Starting phenix.real_space_refine on Fri Feb 16 13:32:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pik_13439/02_2024/7pik_13439.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pik_13439/02_2024/7pik_13439.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pik_13439/02_2024/7pik_13439.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pik_13439/02_2024/7pik_13439.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pik_13439/02_2024/7pik_13439.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pik_13439/02_2024/7pik_13439.pdb" } resolution = 2.68 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= 0.001 sd= 0.045 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 125 5.49 5 S 33 5.16 5 C 9497 2.51 5 N 2741 2.21 5 O 3079 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 59": "OD1" <-> "OD2" Residue "A PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 80": "OE1" <-> "OE2" Residue "B GLU 42": "OE1" <-> "OE2" Residue "B ASP 94": "OD1" <-> "OD2" Residue "B ASP 205": "OD1" <-> "OD2" Residue "B TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 361": "OD1" <-> "OD2" Residue "C PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 493": "OE1" <-> "OE2" Residue "C PHE 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 273": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 15475 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1240 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 9, 'TRANS': 141} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 4272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4272 Classifications: {'peptide': 541} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 29, 'TRANS': 511} Chain breaks: 4 Unresolved non-hydrogen bonds: 149 Unresolved non-hydrogen angles: 182 Unresolved non-hydrogen dihedrals: 118 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 10, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 10, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 106 Chain: "C" Number of atoms: 4513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 4513 Classifications: {'peptide': 557} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 28, 'TRANS': 528} Chain breaks: 4 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 54 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 41 Chain: "D" Number of atoms: 2602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2602 Classifications: {'peptide': 335} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 15, 'TRANS': 319} Chain breaks: 2 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 60 Chain: "K" Number of atoms: 1282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 1282 Classifications: {'DNA': 63} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 62} Chain: "L" Number of atoms: 1298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 1298 Classifications: {'DNA': 63} Link IDs: {'rna3p': 62} Chain: "E" Number of atoms: 268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 268 Classifications: {'peptide': 40} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 1, 'TRANS': 38} Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 36 Time building chain proxies: 8.42, per 1000 atoms: 0.54 Number of scatterers: 15475 At special positions: 0 Unit cell: (129.86, 168.56, 169.42, 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 33 16.00 P 125 15.00 O 3079 8.00 N 2741 7.00 C 9497 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: 5.92 Conformation dependent library (CDL) restraints added in 2.5 seconds 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3092 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 14 sheets defined 47.2% alpha, 15.2% beta 50 base pairs and 116 stacking pairs defined. Time for finding SS restraints: 5.67 Creating SS restraints... Processing helix chain 'A' and resid 42 through 51 removed outlier: 3.648A pdb=" N GLU A 51 " --> pdb=" O GLN A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 65 Processing helix chain 'A' and resid 73 through 91 removed outlier: 3.593A pdb=" N ILE A 86 " --> pdb=" O ASP A 82 " (cutoff:3.500A) Proline residue: A 88 - end of helix Processing helix chain 'A' and resid 97 through 113 Processing helix chain 'A' and resid 115 through 129 Processing helix chain 'A' and resid 132 through 137 removed outlier: 3.530A pdb=" N ILE A 137 " --> pdb=" O ASN A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 143 Processing helix chain 'B' and resid 42 through 52 Processing helix chain 'B' and resid 61 through 66 removed outlier: 3.892A pdb=" N ASP B 65 " --> pdb=" O VAL B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 84 Processing helix chain 'B' and resid 86 through 91 Processing helix chain 'B' and resid 97 through 113 Processing helix chain 'B' and resid 115 through 129 removed outlier: 3.576A pdb=" N VAL B 119 " --> pdb=" O THR B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 137 removed outlier: 3.529A pdb=" N ILE B 137 " --> pdb=" O ASN B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 143 Processing helix chain 'B' and resid 173 through 188 Processing helix chain 'B' and resid 195 through 211 removed outlier: 3.562A pdb=" N ALA B 199 " --> pdb=" O LYS B 195 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASP B 205 " --> pdb=" O ARG B 201 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU B 206 " --> pdb=" O ARG B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 219 Processing helix chain 'B' and resid 221 through 232 Processing helix chain 'B' and resid 318 through 330 removed outlier: 4.525A pdb=" N GLN B 324 " --> pdb=" O VAL B 320 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ALA B 325 " --> pdb=" O VAL B 321 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N CYS B 330 " --> pdb=" O PHE B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 340 Processing helix chain 'B' and resid 366 through 376 Processing helix chain 'B' and resid 389 through 396 removed outlier: 3.536A pdb=" N GLY B 393 " --> pdb=" O GLY B 389 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE B 394 " --> pdb=" O ASP B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 452 Processing helix chain 'B' and resid 471 through 483 Processing helix chain 'B' and resid 491 through 499 removed outlier: 3.519A pdb=" N LEU B 499 " --> pdb=" O LEU B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 528 removed outlier: 4.097A pdb=" N ARG B 526 " --> pdb=" O SER B 522 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N GLU B 527 " --> pdb=" O GLU B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 578 removed outlier: 3.760A pdb=" N PHE B 577 " --> pdb=" O SER B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 596 Processing helix chain 'C' and resid 41 through 52 removed outlier: 3.665A pdb=" N LEU C 45 " --> pdb=" O ALA C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 67 removed outlier: 3.642A pdb=" N LEU C 64 " --> pdb=" O TYR C 61 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU C 67 " --> pdb=" O LEU C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 92 Proline residue: C 88 - end of helix removed outlier: 3.793A pdb=" N SER C 92 " --> pdb=" O PRO C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 113 removed outlier: 3.603A pdb=" N GLU C 111 " --> pdb=" O HIS C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 130 removed outlier: 3.562A pdb=" N VAL C 119 " --> pdb=" O THR C 115 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLY C 130 " --> pdb=" O TYR C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 137 removed outlier: 4.041A pdb=" N ILE C 137 " --> pdb=" O ASN C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 143 Processing helix chain 'C' and resid 173 through 188 Processing helix chain 'C' and resid 195 through 211 removed outlier: 3.625A pdb=" N ALA C 199 " --> pdb=" O LYS C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 219 removed outlier: 3.621A pdb=" N ASP C 218 " --> pdb=" O PRO C 215 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TYR C 219 " --> pdb=" O GLN C 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 215 through 219' Processing helix chain 'C' and resid 221 through 233 Processing helix chain 'C' and resid 321 through 330 removed outlier: 4.078A pdb=" N ALA C 325 " --> pdb=" O VAL C 321 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N CYS C 330 " --> pdb=" O PHE C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 340 Processing helix chain 'C' and resid 361 through 365 removed outlier: 3.555A pdb=" N GLU C 364 " --> pdb=" O ASP C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 375 Processing helix chain 'C' and resid 389 through 396 Processing helix chain 'C' and resid 434 through 452 Processing helix chain 'C' and resid 471 through 483 Processing helix chain 'C' and resid 491 through 499 removed outlier: 3.648A pdb=" N LEU C 495 " --> pdb=" O GLU C 491 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU C 499 " --> pdb=" O LEU C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 527 removed outlier: 3.847A pdb=" N LEU C 525 " --> pdb=" O GLY C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 528 through 533 removed outlier: 3.964A pdb=" N ARG C 532 " --> pdb=" O GLY C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 578 removed outlier: 3.565A pdb=" N ARG C 575 " --> pdb=" O GLU C 572 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N GLN C 576 " --> pdb=" O ARG C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 624 removed outlier: 5.501A pdb=" N LYS C 600 " --> pdb=" O LYS C 596 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N GLN C 601 " --> pdb=" O ALA C 597 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU C 604 " --> pdb=" O LYS C 600 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR C 605 " --> pdb=" O GLN C 601 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU C 624 " --> pdb=" O LYS C 620 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 330 removed outlier: 4.784A pdb=" N GLN D 324 " --> pdb=" O VAL D 320 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ALA D 325 " --> pdb=" O VAL D 321 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE D 326 " --> pdb=" O ALA D 322 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N CYS D 330 " --> pdb=" O PHE D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 340 Processing helix chain 'D' and resid 361 through 365 removed outlier: 3.659A pdb=" N LEU D 365 " --> pdb=" O ARG D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 376 Processing helix chain 'D' and resid 389 through 396 Processing helix chain 'D' and resid 435 through 452 Processing helix chain 'D' and resid 471 through 483 Processing helix chain 'D' and resid 491 through 499 removed outlier: 3.545A pdb=" N LEU D 495 " --> pdb=" O GLU D 491 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 578 removed outlier: 5.731A pdb=" N GLN D 576 " --> pdb=" O ARG D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 595 Processing helix chain 'D' and resid 598 through 625 Processing helix chain 'E' and resid 588 through 599 removed outlier: 4.267A pdb=" N ALA E 599 " --> pdb=" O ASN E 595 " (cutoff:3.500A) Processing helix chain 'E' and resid 600 through 625 Processing sheet with id=AA1, first strand: chain 'A' and resid 38 through 41 removed outlier: 6.834A pdb=" N GLN A 24 " --> pdb=" O ILE A 20 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ILE A 20 " --> pdb=" O GLN A 24 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL A 26 " --> pdb=" O LEU A 18 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 38 through 41 removed outlier: 3.659A pdb=" N ALA B 19 " --> pdb=" O VAL B 26 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N MET B 28 " --> pdb=" O ILE B 17 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N ILE B 17 " --> pdb=" O MET B 28 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 307 through 313 removed outlier: 6.673A pdb=" N VAL B 299 " --> pdb=" O THR B 308 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N PHE B 310 " --> pdb=" O TYR B 297 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N TYR B 297 " --> pdb=" O PHE B 310 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ILE B 312 " --> pdb=" O THR B 295 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N THR B 295 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N TYR B 270 " --> pdb=" O LEU B 359 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU B 382 " --> pdb=" O LEU B 358 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 307 through 313 removed outlier: 6.673A pdb=" N VAL B 299 " --> pdb=" O THR B 308 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N PHE B 310 " --> pdb=" O TYR B 297 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N TYR B 297 " --> pdb=" O PHE B 310 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ILE B 312 " --> pdb=" O THR B 295 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N THR B 295 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ILE B 276 " --> pdb=" O LEU B 402 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 281 through 282 removed outlier: 3.657A pdb=" N GLY B 292 " --> pdb=" O LEU B 281 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 502 through 504 removed outlier: 4.434A pdb=" N GLU B 543 " --> pdb=" O PHE B 557 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 38 through 40 removed outlier: 7.166A pdb=" N GLN C 24 " --> pdb=" O ILE C 20 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N ILE C 20 " --> pdb=" O GLN C 24 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N VAL C 26 " --> pdb=" O LEU C 18 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 307 through 313 removed outlier: 6.328A pdb=" N ILE C 307 " --> pdb=" O ASP C 301 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ASP C 301 " --> pdb=" O ILE C 307 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLY C 309 " --> pdb=" O VAL C 299 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE C 276 " --> pdb=" O LEU C 402 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU C 402 " --> pdb=" O ILE C 276 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 357 through 359 Processing sheet with id=AB1, first strand: chain 'C' and resid 502 through 508 removed outlier: 4.395A pdb=" N GLU C 543 " --> pdb=" O PHE C 557 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N LEU C 542 " --> pdb=" O VAL C 505 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 306 through 313 removed outlier: 3.593A pdb=" N MET D 306 " --> pdb=" O ASP D 301 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL D 299 " --> pdb=" O THR D 308 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N PHE D 310 " --> pdb=" O TYR D 297 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N TYR D 297 " --> pdb=" O PHE D 310 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ILE D 312 " --> pdb=" O THR D 295 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N THR D 295 " --> pdb=" O ILE D 312 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N TYR D 270 " --> pdb=" O LEU D 359 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 306 through 313 removed outlier: 3.593A pdb=" N MET D 306 " --> pdb=" O ASP D 301 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL D 299 " --> pdb=" O THR D 308 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N PHE D 310 " --> pdb=" O TYR D 297 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N TYR D 297 " --> pdb=" O PHE D 310 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ILE D 312 " --> pdb=" O THR D 295 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N THR D 295 " --> pdb=" O ILE D 312 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ILE D 276 " --> pdb=" O LEU D 402 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU D 402 " --> pdb=" O ILE D 276 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 281 through 282 Processing sheet with id=AB5, first strand: chain 'D' and resid 502 through 504 removed outlier: 4.432A pdb=" N GLU D 543 " --> pdb=" O PHE D 557 " (cutoff:3.500A) 604 hydrogen bonds defined for protein. 1677 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 110 hydrogen bonds 216 hydrogen bond angles 0 basepair planarities 50 basepair parallelities 116 stacking parallelities Total time for adding SS restraints: 6.38 Time building geometry restraints manager: 6.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2455 1.32 - 1.44: 4927 1.44 - 1.57: 8403 1.57 - 1.69: 249 1.69 - 1.81: 54 Bond restraints: 16088 Sorted by residual: bond pdb=" C SER D 346 " pdb=" O SER D 346 " ideal model delta sigma weight residual 1.237 1.201 0.036 1.17e-02 7.31e+03 9.55e+00 bond pdb=" C VAL A 26 " pdb=" O VAL A 26 " ideal model delta sigma weight residual 1.238 1.202 0.036 1.17e-02 7.31e+03 9.46e+00 bond pdb=" N VAL C 26 " pdb=" CA VAL C 26 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.27e-02 6.20e+03 7.61e+00 bond pdb=" C VAL C 26 " pdb=" O VAL C 26 " ideal model delta sigma weight residual 1.238 1.206 0.032 1.17e-02 7.31e+03 7.39e+00 bond pdb=" C VAL B 26 " pdb=" O VAL B 26 " ideal model delta sigma weight residual 1.238 1.208 0.029 1.17e-02 7.31e+03 6.34e+00 ... (remaining 16083 not shown) Histogram of bond angle deviations from ideal: 98.37 - 106.13: 1082 106.13 - 113.89: 8944 113.89 - 121.66: 8513 121.66 - 129.42: 3685 129.42 - 137.19: 163 Bond angle restraints: 22387 Sorted by residual: angle pdb=" CA TRP A 27 " pdb=" CB TRP A 27 " pdb=" CG TRP A 27 " ideal model delta sigma weight residual 113.60 120.92 -7.32 1.90e+00 2.77e-01 1.48e+01 angle pdb=" CA GLY C 353 " pdb=" C GLY C 353 " pdb=" O GLY C 353 " ideal model delta sigma weight residual 122.33 119.24 3.09 8.10e-01 1.52e+00 1.46e+01 angle pdb=" CA GLY C 353 " pdb=" C GLY C 353 " pdb=" N LEU C 354 " ideal model delta sigma weight residual 114.23 117.33 -3.10 8.80e-01 1.29e+00 1.24e+01 angle pdb=" N GLY C 353 " pdb=" CA GLY C 353 " pdb=" C GLY C 353 " ideal model delta sigma weight residual 111.85 115.58 -3.73 1.06e+00 8.90e-01 1.24e+01 angle pdb=" N TRP A 27 " pdb=" CA TRP A 27 " pdb=" C TRP A 27 " ideal model delta sigma weight residual 109.23 114.49 -5.26 1.55e+00 4.16e-01 1.15e+01 ... (remaining 22382 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 7768 17.82 - 35.64: 951 35.64 - 53.46: 515 53.46 - 71.28: 89 71.28 - 89.10: 15 Dihedral angle restraints: 9338 sinusoidal: 4574 harmonic: 4764 Sorted by residual: dihedral pdb=" CA LYS D 407 " pdb=" C LYS D 407 " pdb=" N SER D 408 " pdb=" CA SER D 408 " ideal model delta harmonic sigma weight residual -180.00 -157.32 -22.68 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA GLU B 232 " pdb=" C GLU B 232 " pdb=" N TYR B 233 " pdb=" CA TYR B 233 " ideal model delta harmonic sigma weight residual 180.00 160.22 19.78 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA GLU D 491 " pdb=" C GLU D 491 " pdb=" N GLN D 492 " pdb=" CA GLN D 492 " ideal model delta harmonic sigma weight residual -180.00 -160.81 -19.19 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 9335 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 2035 0.051 - 0.102: 339 0.102 - 0.154: 103 0.154 - 0.205: 8 0.205 - 0.256: 3 Chirality restraints: 2488 Sorted by residual: chirality pdb=" CA TRP C 27 " pdb=" N TRP C 27 " pdb=" C TRP C 27 " pdb=" CB TRP C 27 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CA TRP B 27 " pdb=" N TRP B 27 " pdb=" C TRP B 27 " pdb=" CB TRP B 27 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA ASP D 348 " pdb=" N ASP D 348 " pdb=" C ASP D 348 " pdb=" CB ASP D 348 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 2485 not shown) Planarity restraints: 2445 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 347 " 0.012 2.00e-02 2.50e+03 2.54e-02 6.48e+00 pdb=" C SER B 347 " -0.044 2.00e-02 2.50e+03 pdb=" O SER B 347 " 0.017 2.00e-02 2.50e+03 pdb=" N ASP B 348 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 527 " -0.013 2.00e-02 2.50e+03 2.53e-02 6.39e+00 pdb=" C GLU C 527 " 0.044 2.00e-02 2.50e+03 pdb=" O GLU C 527 " -0.016 2.00e-02 2.50e+03 pdb=" N GLY C 528 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR C 173 " 0.039 5.00e-02 4.00e+02 5.88e-02 5.54e+00 pdb=" N PRO C 174 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO C 174 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 174 " 0.033 5.00e-02 4.00e+02 ... (remaining 2442 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 3724 2.81 - 3.33: 12753 3.33 - 3.85: 24689 3.85 - 4.38: 30405 4.38 - 4.90: 48936 Nonbonded interactions: 120507 Sorted by model distance: nonbonded pdb=" N2 DG K 60 " pdb=" O2 DC L 11 " model vdw 2.284 2.520 nonbonded pdb=" NH1 ARG B 460 " pdb=" O LEU B 468 " model vdw 2.288 2.520 nonbonded pdb=" O PHE B 303 " pdb=" OH TYR B 458 " model vdw 2.294 2.440 nonbonded pdb=" OD1 ASN C 5 " pdb=" NE2 GLN C 131 " model vdw 2.322 2.520 nonbonded pdb=" NE2 GLN C 47 " pdb=" OE2 GLU C 51 " model vdw 2.322 2.520 ... (remaining 120502 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 'B' and (resid 1 through 93 or (resid 94 and (name N or name CA or name C \ or name O or name CB )) or resid 95 through 150 or resid 169 through 177 or (re \ sid 178 and (name N or name CA or name C or name O or name CB )) or resid 179 th \ rough 184 or (resid 185 and (name N or name CA or name C or name O or name CB )) \ or resid 186 through 234 or (resid 235 through 236 and (name N or name CA or na \ me C or name O or name CB )) or resid 264 through 315 or (resid 316 and (name N \ or name CA or name C or name O or name CB )) or resid 317 through 529 or resid 5 \ 40 through 597)) selection = (chain 'C' and (resid 1 through 49 or (resid 50 and (name N or name CA or name C \ or name O or name CB )) or resid 51 through 102 or (resid 103 and (name N or na \ me CA or name C or name O or name CB )) or resid 104 through 172 or (resid 173 a \ nd (name N or name CA or name C or name O or name CB )) or resid 174 through 185 \ or (resid 186 and (name N or name CA or name C or name O or name CB or name CG \ or name CD )) or resid 187 through 189 or (resid 190 and (name N or name CA or n \ ame C or name O or name CB )) or resid 191 through 216 or (resid 217 through 218 \ and (name N or name CA or name C or name O or name CB )) or resid 219 through 2 \ 81 or (resid 282 through 283 and (name N or name CA or name C or name O or name \ CB )) or resid 284 through 285 or (resid 286 through 290 and (name N or name CA \ or name C or name O or name CB )) or resid 291 through 314 or (resid 315 through \ 316 and (name N or name CA or name C or name O or name CB )) or resid 317 throu \ gh 340 or (resid 341 and (name N or name CA or name C or name O or name CB )) or \ resid 342 through 387 or (resid 388 and (name N or name CA or name C or name O \ or name CB )) or resid 389 through 399 or (resid 400 and (name N or name CA or n \ ame C or name O or name CB )) or resid 401 or (resid 402 and (name N or name CA \ or name C or name O or name CB )) or resid 403 through 412 or resid 431 through \ 458 or (resid 459 and (name N or name CA or name C or name O or name CB )) or re \ sid 460 or (resid 461 through 463 and (name N or name CA or name C or name O or \ name CB )) or resid 464 through 492 or (resid 493 and (name N or name CA or name \ C or name O or name CB )) or resid 494 through 526 or (resid 527 and (name N or \ name CA or name C or name O or name CB )) or resid 528 through 529 or (resid 53 \ 1 and (name N or name CA or name C or name O or name CB )) or resid 541 through \ 571 or (resid 572 and (name N or name CA or name C or name O or name CB )) or re \ sid 573 through 586 or (resid 587 and (name N or name CA or name C or name O or \ name CB )) or resid 588 through 592 or (resid 593 through 594 and (name N or nam \ e CA or name C or name O or name CB )) or resid 595 or (resid 596 through 597 an \ d (name N or name CA or name C or name O or name CB )))) } 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: 9.120 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: 26.990 Check model and map are aligned: 0.220 Set scattering table: 0.140 Process input model: 46.640 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.060 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:11.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 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 : 0.003 0.042 16088 Z= 0.214 Angle : 0.613 12.186 22387 Z= 0.355 Chirality : 0.043 0.256 2488 Planarity : 0.005 0.059 2445 Dihedral : 19.276 89.096 6246 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.08 % Allowed : 1.28 % Favored : 98.65 % 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: 0.06 (0.21), residues: 1594 helix: 1.30 (0.21), residues: 629 sheet: 0.30 (0.41), residues: 144 loop : -1.03 (0.21), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 586 HIS 0.004 0.001 HIS B 368 PHE 0.024 0.001 PHE B 228 TYR 0.020 0.001 TYR C 48 ARG 0.004 0.000 ARG A 84 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 198 time to evaluate : 1.555 Fit side-chains revert: symmetry clash REVERT: A 93 LYS cc_start: 0.8132 (pttp) cc_final: 0.7719 (tmtt) REVERT: D 323 MET cc_start: 0.8598 (mmp) cc_final: 0.8363 (mmp) outliers start: 1 outliers final: 2 residues processed: 199 average time/residue: 1.6529 time to fit residues: 355.9139 Evaluate side-chains 148 residues out of total 1440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 146 time to evaluate : 1.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain D residue 615 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 146 optimal weight: 0.9990 chunk 131 optimal weight: 4.9990 chunk 72 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 88 optimal weight: 0.0770 chunk 70 optimal weight: 0.9990 chunk 135 optimal weight: 0.0970 chunk 52 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 157 optimal weight: 2.9990 overall best weight: 0.5940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 ASN C 128 GLN ** D 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.0935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16088 Z= 0.201 Angle : 0.571 9.791 22387 Z= 0.324 Chirality : 0.042 0.174 2488 Planarity : 0.005 0.064 2445 Dihedral : 21.233 73.691 3236 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.65 % Allowed : 9.17 % Favored : 89.18 % 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: 0.39 (0.21), residues: 1594 helix: 1.59 (0.21), residues: 639 sheet: 0.55 (0.41), residues: 140 loop : -0.90 (0.21), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 586 HIS 0.005 0.001 HIS D 340 PHE 0.024 0.001 PHE B 228 TYR 0.039 0.001 TYR C 48 ARG 0.006 0.000 ARG C 607 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 149 time to evaluate : 1.448 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 LYS cc_start: 0.8093 (pttp) cc_final: 0.7685 (tmtt) REVERT: B 13 ASP cc_start: 0.7841 (OUTLIER) cc_final: 0.7516 (m-30) REVERT: B 366 MET cc_start: 0.6974 (mmm) cc_final: 0.6576 (mmm) REVERT: C 529 TRP cc_start: 0.7511 (OUTLIER) cc_final: 0.6561 (m100) REVERT: D 289 LYS cc_start: 0.6802 (OUTLIER) cc_final: 0.6589 (mtmt) REVERT: D 323 MET cc_start: 0.8637 (mmp) cc_final: 0.8239 (mmp) outliers start: 22 outliers final: 7 residues processed: 161 average time/residue: 1.5583 time to fit residues: 272.7807 Evaluate side-chains 145 residues out of total 1440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 135 time to evaluate : 1.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain B residue 13 ASP Chi-restraints excluded: chain B residue 480 MET Chi-restraints excluded: chain C residue 293 ARG Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 529 TRP Chi-restraints excluded: chain C residue 543 GLU Chi-restraints excluded: chain D residue 289 LYS Chi-restraints excluded: chain D residue 559 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 87 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 chunk 170 optimal weight: 6.9990 chunk 140 optimal weight: 3.9990 chunk 156 optimal weight: 3.9990 chunk 53 optimal weight: 0.5980 chunk 126 optimal weight: 2.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 482 HIS B 513 ASN C 77 GLN C 368 HIS ** D 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 615 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.059 16088 Z= 0.479 Angle : 0.781 8.123 22387 Z= 0.436 Chirality : 0.052 0.197 2488 Planarity : 0.007 0.067 2445 Dihedral : 21.860 86.186 3233 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.85 % Allowed : 11.95 % Favored : 85.20 % 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: -0.24 (0.20), residues: 1594 helix: 1.02 (0.20), residues: 639 sheet: -0.00 (0.41), residues: 131 loop : -1.17 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 529 HIS 0.006 0.001 HIS B 368 PHE 0.022 0.003 PHE B 228 TYR 0.039 0.003 TYR C 48 ARG 0.007 0.001 ARG A 101 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 144 time to evaluate : 1.717 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.7846 (OUTLIER) cc_final: 0.7319 (mp10) REVERT: A 84 ARG cc_start: 0.7814 (OUTLIER) cc_final: 0.7459 (mtp180) REVERT: A 93 LYS cc_start: 0.8145 (pttp) cc_final: 0.7672 (tmtt) REVERT: B 13 ASP cc_start: 0.7898 (OUTLIER) cc_final: 0.7578 (m-30) REVERT: B 366 MET cc_start: 0.7319 (mmm) cc_final: 0.6892 (mmm) REVERT: C 65 ASP cc_start: 0.7204 (m-30) cc_final: 0.6959 (m-30) REVERT: C 269 ARG cc_start: 0.8066 (OUTLIER) cc_final: 0.6659 (ptm-80) REVERT: C 526 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.7913 (ptp-170) REVERT: C 529 TRP cc_start: 0.7918 (OUTLIER) cc_final: 0.7122 (m100) REVERT: D 289 LYS cc_start: 0.6930 (OUTLIER) cc_final: 0.6623 (mtmt) REVERT: D 323 MET cc_start: 0.8658 (mmp) cc_final: 0.8384 (mmp) outliers start: 38 outliers final: 15 residues processed: 166 average time/residue: 1.6045 time to fit residues: 289.1384 Evaluate side-chains 164 residues out of total 1440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 142 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 40 ARG Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain B residue 13 ASP Chi-restraints excluded: chain B residue 77 GLN Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 504 LYS Chi-restraints excluded: chain C residue 269 ARG Chi-restraints excluded: chain C residue 306 MET Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain C residue 526 ARG Chi-restraints excluded: chain C residue 529 TRP Chi-restraints excluded: chain C residue 543 GLU Chi-restraints excluded: chain C residue 592 GLU Chi-restraints excluded: chain D residue 289 LYS Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 466 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 155 optimal weight: 7.9990 chunk 118 optimal weight: 0.5980 chunk 81 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 105 optimal weight: 4.9990 chunk 157 optimal weight: 2.9990 chunk 167 optimal weight: 0.9990 chunk 82 optimal weight: 0.2980 chunk 149 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 ASN C 77 GLN ** D 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16088 Z= 0.204 Angle : 0.566 10.292 22387 Z= 0.322 Chirality : 0.042 0.159 2488 Planarity : 0.005 0.068 2445 Dihedral : 21.331 71.581 3232 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.40 % Allowed : 13.45 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.21), residues: 1594 helix: 1.53 (0.21), residues: 640 sheet: 0.43 (0.43), residues: 134 loop : -0.98 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 586 HIS 0.004 0.001 HIS B 368 PHE 0.021 0.001 PHE B 228 TYR 0.034 0.001 TYR C 48 ARG 0.004 0.000 ARG D 575 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 143 time to evaluate : 1.675 Fit side-chains revert: symmetry clash REVERT: A 38 GLN cc_start: 0.7788 (OUTLIER) cc_final: 0.7323 (mp10) REVERT: A 40 ARG cc_start: 0.7934 (OUTLIER) cc_final: 0.7545 (ptp-170) REVERT: A 93 LYS cc_start: 0.8107 (pttp) cc_final: 0.7673 (tmtt) REVERT: B 13 ASP cc_start: 0.7872 (OUTLIER) cc_final: 0.7533 (m-30) REVERT: B 366 MET cc_start: 0.6987 (mmm) cc_final: 0.6562 (mmm) REVERT: B 451 ASN cc_start: 0.7442 (m110) cc_final: 0.7195 (m-40) REVERT: C 106 GLU cc_start: 0.6922 (OUTLIER) cc_final: 0.6642 (mp0) REVERT: C 269 ARG cc_start: 0.7975 (OUTLIER) cc_final: 0.6621 (ptm-80) REVERT: C 529 TRP cc_start: 0.7637 (OUTLIER) cc_final: 0.6715 (m100) REVERT: C 607 ARG cc_start: 0.7628 (ttm110) cc_final: 0.7316 (ttm110) REVERT: C 611 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.6676 (mp0) REVERT: D 289 LYS cc_start: 0.6825 (OUTLIER) cc_final: 0.6530 (mtmt) outliers start: 32 outliers final: 6 residues processed: 160 average time/residue: 1.5622 time to fit residues: 272.3422 Evaluate side-chains 149 residues out of total 1440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 135 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 40 ARG Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain B residue 13 ASP Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 269 ARG Chi-restraints excluded: chain C residue 306 MET Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain C residue 529 TRP Chi-restraints excluded: chain C residue 611 GLU Chi-restraints excluded: chain D residue 289 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 139 optimal weight: 8.9990 chunk 94 optimal weight: 2.9990 chunk 2 optimal weight: 0.3980 chunk 124 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 142 optimal weight: 9.9990 chunk 115 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 150 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 482 HIS C 12 ASN ** D 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 16088 Z= 0.301 Angle : 0.647 9.953 22387 Z= 0.364 Chirality : 0.045 0.192 2488 Planarity : 0.006 0.068 2445 Dihedral : 21.481 71.014 3232 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.48 % Allowed : 14.65 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.21), residues: 1594 helix: 1.44 (0.21), residues: 639 sheet: 0.10 (0.42), residues: 131 loop : -1.04 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 586 HIS 0.006 0.001 HIS B 368 PHE 0.023 0.002 PHE B 228 TYR 0.036 0.002 TYR C 48 ARG 0.006 0.000 ARG D 575 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 142 time to evaluate : 1.623 Fit side-chains revert: symmetry clash REVERT: A 38 GLN cc_start: 0.7822 (OUTLIER) cc_final: 0.7320 (mp10) REVERT: A 40 ARG cc_start: 0.7942 (OUTLIER) cc_final: 0.7462 (ptp-170) REVERT: A 84 ARG cc_start: 0.7810 (OUTLIER) cc_final: 0.7460 (mtp180) REVERT: A 93 LYS cc_start: 0.8122 (pttp) cc_final: 0.7694 (tmtt) REVERT: B 13 ASP cc_start: 0.7890 (OUTLIER) cc_final: 0.7561 (m-30) REVERT: B 38 GLN cc_start: 0.7802 (OUTLIER) cc_final: 0.6914 (mp-120) REVERT: B 366 MET cc_start: 0.7131 (mmm) cc_final: 0.6658 (mmm) REVERT: C 218 ASP cc_start: 0.7241 (m-30) cc_final: 0.6981 (m-30) REVERT: C 269 ARG cc_start: 0.8036 (OUTLIER) cc_final: 0.6665 (ptm-80) REVERT: C 529 TRP cc_start: 0.7713 (OUTLIER) cc_final: 0.6787 (m100) REVERT: C 611 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.6803 (mp0) REVERT: D 289 LYS cc_start: 0.6844 (OUTLIER) cc_final: 0.6550 (mtmt) outliers start: 33 outliers final: 9 residues processed: 164 average time/residue: 1.5524 time to fit residues: 276.7638 Evaluate side-chains 151 residues out of total 1440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 133 time to evaluate : 1.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 40 ARG Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain B residue 13 ASP Chi-restraints excluded: chain B residue 38 GLN Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain C residue 269 ARG Chi-restraints excluded: chain C residue 306 MET Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain C residue 529 TRP Chi-restraints excluded: chain C residue 543 GLU Chi-restraints excluded: chain C residue 584 GLU Chi-restraints excluded: chain C residue 611 GLU Chi-restraints excluded: chain D residue 289 LYS Chi-restraints excluded: chain D residue 344 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 56 optimal weight: 5.9990 chunk 150 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 98 optimal weight: 0.0980 chunk 41 optimal weight: 0.0040 chunk 167 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 13 optimal weight: 0.0670 chunk 55 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 overall best weight: 0.4332 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16088 Z= 0.176 Angle : 0.543 10.908 22387 Z= 0.308 Chirality : 0.040 0.157 2488 Planarity : 0.005 0.067 2445 Dihedral : 21.139 69.559 3232 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.40 % Allowed : 15.40 % Favored : 82.19 % 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: 0.53 (0.21), residues: 1594 helix: 1.77 (0.21), residues: 640 sheet: 0.52 (0.43), residues: 129 loop : -0.85 (0.21), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 586 HIS 0.003 0.001 HIS B 368 PHE 0.025 0.001 PHE B 228 TYR 0.032 0.001 TYR C 48 ARG 0.009 0.000 ARG C 607 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 140 time to evaluate : 1.704 Fit side-chains revert: symmetry clash REVERT: A 40 ARG cc_start: 0.7846 (OUTLIER) cc_final: 0.7358 (ptp-170) REVERT: A 93 LYS cc_start: 0.8098 (pttp) cc_final: 0.7659 (tmtt) REVERT: B 13 ASP cc_start: 0.7928 (OUTLIER) cc_final: 0.7599 (m-30) REVERT: B 366 MET cc_start: 0.6889 (mmm) cc_final: 0.6561 (mmm) REVERT: B 451 ASN cc_start: 0.7441 (m110) cc_final: 0.7210 (m-40) REVERT: C 529 TRP cc_start: 0.7588 (OUTLIER) cc_final: 0.6667 (m100) REVERT: C 611 GLU cc_start: 0.7463 (OUTLIER) cc_final: 0.6673 (mp0) REVERT: D 289 LYS cc_start: 0.6808 (OUTLIER) cc_final: 0.6546 (mtmt) outliers start: 32 outliers final: 8 residues processed: 158 average time/residue: 1.4576 time to fit residues: 252.7289 Evaluate side-chains 151 residues out of total 1440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 138 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ARG Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain B residue 13 ASP Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain C residue 529 TRP Chi-restraints excluded: chain C residue 584 GLU Chi-restraints excluded: chain C residue 592 GLU Chi-restraints excluded: chain C residue 611 GLU Chi-restraints excluded: chain D residue 289 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 161 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 95 optimal weight: 0.5980 chunk 122 optimal weight: 5.9990 chunk 94 optimal weight: 0.5980 chunk 140 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 166 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 101 optimal weight: 0.5980 chunk 76 optimal weight: 0.8980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 482 HIS C 12 ASN C 187 HIS C 209 GLN ** D 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16088 Z= 0.220 Angle : 0.583 10.951 22387 Z= 0.328 Chirality : 0.042 0.176 2488 Planarity : 0.005 0.067 2445 Dihedral : 21.219 69.457 3232 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.48 % Allowed : 15.70 % Favored : 81.82 % 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: 0.50 (0.21), residues: 1594 helix: 1.76 (0.21), residues: 639 sheet: 0.47 (0.42), residues: 134 loop : -0.88 (0.21), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 586 HIS 0.005 0.001 HIS B 368 PHE 0.024 0.001 PHE B 228 TYR 0.032 0.001 TYR C 48 ARG 0.007 0.000 ARG C 607 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 143 time to evaluate : 1.590 Fit side-chains revert: symmetry clash REVERT: A 40 ARG cc_start: 0.7895 (OUTLIER) cc_final: 0.7299 (ptp-170) REVERT: A 93 LYS cc_start: 0.8099 (pttp) cc_final: 0.7671 (tmtt) REVERT: B 13 ASP cc_start: 0.7917 (OUTLIER) cc_final: 0.7619 (m-30) REVERT: B 366 MET cc_start: 0.6990 (mmm) cc_final: 0.6450 (mmm) REVERT: B 451 ASN cc_start: 0.7467 (m110) cc_final: 0.7256 (m-40) REVERT: C 40 ARG cc_start: 0.7265 (OUTLIER) cc_final: 0.6739 (ptp-170) REVERT: C 529 TRP cc_start: 0.7602 (OUTLIER) cc_final: 0.6688 (m100) REVERT: C 611 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.6750 (mp0) REVERT: D 289 LYS cc_start: 0.6814 (OUTLIER) cc_final: 0.6527 (mtmt) outliers start: 33 outliers final: 14 residues processed: 162 average time/residue: 1.5334 time to fit residues: 273.3181 Evaluate side-chains 156 residues out of total 1440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 136 time to evaluate : 1.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ARG Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain B residue 13 ASP Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 504 LYS Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 40 ARG Chi-restraints excluded: chain C residue 382 GLU Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 529 TRP Chi-restraints excluded: chain C residue 584 GLU Chi-restraints excluded: chain C residue 592 GLU Chi-restraints excluded: chain C residue 611 GLU Chi-restraints excluded: chain D residue 289 LYS Chi-restraints excluded: chain D residue 466 THR Chi-restraints excluded: chain D residue 473 VAL Chi-restraints excluded: chain D residue 480 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 103 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 113 optimal weight: 0.0270 chunk 82 optimal weight: 0.0570 chunk 15 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 chunk 151 optimal weight: 1.9990 overall best weight: 0.9960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 482 HIS C 12 ASN C 77 GLN ** D 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16088 Z= 0.264 Angle : 0.629 11.541 22387 Z= 0.352 Chirality : 0.044 0.180 2488 Planarity : 0.005 0.067 2445 Dihedral : 21.316 69.316 3232 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.25 % Allowed : 16.75 % Favored : 80.99 % 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: 0.38 (0.21), residues: 1594 helix: 1.67 (0.21), residues: 639 sheet: 0.36 (0.42), residues: 134 loop : -0.94 (0.21), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 586 HIS 0.006 0.001 HIS B 368 PHE 0.021 0.002 PHE B 228 TYR 0.031 0.002 TYR C 48 ARG 0.007 0.000 ARG D 575 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 138 time to evaluate : 2.211 Fit side-chains revert: symmetry clash REVERT: A 38 GLN cc_start: 0.7827 (OUTLIER) cc_final: 0.7395 (mp10) REVERT: A 40 ARG cc_start: 0.7924 (OUTLIER) cc_final: 0.7379 (ptp-170) REVERT: A 93 LYS cc_start: 0.8109 (pttp) cc_final: 0.7685 (tmtt) REVERT: B 13 ASP cc_start: 0.7878 (OUTLIER) cc_final: 0.7580 (m-30) REVERT: B 366 MET cc_start: 0.7083 (mmm) cc_final: 0.6489 (mmm) REVERT: C 40 ARG cc_start: 0.7207 (OUTLIER) cc_final: 0.6527 (ptp-110) REVERT: C 529 TRP cc_start: 0.7715 (OUTLIER) cc_final: 0.6748 (m100) REVERT: C 611 GLU cc_start: 0.7491 (OUTLIER) cc_final: 0.6828 (mp0) REVERT: D 289 LYS cc_start: 0.6822 (OUTLIER) cc_final: 0.6534 (mtmt) outliers start: 30 outliers final: 14 residues processed: 158 average time/residue: 1.5366 time to fit residues: 265.8164 Evaluate side-chains 153 residues out of total 1440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 132 time to evaluate : 1.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 40 ARG Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain B residue 13 ASP Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 504 LYS Chi-restraints excluded: chain C residue 40 ARG Chi-restraints excluded: chain C residue 382 GLU Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 529 TRP Chi-restraints excluded: chain C residue 541 HIS Chi-restraints excluded: chain C residue 584 GLU Chi-restraints excluded: chain C residue 592 GLU Chi-restraints excluded: chain C residue 611 GLU Chi-restraints excluded: chain D residue 289 LYS Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 466 THR Chi-restraints excluded: chain D residue 473 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 159 optimal weight: 1.9990 chunk 145 optimal weight: 0.0060 chunk 155 optimal weight: 3.9990 chunk 93 optimal weight: 8.9990 chunk 67 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 chunk 146 optimal weight: 0.8980 chunk 154 optimal weight: 8.9990 chunk 102 optimal weight: 0.6980 overall best weight: 1.1200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN C 77 GLN ** D 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 16088 Z= 0.286 Angle : 0.647 11.752 22387 Z= 0.363 Chirality : 0.045 0.183 2488 Planarity : 0.006 0.067 2445 Dihedral : 21.403 69.571 3232 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.33 % Allowed : 16.90 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.21), residues: 1594 helix: 1.60 (0.21), residues: 639 sheet: 0.30 (0.42), residues: 134 loop : -0.98 (0.21), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 586 HIS 0.006 0.001 HIS B 368 PHE 0.024 0.002 PHE B 228 TYR 0.045 0.002 TYR C 48 ARG 0.007 0.000 ARG D 575 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 132 time to evaluate : 1.697 Fit side-chains revert: symmetry clash REVERT: A 38 GLN cc_start: 0.7803 (OUTLIER) cc_final: 0.7390 (mp10) REVERT: A 40 ARG cc_start: 0.7943 (OUTLIER) cc_final: 0.7513 (ptp-170) REVERT: A 84 ARG cc_start: 0.7803 (OUTLIER) cc_final: 0.7471 (mtp180) REVERT: A 93 LYS cc_start: 0.8114 (pttp) cc_final: 0.7686 (tmtt) REVERT: B 13 ASP cc_start: 0.7902 (OUTLIER) cc_final: 0.7602 (m-30) REVERT: B 366 MET cc_start: 0.7106 (mmm) cc_final: 0.6620 (mmm) REVERT: C 40 ARG cc_start: 0.7209 (OUTLIER) cc_final: 0.6487 (ptp-110) REVERT: C 529 TRP cc_start: 0.7780 (OUTLIER) cc_final: 0.6779 (m100) REVERT: C 611 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.6980 (mp0) REVERT: D 289 LYS cc_start: 0.6829 (OUTLIER) cc_final: 0.6556 (mtmt) outliers start: 31 outliers final: 12 residues processed: 154 average time/residue: 1.5607 time to fit residues: 261.9999 Evaluate side-chains 150 residues out of total 1440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 130 time to evaluate : 1.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 40 ARG Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain B residue 13 ASP Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 504 LYS Chi-restraints excluded: chain C residue 40 ARG Chi-restraints excluded: chain C residue 382 GLU Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain C residue 529 TRP Chi-restraints excluded: chain C residue 584 GLU Chi-restraints excluded: chain C residue 592 GLU Chi-restraints excluded: chain C residue 611 GLU Chi-restraints excluded: chain D residue 289 LYS Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 466 THR Chi-restraints excluded: chain D residue 473 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 164 optimal weight: 0.9990 chunk 100 optimal weight: 0.5980 chunk 77 optimal weight: 0.0370 chunk 114 optimal weight: 0.1980 chunk 172 optimal weight: 4.9990 chunk 158 optimal weight: 1.9990 chunk 137 optimal weight: 0.0970 chunk 14 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 84 optimal weight: 0.0270 chunk 109 optimal weight: 7.9990 overall best weight: 0.1914 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 187 HIS C 77 GLN ** D 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16088 Z= 0.157 Angle : 0.533 13.104 22387 Z= 0.298 Chirality : 0.039 0.159 2488 Planarity : 0.005 0.067 2445 Dihedral : 20.954 68.951 3232 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.05 % Allowed : 18.26 % Favored : 80.69 % 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: 0.78 (0.21), residues: 1594 helix: 2.05 (0.21), residues: 639 sheet: 0.65 (0.43), residues: 142 loop : -0.78 (0.22), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B 586 HIS 0.004 0.001 HIS B 187 PHE 0.023 0.001 PHE B 228 TYR 0.045 0.001 TYR C 48 ARG 0.007 0.000 ARG B 526 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 139 time to evaluate : 1.777 Fit side-chains revert: symmetry clash REVERT: A 93 LYS cc_start: 0.8083 (pttp) cc_final: 0.7591 (tppt) REVERT: B 13 ASP cc_start: 0.7869 (OUTLIER) cc_final: 0.7587 (m-30) REVERT: C 529 TRP cc_start: 0.7475 (OUTLIER) cc_final: 0.6581 (m100) REVERT: C 611 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.6666 (mp0) outliers start: 14 outliers final: 7 residues processed: 148 average time/residue: 1.4426 time to fit residues: 233.9937 Evaluate side-chains 147 residues out of total 1440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 137 time to evaluate : 1.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 ASP Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 77 GLN Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 529 TRP Chi-restraints excluded: chain C residue 584 GLU Chi-restraints excluded: chain C residue 592 GLU Chi-restraints excluded: chain C residue 611 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 146 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 126 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 137 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 141 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 187 HIS B 482 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.194147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.164375 restraints weight = 13056.473| |-----------------------------------------------------------------------------| r_work (start): 0.3988 rms_B_bonded: 0.97 r_work: 0.3732 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.3603 rms_B_bonded: 2.48 restraints_weight: 0.2500 r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 16088 Z= 0.260 Angle : 0.781 59.197 22387 Z= 0.456 Chirality : 0.041 0.162 2488 Planarity : 0.005 0.067 2445 Dihedral : 20.957 69.070 3232 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.75 % Allowed : 18.56 % Favored : 80.69 % 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: 0.76 (0.21), residues: 1594 helix: 2.02 (0.21), residues: 635 sheet: 0.69 (0.43), residues: 142 loop : -0.79 (0.22), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 586 HIS 0.004 0.001 HIS B 368 PHE 0.022 0.001 PHE B 228 TYR 0.048 0.002 TYR C 48 ARG 0.006 0.000 ARG D 575 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6147.09 seconds wall clock time: 110 minutes 40.87 seconds (6640.87 seconds total)