Starting phenix.real_space_refine on Sat Aug 3 14:25:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w6g_37322/08_2024/8w6g_37322.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w6g_37322/08_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_37322/08_2024/8w6g_37322.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w6g_37322/08_2024/8w6g_37322.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w6g_37322/08_2024/8w6g_37322.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w6g_37322/08_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-5409/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: 5.83, per 1000 atoms: 0.70 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: 3.68 Conformation dependent library (CDL) restraints added in 1.6 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: 0.97 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: 2.16 Time building geometry restraints manager: 3.97 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 3.040 nonbonded pdb=" O ALA B 460 " pdb=" OG SER B 464 " model vdw 2.313 3.040 nonbonded pdb=" O ILE A 524 " pdb=" OG SER A 527 " model vdw 2.321 3.040 nonbonded pdb=" O ILE B 524 " pdb=" OG SER B 527 " model vdw 2.321 3.040 nonbonded pdb=" NH2 ARG A 108 " pdb=" O GLY A 323 " model vdw 2.351 3.120 ... (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 Time spend for trying shortcut: 0.00 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: 2.020 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: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 27.130 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.500 ------------------------------------------------------------------------------- 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 : 0.937 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: 0.2497 time to fit residues: 37.2505 Evaluate side-chains 87 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.860 ------------------------------------------------------------------------------- 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: 0.9990 chunk 78 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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: 0.8576 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8544 Z= 0.259 Angle : 0.715 12.204 11664 Z= 0.362 Chirality : 0.043 0.149 1386 Planarity : 0.008 0.072 1406 Dihedral : 7.902 48.740 1342 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 1.26 % Allowed : 8.26 % Favored : 90.48 % 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: -3.97 (0.22), residues: 1046 helix: -2.10 (0.16), residues: 696 sheet: None (None), residues: 0 loop : -3.54 (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 0.014 0.002 PHE B 376 TYR 0.009 0.001 TYR A 11 ARG 0.003 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 : 0.918 Fit side-chains REVERT: A 295 ARG cc_start: 0.8454 (mtp-110) cc_final: 0.8240 (mtp85) REVERT: A 514 MET cc_start: 0.8870 (mtm) cc_final: 0.8659 (mtp) REVERT: B 514 MET cc_start: 0.8877 (mtm) cc_final: 0.8662 (mtp) outliers start: 11 outliers final: 7 residues processed: 99 average time/residue: 0.2204 time to fit residues: 30.0750 Evaluate side-chains 91 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 84 time to evaluate : 0.877 ------------------------------------------------------------------------------- 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 495 CYS Chi-restraints excluded: chain A residue 558 TRP Chi-restraints excluded: chain B residue 224 CYS 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: 0.9990 chunk 29 optimal weight: 0.8980 chunk 78 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 94 optimal weight: 0.9980 chunk 102 optimal weight: 0.9990 chunk 84 optimal weight: 0.9990 chunk 93 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.8556 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8544 Z= 0.222 Angle : 0.632 12.080 11664 Z= 0.312 Chirality : 0.042 0.150 1386 Planarity : 0.006 0.066 1406 Dihedral : 7.820 50.316 1342 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 0.92 % Allowed : 9.63 % Favored : 89.45 % 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: -0.53 (0.19), residues: 712 sheet: None (None), residues: 0 loop : -3.48 (0.30), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 558 HIS 0.002 0.000 HIS B 153 PHE 0.013 0.001 PHE B 292 TYR 0.006 0.001 TYR A 11 ARG 0.004 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 100 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 92 time to evaluate : 0.939 Fit side-chains REVERT: A 295 ARG cc_start: 0.8473 (mtp-110) cc_final: 0.8271 (mtp85) outliers start: 8 outliers final: 5 residues processed: 93 average time/residue: 0.2189 time to fit residues: 27.8051 Evaluate side-chains 90 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 85 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 495 CYS Chi-restraints excluded: chain B residue 365 GLU 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: 0.9980 chunk 71 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 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: 0.7980 chunk 89 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 83 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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: 0.8560 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8544 Z= 0.249 Angle : 0.630 11.688 11664 Z= 0.310 Chirality : 0.043 0.149 1386 Planarity : 0.006 0.065 1406 Dihedral : 7.849 50.609 1342 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 1.38 % Allowed : 10.55 % Favored : 88.07 % 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: 0.11 (0.20), residues: 712 sheet: None (None), residues: 0 loop : -3.31 (0.31), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 558 HIS 0.002 0.001 HIS A 319 PHE 0.013 0.001 PHE B 292 TYR 0.006 0.001 TYR A 11 ARG 0.005 0.000 ARG B 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 96 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 84 time to evaluate : 0.959 Fit side-chains outliers start: 12 outliers final: 10 residues processed: 92 average time/residue: 0.2235 time to fit residues: 28.1732 Evaluate side-chains 90 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 80 time to evaluate : 0.803 ------------------------------------------------------------------------------- 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 365 GLU Chi-restraints excluded: chain A residue 380 ILE 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 365 GLU 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: 0.2980 chunk 1 optimal weight: 0.8980 chunk 74 optimal weight: 0.0670 chunk 41 optimal weight: 0.7980 chunk 85 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 51 optimal weight: 0.0670 chunk 90 optimal weight: 0.9980 chunk 25 optimal weight: 0.3980 chunk 33 optimal weight: 0.0870 overall best weight: 0.1834 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 GLN B 286 GLN B 297 ASN B 308 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.2523 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= 0.156 Angle : 0.571 10.686 11664 Z= 0.281 Chirality : 0.040 0.148 1386 Planarity : 0.006 0.064 1406 Dihedral : 7.571 54.069 1342 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 1.72 % Allowed : 10.89 % Favored : 87.39 % 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: -0.63 (0.27), residues: 1046 helix: 0.78 (0.21), residues: 694 sheet: None (None), residues: 0 loop : -2.96 (0.32), residues: 352 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 0.012 0.001 PHE B 292 TYR 0.009 0.001 TYR B 11 ARG 0.006 0.001 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 109 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 94 time to evaluate : 0.958 Fit side-chains REVERT: A 344 PHE cc_start: 0.8042 (OUTLIER) cc_final: 0.7202 (t80) REVERT: B 344 PHE cc_start: 0.8017 (OUTLIER) cc_final: 0.7131 (t80) outliers start: 15 outliers final: 4 residues processed: 101 average time/residue: 0.2122 time to fit residues: 29.8265 Evaluate side-chains 93 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 87 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain B residue 344 PHE Chi-restraints excluded: chain B residue 365 GLU Chi-restraints excluded: chain B residue 380 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 90 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 24 optimal weight: 0.0870 chunk 100 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 97 optimal weight: 0.7980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 286 GLN B 297 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8544 Z= 0.202 Angle : 0.611 13.866 11664 Z= 0.294 Chirality : 0.042 0.146 1386 Planarity : 0.005 0.065 1406 Dihedral : 7.537 52.650 1342 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 0.80 % Allowed : 11.58 % Favored : 87.61 % 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: -0.27 (0.27), residues: 1046 helix: 1.08 (0.21), residues: 700 sheet: None (None), residues: 0 loop : -2.96 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 558 HIS 0.002 0.000 HIS A 497 PHE 0.013 0.001 PHE B 292 TYR 0.005 0.001 TYR A 11 ARG 0.007 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 91 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 84 time to evaluate : 0.934 Fit side-chains REVERT: A 344 PHE cc_start: 0.8079 (OUTLIER) cc_final: 0.7234 (t80) REVERT: B 344 PHE cc_start: 0.8094 (OUTLIER) cc_final: 0.7274 (t80) outliers start: 7 outliers final: 5 residues processed: 88 average time/residue: 0.2272 time to fit residues: 27.2343 Evaluate side-chains 90 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 83 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 344 PHE Chi-restraints excluded: chain B residue 365 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 56 optimal weight: 0.4980 chunk 84 optimal weight: 1.9990 chunk 100 optimal weight: 0.0980 chunk 62 optimal weight: 0.5980 chunk 61 optimal weight: 0.5980 chunk 46 optimal weight: 0.2980 chunk 40 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 286 GLN B 297 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8544 Z= 0.175 Angle : 0.590 13.279 11664 Z= 0.285 Chirality : 0.041 0.147 1386 Planarity : 0.005 0.065 1406 Dihedral : 7.489 53.107 1342 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 1.03 % Allowed : 11.93 % Favored : 87.04 % 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: 0.16 (0.28), residues: 1046 helix: 1.44 (0.21), residues: 696 sheet: None (None), residues: 0 loop : -2.79 (0.33), residues: 350 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 0.006 0.001 TYR B 11 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 96 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 87 time to evaluate : 0.915 Fit side-chains REVERT: A 295 ARG cc_start: 0.8432 (mtp-110) cc_final: 0.8227 (mtp85) REVERT: A 344 PHE cc_start: 0.8094 (OUTLIER) cc_final: 0.7278 (t80) REVERT: B 344 PHE cc_start: 0.8090 (OUTLIER) cc_final: 0.7272 (t80) outliers start: 9 outliers final: 6 residues processed: 92 average time/residue: 0.2180 time to fit residues: 27.4076 Evaluate side-chains 91 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 83 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 495 CYS Chi-restraints excluded: chain B residue 344 PHE Chi-restraints excluded: chain B residue 365 GLU Chi-restraints excluded: chain B residue 380 ILE 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: 0.9990 chunk 19 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 87 optimal weight: 0.0870 chunk 93 optimal weight: 0.6980 overall best weight: 0.7360 ------------------------------------------------------------------------------- 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: 0.8526 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8544 Z= 0.222 Angle : 0.616 13.456 11664 Z= 0.297 Chirality : 0.042 0.145 1386 Planarity : 0.005 0.065 1406 Dihedral : 7.610 52.179 1342 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 1.72 % Allowed : 12.04 % Favored : 86.24 % 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: 0.23 (0.28), residues: 1046 helix: 1.49 (0.21), residues: 702 sheet: None (None), residues: 0 loop : -2.85 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 558 HIS 0.002 0.000 HIS B 319 PHE 0.013 0.001 PHE B 292 TYR 0.005 0.001 TYR B 40 ARG 0.002 0.000 ARG A 295 *********************** 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 98 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 83 time to evaluate : 0.933 Fit side-chains REVERT: A 344 PHE cc_start: 0.8200 (OUTLIER) cc_final: 0.7321 (t80) REVERT: A 437 ARG cc_start: 0.7976 (mmm-85) cc_final: 0.7703 (tpp80) REVERT: B 344 PHE cc_start: 0.8196 (OUTLIER) cc_final: 0.7316 (t80) REVERT: B 437 ARG cc_start: 0.7857 (mmm-85) cc_final: 0.7587 (tpp80) outliers start: 15 outliers final: 10 residues processed: 95 average time/residue: 0.2220 time to fit residues: 28.8540 Evaluate side-chains 92 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 80 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 365 GLU Chi-restraints excluded: chain A residue 495 CYS Chi-restraints excluded: chain A residue 558 TRP Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 344 PHE Chi-restraints excluded: chain B residue 365 GLU Chi-restraints excluded: chain B residue 495 CYS Chi-restraints excluded: chain B residue 558 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 96 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 73 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 chunk 84 optimal weight: 0.9980 chunk 88 optimal weight: 0.9990 chunk 93 optimal weight: 0.6980 chunk 61 optimal weight: 0.0870 chunk 98 optimal weight: 0.0040 chunk 60 optimal weight: 0.7980 overall best weight: 0.4170 ------------------------------------------------------------------------------- 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: 0.8496 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8544 Z= 0.171 Angle : 0.588 13.040 11664 Z= 0.284 Chirality : 0.041 0.147 1386 Planarity : 0.005 0.064 1406 Dihedral : 7.551 53.560 1342 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 1.26 % Allowed : 12.61 % Favored : 86.12 % 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: 0.58 (0.28), residues: 1046 helix: 1.78 (0.21), residues: 696 sheet: None (None), residues: 0 loop : -2.68 (0.34), residues: 350 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 0.007 0.001 TYR B 11 ARG 0.002 0.000 ARG A 295 *********************** 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 100 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 89 time to evaluate : 0.946 Fit side-chains REVERT: A 344 PHE cc_start: 0.8044 (OUTLIER) cc_final: 0.7185 (t80) REVERT: A 437 ARG cc_start: 0.8005 (mmm-85) cc_final: 0.7748 (tpp80) REVERT: B 344 PHE cc_start: 0.8042 (OUTLIER) cc_final: 0.7179 (t80) REVERT: B 437 ARG cc_start: 0.7823 (mmm-85) cc_final: 0.7565 (tpp80) outliers start: 11 outliers final: 7 residues processed: 96 average time/residue: 0.2273 time to fit residues: 30.0774 Evaluate side-chains 91 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 82 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 495 CYS Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 344 PHE Chi-restraints excluded: chain B residue 365 GLU 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: 0.5980 chunk 68 optimal weight: 0.3980 chunk 103 optimal weight: 0.7980 chunk 95 optimal weight: 0.6980 chunk 82 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 chunk 87 optimal weight: 0.2980 chunk 25 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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: 0.8504 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8544 Z= 0.190 Angle : 0.600 13.310 11664 Z= 0.290 Chirality : 0.041 0.148 1386 Planarity : 0.005 0.065 1406 Dihedral : 7.542 52.938 1342 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 1.38 % Allowed : 12.39 % Favored : 86.24 % 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: 0.63 (0.28), residues: 1046 helix: 1.81 (0.21), residues: 702 sheet: None (None), residues: 0 loop : -2.71 (0.33), residues: 344 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 0.005 0.000 ARG A 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 99 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 87 time to evaluate : 0.867 Fit side-chains REVERT: A 344 PHE cc_start: 0.8061 (OUTLIER) cc_final: 0.7196 (t80) REVERT: A 437 ARG cc_start: 0.7914 (mmm-85) cc_final: 0.7649 (tpp80) REVERT: B 344 PHE cc_start: 0.8059 (OUTLIER) cc_final: 0.7197 (t80) REVERT: B 437 ARG cc_start: 0.7822 (mmm-85) cc_final: 0.7559 (tpp80) outliers start: 12 outliers final: 7 residues processed: 95 average time/residue: 0.2132 time to fit residues: 27.7171 Evaluate side-chains 93 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 84 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 495 CYS Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 344 PHE Chi-restraints excluded: chain B residue 365 GLU 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: 0.0000 chunk 12 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 82 optimal weight: 0.5980 chunk 34 optimal weight: 7.9990 chunk 84 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 72 optimal weight: 0.0570 chunk 4 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 overall best weight: 0.4102 ------------------------------------------------------------------------------- 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 = 0.3167 r_free = 0.3167 target = 0.100489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.084230 restraints weight = 12765.586| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 2.03 r_work: 0.2819 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2702 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8544 Z= 0.169 Angle : 0.585 12.970 11664 Z= 0.283 Chirality : 0.041 0.153 1386 Planarity : 0.005 0.065 1406 Dihedral : 7.500 53.308 1342 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 1.26 % Allowed : 12.61 % Favored : 86.12 % 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: 0.87 (0.29), residues: 1046 helix: 1.98 (0.21), residues: 696 sheet: None (None), residues: 0 loop : -2.52 (0.35), residues: 350 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 B 11 ARG 0.006 0.000 ARG A 320 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1837.35 seconds wall clock time: 33 minutes 47.09 seconds (2027.09 seconds total)