N SER B 453 " --> pdb=" O PRO B 450 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 447 through 453' Processing helix chain 'B' and resid 455 through 457 No H-bonds generated for 'chain 'B' and resid 455 through 457' Processing helix chain 'B' and resid 458 through 471 Processing helix chain 'B' and resid 475 through 492 removed outlier: 3.570A pdb=" N ILE B 482 " --> pdb=" O ALA B 478 " (cutoff:3.500A) Proline residue: B 485 - end of helix Processing helix chain 'B' and resid 502 through 508 Processing helix chain 'B' and resid 509 through 511 No H-bonds generated for 'chain 'B' and resid 509 through 511' Processing helix chain 'B' and resid 520 through 525 removed outlier: 3.622A pdb=" N ILE B 524 " --> pdb=" O PRO B 520 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL B 525 " --> pdb=" O PRO B 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 520 through 525' Processing helix chain 'B' and resid 532 through 555 removed outlier: 3.642A pdb=" N PHE B 541 " --> pdb=" O ALA B 537 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N LEU B 542 " --> pdb=" O ARG B 538 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU B 543 " --> pdb=" O ALA B 539 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE B 545 " --> pdb=" O PHE B 541 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU B 553 " --> pdb=" O LEU B 549 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 392 through 393 removed outlier: 3.582A pdb=" N THR A 392 " --> pdb=" O LYS A 402 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 392 through 393 removed outlier: 3.581A pdb=" N THR B 392 " --> pdb=" O LYS B 402 " (cutoff:3.500A) 400 hydrogen bonds defined for protein. 1188 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: 2.11 Time building geometry restraints manager: 3.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1236 1.31 - 1.43: 2250 1.43 - 1.56: 4958 1.56 - 1.68: 4 1.68 - 1.81: 96 Bond restraints: 8544 Sorted by residual: bond pdb=" C THR B 449 " pdb=" N PRO B 450 " ideal model delta sigma weight residual 1.334 1.375 -0.041 8.40e-03 1.42e+04 2.40e+01 bond pdb=" O11 3PH A 603 " pdb=" P 3PH A 603 " ideal model delta sigma weight residual 1.703 1.609 0.094 2.00e-02 2.50e+03 2.20e+01 bond pdb=" C20 VIJ A 601 " pdb=" N04 VIJ A 601 " ideal model delta sigma weight residual 1.353 1.446 -0.093 2.00e-02 2.50e+03 2.18e+01 bond pdb=" O11 3PH B 603 " pdb=" P 3PH B 603 " ideal model delta sigma weight residual 1.703 1.610 0.093 2.00e-02 2.50e+03 2.15e+01 bond pdb=" C20 VIJ B 601 " pdb=" N04 VIJ B 601 " ideal model delta sigma weight residual 1.353 1.445 -0.092 2.00e-02 2.50e+03 2.13e+01 ... (remaining 8539 not shown) Histogram of bond angle deviations from ideal: 98.76 - 105.87: 278 105.87 - 112.98: 4622 112.98 - 120.08: 3375 120.08 - 127.19: 3252 127.19 - 134.29: 137 Bond angle restraints: 11664 Sorted by residual: angle pdb=" CA LEU B 322 " pdb=" CB LEU B 322 " pdb=" CG LEU B 322 " ideal model delta sigma weight residual 116.30 133.68 -17.38 3.50e+00 8.16e-02 2.47e+01 angle pdb=" CA LEU A 322 " pdb=" CB LEU A 322 " pdb=" CG LEU A 322 " ideal model delta sigma weight residual 116.30 133.63 -17.33 3.50e+00 8.16e-02 2.45e+01 angle pdb=" C PRO A 455 " pdb=" N ALA A 456 " pdb=" CA ALA A 456 " ideal model delta sigma weight residual 120.06 125.80 -5.74 1.19e+00 7.06e-01 2.33e+01 angle pdb=" C PRO B 455 " pdb=" N ALA B 456 " pdb=" CA ALA B 456 " ideal model delta sigma weight residual 120.06 125.78 -5.72 1.19e+00 7.06e-01 2.31e+01 angle pdb=" N PRO B 520 " pdb=" CA PRO B 520 " pdb=" C PRO B 520 " ideal model delta sigma weight residual 110.70 116.37 -5.67 1.22e+00 6.72e-01 2.16e+01 ... (remaining 11659 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.97: 4605 16.97 - 33.94: 411 33.94 - 50.91: 76 50.91 - 67.88: 12 67.88 - 84.85: 6 Dihedral angle restraints: 5110 sinusoidal: 2066 harmonic: 3044 Sorted by residual: dihedral pdb=" CA PRO B 398 " pdb=" C PRO B 398 " pdb=" N GLY B 399 " pdb=" CA GLY B 399 " ideal model delta harmonic sigma weight residual 180.00 126.99 53.01 0 5.00e+00 4.00e-02 1.12e+02 dihedral pdb=" CA PRO A 398 " pdb=" C PRO A 398 " pdb=" N GLY A 399 " pdb=" CA GLY A 399 " ideal model delta harmonic sigma weight residual 180.00 127.02 52.98 0 5.00e+00 4.00e-02 1.12e+02 dihedral pdb=" CA PRO B 520 " pdb=" C PRO B 520 " pdb=" N PRO B 521 " pdb=" CA PRO B 521 " ideal model delta harmonic sigma weight residual 180.00 155.09 24.91 0 5.00e+00 4.00e-02 2.48e+01 ... (remaining 5107 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1112 0.060 - 0.120: 204 0.120 - 0.180: 60 0.180 - 0.240: 8 0.240 - 0.301: 2 Chirality restraints: 1386 Sorted by residual: chirality pdb=" CA ASN A 397 " pdb=" N ASN A 397 " pdb=" C ASN A 397 " pdb=" CB ASN A 397 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" CA ASN B 397 " pdb=" N ASN B 397 " pdb=" C ASN B 397 " pdb=" CB ASN B 397 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" C2 3PH B 603 " pdb=" C1 3PH B 603 " pdb=" C3 3PH B 603 " pdb=" O21 3PH B 603 " both_signs ideal model delta sigma weight residual False -2.33 -2.55 0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 1383 not shown) Planarity restraints: 1406 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 25 " 0.062 5.00e-02 4.00e+02 9.23e-02 1.36e+01 pdb=" N PRO B 26 " -0.160 5.00e-02 4.00e+02 pdb=" CA PRO B 26 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO B 26 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 25 " -0.062 5.00e-02 4.00e+02 9.23e-02 1.36e+01 pdb=" N PRO A 26 " 0.160 5.00e-02 4.00e+02 pdb=" CA PRO A 26 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 26 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 520 " -0.053 5.00e-02 4.00e+02 8.00e-02 1.02e+01 pdb=" N PRO B 521 " 0.138 5.00e-02 4.00e+02 pdb=" CA PRO B 521 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 521 " -0.045 5.00e-02 4.00e+02 ... (remaining 1403 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 2708 2.83 - 3.35: 7270 3.35 - 3.87: 12413 3.87 - 4.38: 15270 4.38 - 4.90: 26439 Nonbonded interactions: 64100 Sorted by model distance: nonbonded pdb=" O ALA A 460 " pdb=" OG SER A 464 " model vdw 2.313 2.440 nonbonded pdb=" O ALA B 460 " pdb=" OG SER B 464 " model vdw 2.313 2.440 nonbonded pdb=" O ILE A 524 " pdb=" OG SER A 527 " model vdw 2.321 2.440 nonbonded pdb=" O ILE B 524 " pdb=" OG SER B 527 " model vdw 2.321 2.440 nonbonded pdb=" NH2 ARG A 108 " pdb=" O GLY A 323 " model vdw 2.351 2.520 ... (remaining 64095 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 7.340 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: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 25.570 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 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 : 0.008 0.094 8544 Z= 0.525 Angle : 1.063 17.379 11664 Z= 0.566 Chirality : 0.055 0.301 1386 Planarity : 0.010 0.092 1406 Dihedral : 13.355 84.845 3134 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -6.99 (0.15), residues: 1046 helix: -4.76 (0.06), residues: 692 sheet: None (None), residues: 0 loop : -3.90 (0.28), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP A 558 HIS 0.006 0.001 HIS A 566 PHE 0.019 0.002 PHE B 351 TYR 0.010 0.001 TYR A 40 ARG 0.002 0.000 ARG B 538 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 0.862 Fit side-chains REVERT: A 295 ARG cc_start: 0.8456 (mtp-110) cc_final: 0.8228 (mtp85) REVERT: A 514 MET cc_start: 0.8977 (mtm) cc_final: 0.8691 (mtp) REVERT: B 514 MET cc_start: 0.8973 (mtm) cc_final: 0.8685 (mtp) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.2482 time to fit residues: 36.7367 Evaluate side-chains 87 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 60 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 ASN A 356 ASN A 556 ASN B 243 ASN B 356 ASN B 556 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8544 Z= 0.244 Angle : 0.691 11.937 11664 Z= 0.348 Chirality : 0.043 0.156 1386 Planarity : 0.007 0.072 1406 Dihedral : 7.899 48.334 1342 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 1.26 % Allowed : 8.94 % Favored : 89.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -4.08 (0.21), residues: 1046 helix: -2.18 (0.16), residues: 696 sheet: None (None), residues: 0 loop : -3.57 (0.30), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 558 HIS 0.001 0.001 HIS A 153 PHE 0.012 0.002 PHE B 376 TYR 0.005 0.001 TYR B 40 ARG 0.005 0.000 ARG A 320 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 92 time to evaluate : 0.895 Fit side-chains REVERT: A 295 ARG cc_start: 0.8470 (mtp-110) cc_final: 0.8269 (mtp85) REVERT: A 514 MET cc_start: 0.8878 (mtm) cc_final: 0.8669 (mtp) REVERT: B 514 MET cc_start: 0.8885 (mtm) cc_final: 0.8671 (mtp) outliers start: 11 outliers final: 9 residues processed: 99 average time/residue: 0.2130 time to fit residues: 29.2213 Evaluate side-chains 94 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 85 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 495 CYS Chi-restraints excluded: chain A residue 558 TRP Chi-restraints excluded: chain B residue 224 CYS Chi-restraints excluded: chain B residue 409 ASP Chi-restraints excluded: chain B residue 495 CYS Chi-restraints excluded: chain B residue 558 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 52 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 78 optimal weight: 0.5980 chunk 64 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 94 optimal weight: 3.9990 chunk 102 optimal weight: 0.8980 chunk 84 optimal weight: 0.9980 chunk 93 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8544 Z= 0.204 Angle : 0.613 11.544 11664 Z= 0.302 Chirality : 0.041 0.150 1386 Planarity : 0.006 0.064 1406 Dihedral : 7.756 50.135 1342 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 1.26 % Allowed : 10.78 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -2.21 (0.25), residues: 1046 helix: -0.49 (0.19), residues: 698 sheet: None (None), residues: 0 loop : -3.49 (0.30), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 558 HIS 0.002 0.001 HIS A 153 PHE 0.013 0.001 PHE B 292 TYR 0.004 0.001 TYR B 40 ARG 0.006 0.000 ARG B 320 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 91 time to evaluate : 0.874 Fit side-chains outliers start: 11 outliers final: 7 residues processed: 96 average time/residue: 0.2115 time to fit residues: 27.9612 Evaluate side-chains 91 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 84 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 495 CYS Chi-restraints excluded: chain B residue 224 CYS Chi-restraints excluded: chain B residue 409 ASP Chi-restraints excluded: chain B residue 495 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 93 optimal weight: 0.9990 chunk 71 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 100 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8544 Z= 0.255 Angle : 0.621 11.353 11664 Z= 0.303 Chirality : 0.042 0.148 1386 Planarity : 0.006 0.063 1406 Dihedral : 7.813 50.398 1342 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 1.49 % Allowed : 12.16 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -1.43 (0.26), residues: 1046 helix: 0.16 (0.20), residues: 698 sheet: None (None), residues: 0 loop : -3.29 (0.31), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 558 HIS 0.002 0.001 HIS B 319 PHE 0.013 0.001 PHE B 292 TYR 0.005 0.001 TYR A 40 ARG 0.005 0.000 ARG A 320 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 82 time to evaluate : 0.938 Fit side-chains outliers start: 13 outliers final: 11 residues processed: 93 average time/residue: 0.2367 time to fit residues: 29.9792 Evaluate side-chains 92 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 81 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 495 CYS Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 224 CYS Chi-restraints excluded: chain B residue 409 ASP Chi-restraints excluded: chain B residue 495 CYS Chi-restraints excluded: chain B residue 542 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 57 optimal weight: 0.0980 chunk 1 optimal weight: 0.9990 chunk 74 optimal weight: 0.0040 chunk 41 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 90 optimal weight: 0.8980 chunk 25 optimal weight: 0.0470 chunk 33 optimal weight: 0.6980 overall best weight: 0.3490 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 GLN B 308 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8544 Z= 0.163 Angle : 0.565 10.687 11664 Z= 0.276 Chirality : 0.040 0.148 1386 Planarity : 0.006 0.063 1406 Dihedral : 7.583 53.454 1342 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 1.61 % Allowed : 12.50 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -0.76 (0.27), residues: 1046 helix: 0.65 (0.20), residues: 712 sheet: None (None), residues: 0 loop : -3.12 (0.32), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 558 HIS 0.002 0.000 HIS A 497 PHE 0.013 0.001 PHE B 292 TYR 0.005 0.001 TYR A 40 ARG 0.006 0.000 ARG A 320 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 89 time to evaluate : 0.893 Fit side-chains REVERT: B 344 PHE cc_start: 0.8054 (OUTLIER) cc_final: 0.7182 (t80) outliers start: 14 outliers final: 5 residues processed: 101 average time/residue: 0.2072 time to fit residues: 28.8938 Evaluate side-chains 92 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 86 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 476 ASN Chi-restraints excluded: chain B residue 344 PHE Chi-restraints excluded: chain B residue 409 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 90 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 100 optimal weight: 0.2980 chunk 83 optimal weight: 0.9990 chunk 46 optimal weight: 0.1980 chunk 8 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8544 Z= 0.187 Angle : 0.597 13.517 11664 Z= 0.287 Chirality : 0.041 0.146 1386 Planarity : 0.005 0.064 1406 Dihedral : 7.510 52.498 1342 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 1.72 % Allowed : 12.73 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -0.29 (0.27), residues: 1046 helix: 1.06 (0.20), residues: 710 sheet: None (None), residues: 0 loop : -3.06 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 558 HIS 0.002 0.000 HIS A 497 PHE 0.013 0.001 PHE B 292 TYR 0.005 0.001 TYR A 40 ARG 0.002 0.000 ARG A 320 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 86 time to evaluate : 0.913 Fit side-chains REVERT: A 344 PHE cc_start: 0.8120 (OUTLIER) cc_final: 0.7268 (t80) REVERT: B 344 PHE cc_start: 0.8112 (OUTLIER) cc_final: 0.7262 (t80) REVERT: B 437 ARG cc_start: 0.7937 (mmm-85) cc_final: 0.7705 (tpp80) outliers start: 15 outliers final: 13 residues processed: 99 average time/residue: 0.2180 time to fit residues: 29.8311 Evaluate side-chains 98 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 83 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 476 ASN Chi-restraints excluded: chain A residue 495 CYS Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 224 CYS Chi-restraints excluded: chain B residue 344 PHE Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain B residue 409 ASP Chi-restraints excluded: chain B residue 476 ASN Chi-restraints excluded: chain B residue 495 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 0.4980 chunk 57 optimal weight: 2.9990 chunk 73 optimal weight: 0.0970 chunk 56 optimal weight: 0.5980 chunk 84 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 61 optimal weight: 0.3980 chunk 46 optimal weight: 0.0970 chunk 40 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 overall best weight: 0.3376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8544 Z= 0.157 Angle : 0.568 12.885 11664 Z= 0.273 Chirality : 0.040 0.145 1386 Planarity : 0.005 0.064 1406 Dihedral : 7.418 53.366 1342 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 1.72 % Allowed : 12.96 % Favored : 85.32 % 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: 0.14 (0.28), residues: 1046 helix: 1.41 (0.21), residues: 712 sheet: None (None), residues: 0 loop : -3.00 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 558 HIS 0.002 0.000 HIS A 497 PHE 0.013 0.001 PHE B 292 TYR 0.006 0.001 TYR B 40 ARG 0.003 0.000 ARG B 437 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 91 time to evaluate : 0.887 Fit side-chains REVERT: A 344 PHE cc_start: 0.8026 (OUTLIER) cc_final: 0.7146 (t80) REVERT: A 437 ARG cc_start: 0.7980 (mmm-85) cc_final: 0.7699 (tpp80) REVERT: B 344 PHE cc_start: 0.8015 (OUTLIER) cc_final: 0.7140 (t80) REVERT: B 437 ARG cc_start: 0.7835 (mmm-85) cc_final: 0.7614 (tpp80) outliers start: 15 outliers final: 13 residues processed: 103 average time/residue: 0.2059 time to fit residues: 29.2757 Evaluate side-chains 100 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 85 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 476 ASN Chi-restraints excluded: chain A residue 495 CYS Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 224 CYS Chi-restraints excluded: chain B residue 344 PHE Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain B residue 409 ASP Chi-restraints excluded: chain B residue 476 ASN Chi-restraints excluded: chain B residue 495 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 30 optimal weight: 0.0000 chunk 19 optimal weight: 0.5980 chunk 63 optimal weight: 0.8980 chunk 68 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 93 optimal weight: 0.6980 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8544 Z= 0.198 Angle : 0.589 13.127 11664 Z= 0.284 Chirality : 0.041 0.144 1386 Planarity : 0.005 0.064 1406 Dihedral : 7.486 52.531 1342 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 1.49 % Allowed : 13.65 % Favored : 84.86 % 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: 0.34 (0.28), residues: 1046 helix: 1.56 (0.21), residues: 712 sheet: None (None), residues: 0 loop : -2.92 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 558 HIS 0.002 0.000 HIS A 319 PHE 0.013 0.001 PHE A 292 TYR 0.005 0.001 TYR B 40 ARG 0.006 0.000 ARG B 320 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 87 time to evaluate : 1.001 Fit side-chains REVERT: A 344 PHE cc_start: 0.8137 (OUTLIER) cc_final: 0.7279 (t80) REVERT: B 320 ARG cc_start: 0.8139 (tpp80) cc_final: 0.7852 (tpp80) REVERT: B 344 PHE cc_start: 0.8130 (OUTLIER) cc_final: 0.7273 (t80) outliers start: 13 outliers final: 11 residues processed: 99 average time/residue: 0.2185 time to fit residues: 29.9010 Evaluate side-chains 94 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 81 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 476 ASN Chi-restraints excluded: chain A residue 495 CYS Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 224 CYS Chi-restraints excluded: chain B residue 344 PHE Chi-restraints excluded: chain B residue 409 ASP Chi-restraints excluded: chain B residue 476 ASN Chi-restraints excluded: chain B residue 495 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 96 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 40 optimal weight: 0.0030 chunk 73 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 84 optimal weight: 0.5980 chunk 88 optimal weight: 0.2980 chunk 93 optimal weight: 0.9990 chunk 61 optimal weight: 0.0970 chunk 98 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 overall best weight: 0.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8544 Z= 0.157 Angle : 0.570 12.465 11664 Z= 0.276 Chirality : 0.040 0.145 1386 Planarity : 0.005 0.064 1406 Dihedral : 7.405 53.759 1342 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 1.61 % Allowed : 14.11 % Favored : 84.29 % 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: 0.61 (0.28), residues: 1046 helix: 1.78 (0.21), residues: 714 sheet: None (None), residues: 0 loop : -2.88 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 558 HIS 0.002 0.000 HIS A 497 PHE 0.013 0.001 PHE B 292 TYR 0.005 0.001 TYR A 40 ARG 0.006 0.000 ARG B 320 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 88 time to evaluate : 1.045 Fit side-chains REVERT: A 344 PHE cc_start: 0.8036 (OUTLIER) cc_final: 0.7179 (t80) REVERT: B 320 ARG cc_start: 0.8109 (tpp80) cc_final: 0.7810 (tpp80) REVERT: B 344 PHE cc_start: 0.8067 (OUTLIER) cc_final: 0.7205 (t80) outliers start: 14 outliers final: 9 residues processed: 99 average time/residue: 0.2098 time to fit residues: 28.6570 Evaluate side-chains 96 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 85 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 476 ASN Chi-restraints excluded: chain A residue 495 CYS Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 344 PHE Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain B residue 409 ASP Chi-restraints excluded: chain B residue 476 ASN Chi-restraints excluded: chain B residue 495 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 46 optimal weight: 0.4980 chunk 68 optimal weight: 0.0070 chunk 103 optimal weight: 0.8980 chunk 95 optimal weight: 0.6980 chunk 82 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 50 optimal weight: 0.5980 chunk 65 optimal weight: 0.6980 chunk 87 optimal weight: 0.0170 chunk 25 optimal weight: 0.9980 overall best weight: 0.3436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8544 Z= 0.158 Angle : 0.569 12.717 11664 Z= 0.275 Chirality : 0.040 0.147 1386 Planarity : 0.005 0.064 1406 Dihedral : 7.296 53.547 1342 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 1.49 % Allowed : 14.33 % Favored : 84.17 % 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: 0.82 (0.29), residues: 1046 helix: 1.93 (0.21), residues: 714 sheet: None (None), residues: 0 loop : -2.76 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 558 HIS 0.002 0.000 HIS A 497 PHE 0.013 0.001 PHE B 292 TYR 0.005 0.001 TYR B 40 ARG 0.006 0.000 ARG B 320 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 88 time to evaluate : 0.885 Fit side-chains REVERT: A 344 PHE cc_start: 0.8031 (OUTLIER) cc_final: 0.7199 (t80) REVERT: A 437 ARG cc_start: 0.7825 (mmm-85) cc_final: 0.7609 (tpp80) REVERT: B 320 ARG cc_start: 0.8117 (tpp80) cc_final: 0.7812 (tpp80) REVERT: B 344 PHE cc_start: 0.8027 (OUTLIER) cc_final: 0.7194 (t80) outliers start: 13 outliers final: 9 residues processed: 100 average time/residue: 0.2199 time to fit residues: 30.1619 Evaluate side-chains 93 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 82 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 476 ASN Chi-restraints excluded: chain A residue 495 CYS Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 344 PHE Chi-restraints excluded: chain B residue 409 ASP Chi-restraints excluded: chain B residue 476 ASN Chi-restraints excluded: chain B residue 495 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 76 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 82 optimal weight: 0.0470 chunk 34 optimal weight: 9.9990 chunk 84 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 72 optimal weight: 0.4980 chunk 4 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.100106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.083647 restraints weight = 12592.888| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 2.11 r_work: 0.2772 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2655 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8544 Z= 0.189 Angle : 0.585 12.683 11664 Z= 0.282 Chirality : 0.041 0.147 1386 Planarity : 0.005 0.063 1406 Dihedral : 7.409 52.516 1342 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 1.72 % Allowed : 13.99 % Favored : 84.29 % 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: 0.77 (0.29), residues: 1046 helix: 1.84 (0.21), residues: 724 sheet: None (None), residues: 0 loop : -2.80 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 558 HIS 0.003 0.000 HIS A 319 PHE 0.013 0.001 PHE B 292 TYR 0.005 0.001 TYR A 40 ARG 0.006 0.001 ARG B 320 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1837.41 seconds wall clock time: 33 minutes 32.50 seconds (2012.50 seconds total)