Starting phenix.real_space_refine on Sun Dec 10 05:51:08 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l2t_0814/12_2023/6l2t_0814.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l2t_0814/12_2023/6l2t_0814.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l2t_0814/12_2023/6l2t_0814.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l2t_0814/12_2023/6l2t_0814.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l2t_0814/12_2023/6l2t_0814.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l2t_0814/12_2023/6l2t_0814.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.038 sd= 1.120 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: 4 Type Number sf(0) Gaussians S 47 5.16 5 C 8728 2.51 5 N 2362 2.21 5 O 2467 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 78": "NH1" <-> "NH2" Residue "A ARG 192": "NH1" <-> "NH2" Residue "A GLU 202": "OE1" <-> "OE2" Residue "A TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 212": "NH1" <-> "NH2" Residue "A TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 366": "OD1" <-> "OD2" Residue "A PHE 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 478": "OD1" <-> "OD2" Residue "A ASP 510": "OD1" <-> "OD2" Residue "A TYR 530": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 29": "NH1" <-> "NH2" Residue "B PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 78": "NH1" <-> "NH2" Residue "B ARG 163": "NH1" <-> "NH2" Residue "B ARG 192": "NH1" <-> "NH2" Residue "B TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 212": "NH1" <-> "NH2" Residue "B TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 294": "OD1" <-> "OD2" Residue "B TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 366": "OD1" <-> "OD2" Residue "B GLU 422": "OE1" <-> "OE2" Residue "B TYR 530": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 575": "OD1" <-> "OD2" Residue "B TYR 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 632": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 78": "NH1" <-> "NH2" Residue "C PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 192": "NH1" <-> "NH2" Residue "C GLU 202": "OE1" <-> "OE2" Residue "C TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 212": "NH1" <-> "NH2" Residue "C PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 486": "OD1" <-> "OD2" Residue "C ASP 512": "OD1" <-> "OD2" Residue "C TYR 530": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 564": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 606": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 632": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 13604 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 628, 4511 Classifications: {'peptide': 628} Incomplete info: {'truncation_to_alanine': 141} Link IDs: {'PTRANS': 48, 'TRANS': 579} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 556 Unresolved non-hydrogen angles: 702 Unresolved non-hydrogen dihedrals: 456 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 10, 'ASP:plan': 22, 'TYR:plan': 3, 'ASN:plan1': 9, 'TRP:plan': 1, 'HIS:plan': 7, 'PHE:plan': 7, 'GLU:plan': 16, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 379 Chain: "B" Number of atoms: 4554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 628, 4554 Classifications: {'peptide': 628} Incomplete info: {'truncation_to_alanine': 125} Link IDs: {'PTRANS': 48, 'TRANS': 579} Chain breaks: 1 Unresolved non-hydrogen bonds: 511 Unresolved non-hydrogen angles: 643 Unresolved non-hydrogen dihedrals: 423 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 10, 'ASP:plan': 19, 'TYR:plan': 3, 'ASN:plan1': 8, 'TRP:plan': 1, 'HIS:plan': 7, 'PHE:plan': 7, 'GLU:plan': 16, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 367 Chain: "C" Number of atoms: 4539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 633, 4539 Classifications: {'peptide': 633} Incomplete info: {'truncation_to_alanine': 135} Link IDs: {'PTRANS': 48, 'TRANS': 584} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 553 Unresolved non-hydrogen angles: 695 Unresolved non-hydrogen dihedrals: 459 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 24, 'TYR:plan': 3, 'ASN:plan1': 7, 'TRP:plan': 1, 'HIS:plan': 8, 'PHE:plan': 7, 'GLU:plan': 16, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 385 Time building chain proxies: 7.07, per 1000 atoms: 0.52 Number of scatterers: 13604 At special positions: 0 Unit cell: (95.85, 98.55, 132.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 47 16.00 O 2467 8.00 N 2362 7.00 C 8728 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: 4.50 Conformation dependent library (CDL) restraints added in 2.5 seconds 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3552 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 26 sheets defined 11.5% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.60 Creating SS restraints... Processing helix chain 'A' and resid 17 through 22 Processing helix chain 'A' and resid 22 through 40 Processing helix chain 'A' and resid 138 through 142 Processing helix chain 'A' and resid 183 through 187 removed outlier: 3.724A pdb=" N LEU A 187 " --> pdb=" O GLY A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 213 removed outlier: 4.136A pdb=" N LYS A 213 " --> pdb=" O THR A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 228 removed outlier: 3.976A pdb=" N TYR A 224 " --> pdb=" O LYS A 220 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL A 228 " --> pdb=" O TYR A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 422 through 426 removed outlier: 3.874A pdb=" N ASN A 425 " --> pdb=" O GLU A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 476 No H-bonds generated for 'chain 'A' and resid 474 through 476' Processing helix chain 'A' and resid 555 through 560 removed outlier: 3.505A pdb=" N SER A 560 " --> pdb=" O GLN A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 566 Processing helix chain 'B' and resid 17 through 22 Processing helix chain 'B' and resid 22 through 40 Processing helix chain 'B' and resid 51 through 55 removed outlier: 4.036A pdb=" N GLU B 54 " --> pdb=" O GLN B 51 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N THR B 55 " --> pdb=" O ILE B 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 51 through 55' Processing helix chain 'B' and resid 138 through 142 Processing helix chain 'B' and resid 183 through 186 Processing helix chain 'B' and resid 205 through 210 Processing helix chain 'B' and resid 220 through 228 Processing helix chain 'B' and resid 271 through 276 removed outlier: 3.507A pdb=" N PHE B 275 " --> pdb=" O THR B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 566 Processing helix chain 'C' and resid 17 through 22 Processing helix chain 'C' and resid 22 through 39 Processing helix chain 'C' and resid 50 through 55 removed outlier: 3.907A pdb=" N GLU C 54 " --> pdb=" O GLN C 51 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N THR C 55 " --> pdb=" O ILE C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 188 removed outlier: 4.252A pdb=" N TYR C 188 " --> pdb=" O GLY C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 228 Processing helix chain 'C' and resid 271 through 278 removed outlier: 3.827A pdb=" N PHE C 275 " --> pdb=" O THR C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 426 removed outlier: 3.584A pdb=" N ASN C 425 " --> pdb=" O GLU C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 474 through 476 No H-bonds generated for 'chain 'C' and resid 474 through 476' Processing helix chain 'C' and resid 554 through 560 removed outlier: 3.641A pdb=" N CYS C 558 " --> pdb=" O PRO C 554 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER C 560 " --> pdb=" O GLN C 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 561 through 566 removed outlier: 3.797A pdb=" N TYR C 566 " --> pdb=" O ILE C 562 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 331 through 332 removed outlier: 3.693A pdb=" N ILE A 331 " --> pdb=" O GLY A 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 198 through 204 removed outlier: 7.181A pdb=" N PHE A 193 " --> pdb=" O LEU A 200 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N GLU A 202 " --> pdb=" O VAL A 191 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL A 191 " --> pdb=" O GLU A 202 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN A 190 " --> pdb=" O LYS A 360 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU A 194 " --> pdb=" O PHE A 356 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE A 356 " --> pdb=" O GLU A 194 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 233 through 234 removed outlier: 3.548A pdb=" N SER A 313 " --> pdb=" O VAL A 234 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 241 through 242 removed outlier: 3.858A pdb=" N ARG A 307 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG A 308 " --> pdb=" O CYS C 314 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ASN C 315 " --> pdb=" O VAL C 232 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL C 232 " --> pdb=" O ASN C 315 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 433 through 441 removed outlier: 3.594A pdb=" N VAL A 438 " --> pdb=" O ALA A 629 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS A 440 " --> pdb=" O SER A 627 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 471 through 472 Processing sheet with id=AA7, first strand: chain 'A' and resid 494 through 495 Processing sheet with id=AA8, first strand: chain 'A' and resid 539 through 544 removed outlier: 6.009A pdb=" N ILE A 540 " --> pdb=" O ASP A 551 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N ASP A 551 " --> pdb=" O ILE A 540 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL A 542 " --> pdb=" O LEU A 549 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE A 547 " --> pdb=" O ALA A 544 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 70 through 71 Processing sheet with id=AB1, first strand: chain 'B' and resid 327 through 328 removed outlier: 3.659A pdb=" N LEU B 327 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU B 110 " --> pdb=" O LEU B 327 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N HIS B 107 " --> pdb=" O GLU B 411 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE B 109 " --> pdb=" O ASN B 409 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ASN B 409 " --> pdb=" O ILE B 109 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 157 through 158 Processing sheet with id=AB3, first strand: chain 'B' and resid 176 through 179 removed outlier: 3.914A pdb=" N LEU B 176 " --> pdb=" O PHE B 371 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N TYR B 178 " --> pdb=" O ASN B 369 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN B 369 " --> pdb=" O TYR B 178 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 198 through 204 removed outlier: 7.058A pdb=" N PHE B 193 " --> pdb=" O LEU B 200 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N GLU B 202 " --> pdb=" O VAL B 191 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N VAL B 191 " --> pdb=" O GLU B 202 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N SER B 204 " --> pdb=" O GLU B 189 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N GLU B 189 " --> pdb=" O SER B 204 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASN B 190 " --> pdb=" O LYS B 360 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU B 194 " --> pdb=" O PHE B 356 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 232 through 234 removed outlier: 3.817A pdb=" N VAL B 232 " --> pdb=" O ASN B 315 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ASN B 315 " --> pdb=" O VAL B 232 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER B 313 " --> pdb=" O VAL B 234 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG C 307 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU C 241 " --> pdb=" O ARG C 307 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 467 through 472 removed outlier: 3.535A pdb=" N PHE B 467 " --> pdb=" O SER B 626 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 504 through 505 Processing sheet with id=AB8, first strand: chain 'B' and resid 547 through 550 removed outlier: 3.892A pdb=" N ILE B 547 " --> pdb=" O ALA B 544 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL B 542 " --> pdb=" O LEU B 549 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 70 through 71 removed outlier: 3.538A pdb=" N GLY C 71 " --> pdb=" O PHE C 418 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 109 through 110 removed outlier: 3.717A pdb=" N LEU C 110 " --> pdb=" O LEU C 327 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU C 327 " --> pdb=" O LEU C 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'C' and resid 176 through 178 removed outlier: 3.963A pdb=" N LEU C 176 " --> pdb=" O PHE C 371 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N TYR C 178 " --> pdb=" O ASN C 369 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASN C 369 " --> pdb=" O TYR C 178 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 198 through 204 removed outlier: 6.961A pdb=" N PHE C 193 " --> pdb=" O LEU C 200 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLU C 202 " --> pdb=" O VAL C 191 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N VAL C 191 " --> pdb=" O GLU C 202 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN C 190 " --> pdb=" O LYS C 360 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 434 through 436 removed outlier: 3.728A pdb=" N SER C 434 " --> pdb=" O LEU C 633 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU C 633 " --> pdb=" O SER C 434 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 444 through 446 removed outlier: 3.569A pdb=" N THR C 446 " --> pdb=" O ALA C 621 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ALA C 621 " --> pdb=" O THR C 446 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 580 through 582 removed outlier: 3.777A pdb=" N MET C 580 " --> pdb=" O ILE C 468 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE C 468 " --> pdb=" O MET C 580 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE C 582 " --> pdb=" O MET C 466 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N SER C 628 " --> pdb=" O GLU C 464 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 492 through 494 removed outlier: 3.574A pdb=" N HIS C 492 " --> pdb=" O LEU C 534 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU C 534 " --> pdb=" O HIS C 492 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL C 494 " --> pdb=" O ILE C 532 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 541 through 543 173 hydrogen bonds defined for protein. 426 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: 3.46 Time building geometry restraints manager: 5.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3389 1.33 - 1.45: 2789 1.45 - 1.57: 7754 1.57 - 1.69: 0 1.69 - 1.81: 70 Bond restraints: 14002 Sorted by residual: bond pdb=" N ILE A 402 " pdb=" CA ILE A 402 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.12e+00 bond pdb=" N VAL A 401 " pdb=" CA VAL A 401 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.99e+00 bond pdb=" N ASN A 403 " pdb=" CA ASN A 403 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.32e-02 5.74e+03 6.10e+00 bond pdb=" N GLU A 404 " pdb=" CA GLU A 404 " ideal model delta sigma weight residual 1.457 1.485 -0.028 1.16e-02 7.43e+03 5.64e+00 bond pdb=" N ILE A 398 " pdb=" CA ILE A 398 " ideal model delta sigma weight residual 1.468 1.492 -0.024 1.05e-02 9.07e+03 5.26e+00 ... (remaining 13997 not shown) Histogram of bond angle deviations from ideal: 100.03 - 106.82: 691 106.82 - 113.62: 7695 113.62 - 120.41: 4716 120.41 - 127.21: 5915 127.21 - 134.01: 235 Bond angle restraints: 19252 Sorted by residual: angle pdb=" N PRO A 399 " pdb=" CA PRO A 399 " pdb=" C PRO A 399 " ideal model delta sigma weight residual 111.33 120.41 -9.08 1.43e+00 4.89e-01 4.03e+01 angle pdb=" N ILE A 398 " pdb=" CA ILE A 398 " pdb=" C ILE A 398 " ideal model delta sigma weight residual 109.02 103.28 5.74 9.30e-01 1.16e+00 3.81e+01 angle pdb=" N PHE B 397 " pdb=" CA PHE B 397 " pdb=" C PHE B 397 " ideal model delta sigma weight residual 108.38 113.65 -5.27 1.35e+00 5.49e-01 1.52e+01 angle pdb=" CA PHE A 397 " pdb=" C PHE A 397 " pdb=" O PHE A 397 " ideal model delta sigma weight residual 122.13 117.78 4.35 1.13e+00 7.83e-01 1.48e+01 angle pdb=" C THR C 271 " pdb=" N ASN C 272 " pdb=" CA ASN C 272 " ideal model delta sigma weight residual 121.62 127.55 -5.93 1.57e+00 4.06e-01 1.43e+01 ... (remaining 19247 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.63: 7408 15.63 - 31.27: 623 31.27 - 46.90: 129 46.90 - 62.54: 12 62.54 - 78.17: 9 Dihedral angle restraints: 8181 sinusoidal: 2676 harmonic: 5505 Sorted by residual: dihedral pdb=" CA PHE A 283 " pdb=" C PHE A 283 " pdb=" N PRO A 284 " pdb=" CA PRO A 284 " ideal model delta harmonic sigma weight residual 180.00 154.95 25.05 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" CA PHE B 283 " pdb=" C PHE B 283 " pdb=" N PRO B 284 " pdb=" CA PRO B 284 " ideal model delta harmonic sigma weight residual 180.00 156.15 23.85 0 5.00e+00 4.00e-02 2.28e+01 dihedral pdb=" CA PRO A 84 " pdb=" C PRO A 84 " pdb=" N THR A 85 " pdb=" CA THR A 85 " ideal model delta harmonic sigma weight residual 180.00 -158.94 -21.06 0 5.00e+00 4.00e-02 1.77e+01 ... (remaining 8178 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1854 0.063 - 0.125: 349 0.125 - 0.188: 18 0.188 - 0.251: 1 0.251 - 0.314: 1 Chirality restraints: 2223 Sorted by residual: chirality pdb=" CA ILE A 398 " pdb=" N ILE A 398 " pdb=" C ILE A 398 " pdb=" CB ILE A 398 " both_signs ideal model delta sigma weight residual False 2.43 2.75 -0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" CA PRO A 399 " pdb=" N PRO A 399 " pdb=" C PRO A 399 " pdb=" CB PRO A 399 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA ILE A 522 " pdb=" N ILE A 522 " pdb=" C ILE A 522 " pdb=" CB ILE A 522 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.98e-01 ... (remaining 2220 not shown) Planarity restraints: 2509 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 83 " 0.039 5.00e-02 4.00e+02 5.98e-02 5.72e+00 pdb=" N PRO A 84 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 84 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 84 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 83 " -0.035 5.00e-02 4.00e+02 5.25e-02 4.41e+00 pdb=" N PRO B 84 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO B 84 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 84 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 83 " 0.029 5.00e-02 4.00e+02 4.36e-02 3.04e+00 pdb=" N PRO C 84 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO C 84 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 84 " 0.024 5.00e-02 4.00e+02 ... (remaining 2506 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2001 2.76 - 3.29: 13040 3.29 - 3.83: 19903 3.83 - 4.36: 21241 4.36 - 4.90: 38252 Nonbonded interactions: 94437 Sorted by model distance: nonbonded pdb=" OG SER C 116 " pdb=" O GLY C 400 " model vdw 2.222 2.440 nonbonded pdb=" OG1 THR A 446 " pdb=" O ALA A 621 " model vdw 2.226 2.440 nonbonded pdb=" O LYS B 460 " pdb=" OG SER B 601 " model vdw 2.231 2.440 nonbonded pdb=" OG SER B 116 " pdb=" O GLY B 400 " model vdw 2.250 2.440 nonbonded pdb=" OG1 THR C 446 " pdb=" O ALA C 621 " model vdw 2.256 2.440 ... (remaining 94432 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 8 through 17 or (resid 18 and (name N or name CA or name C \ or name O or name CB )) or resid 19 through 41 or (resid 42 and (name N or name \ CA or name C or name O or name CB )) or resid 43 through 98 or (resid 99 and (n \ ame N or name CA or name C or name O or name CB )) or resid 100 through 132 or ( \ resid 133 through 135 and (name N or name CA or name C or name O or name CB )) o \ r resid 136 through 157 or (resid 158 and (name N or name CA or name C or name O \ or name CB )) or resid 160 through 184 or (resid 185 and (name N or name CA or \ name C or name O or name CB )) or resid 186 through 229 or (resid 230 through 23 \ 1 and (name N or name CA or name C or name O or name CB )) or resid 232 through \ 248 or (resid 249 through 257 and (name N or name CA or name C or name O or name \ CB )) or resid 258 through 277 or (resid 278 and (name N or name CA or name C o \ r name O or name CB )) or resid 279 through 281 or (resid 282 and (name N or nam \ e CA or name C or name O or name CB )) or resid 284 or (resid 285 and (name N or \ name CA or name C or name O or name CB )) or resid 286 through 301 or (resid 30 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 303 through \ 317 or (resid 318 and (name N or name CA or name C or name O or name CB )) or re \ sid 319 through 341 or resid 344 through 364 or (resid 365 through 366 and (name \ N or name CA or name C or name O or name CB )) or resid 367 through 406 or (res \ id 407 through 408 and (name N or name CA or name C or name O or name CB )) or r \ esid 409 through 410 or (resid 411 and (name N or name CA or name C or name O or \ name CB )) or resid 412 through 476 or (resid 477 through 478 and (name N or na \ me CA or name C or name O or name CB )) or resid 479 through 484 or (resid 485 a \ nd (name N or name CA or name C or name O or name CB )) or resid 486 through 497 \ or (resid 498 and (name N or name CA or name C or name O or name CB )) or resid \ 499 through 509 or (resid 510 and (name N or name CA or name C or name O or nam \ e CB )) or resid 511 through 520 or (resid 521 and (name N or name CA or name C \ or name O or name CB )) or resid 522 through 540 or (resid 541 and (name N or na \ me CA or name C or name O or name CB )) or resid 542 through 550 or (resid 551 a \ nd (name N or name CA or name C or name O or name CB )) or resid 552 through 574 \ or (resid 575 through 576 and (name N or name CA or name C or name O or name CB \ )) or resid 577 through 618 or (resid 619 and (name N or name CA or name C or n \ ame O or name CB )) or resid 620 through 626 or (resid 627 and (name N or name C \ A or name C or name O or name CB )) or resid 628 through 636)) selection = (chain 'B' and (resid 8 through 16 or (resid 17 through 18 and (name N or name C \ A or name C or name O or name CB )) or resid 19 through 29 or (resid 30 through \ 32 and (name N or name CA or name C or name O or name CB )) or resid 33 or (resi \ d 34 and (name N or name CA or name C or name O or name CB )) or resid 35 or (re \ sid 36 and (name N or name CA or name C or name O or name CB )) or resid 37 thro \ ugh 38 or (resid 39 and (name N or name CA or name C or name O or name CB )) or \ resid 40 through 47 or (resid 48 through 49 and (name N or name CA or name C or \ name O or name CB )) or resid 50 through 51 or (resid 52 and (name N or name CA \ or name C or name O or name CB )) or resid 53 through 54 or (resid 55 and (name \ N or name CA or name C or name O or name CB )) or resid 56 through 62 or (resid \ 63 and (name N or name CA or name C or name O or name CB )) or resid 64 through \ 85 or (resid 86 and (name N or name CA or name C or name O or name CB )) or resi \ d 87 through 93 or (resid 94 and (name N or name CA or name C or name O or name \ CB )) or resid 95 through 103 or (resid 104 and (name N or name CA or name C or \ name O or name CB )) or resid 105 through 122 or (resid 123 and (name N or name \ CA or name C or name O or name CB )) or resid 124 through 144 or (resid 145 and \ (name N or name CA or name C or name O or name CB )) or resid 146 through 158 or \ (resid 160 through 161 and (name N or name CA or name C or name O or name CB )) \ or resid 162 through 184 or (resid 185 and (name N or name CA or name C or name \ O or name CB )) or resid 186 through 218 or (resid 219 and (name N or name CA o \ r name C or name O or name CB )) or resid 220 through 229 or (resid 230 through \ 231 and (name N or name CA or name C or name O or name CB )) or resid 232 throug \ h 234 or (resid 235 and (name N or name CA or name C or name O or name CB )) or \ resid 236 through 248 or (resid 249 through 257 and (name N or name CA or name C \ or name O or name CB )) or resid 258 or (resid 259 through 260 and (name N or n \ ame CA or name C or name O or name CB )) or resid 261 through 275 or (resid 276 \ and (name N or name CA or name C or name O or name CB )) or resid 277 or (resid \ 278 and (name N or name CA or name C or name O or name CB )) or resid 279 throug \ h 282 or resid 284 through 294 or (resid 295 and (name N or name CA or name C or \ name O or name CB )) or resid 296 or (resid 297 and (name N or name CA or name \ C or name O or name CB )) or resid 298 through 301 or (resid 302 and (name N or \ name CA or name C or name O or name CB )) or resid 303 or (resid 304 through 305 \ and (name N or name CA or name C or name O or name CB )) or resid 306 through 3 \ 41 or resid 344 through 362 or (resid 363 through 366 and (name N or name CA or \ name C or name O or name CB )) or resid 367 through 410 or (resid 411 and (name \ N or name CA or name C or name O or name CB )) or resid 412 through 428 or (resi \ d 429 through 430 and (name N or name CA or name C or name O or name CB )) or re \ sid 431 through 477 or (resid 478 and (name N or name CA or name C or name O or \ name CB )) or resid 479 through 484 or (resid 485 and (name N or name CA or name \ C or name O or name CB )) or resid 486 through 497 or (resid 498 and (name N or \ name CA or name C or name O or name CB )) or resid 499 through 509 or (resid 51 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 511 through \ 516 or (resid 517 through 518 and (name N or name CA or name C or name O or name \ CB )) or resid 519 through 540 or (resid 541 and (name N or name CA or name C o \ r name O or name CB )) or resid 542 through 550 or (resid 551 and (name N or nam \ e CA or name C or name O or name CB )) or resid 552 through 554 or (resid 555 an \ d (name N or name CA or name C or name O or name CB )) or resid 556 through 574 \ or (resid 575 through 576 and (name N or name CA or name C or name O or name CB \ )) or resid 577 through 592 or (resid 593 and (name N or name CA or name C or na \ me O or name CB )) or resid 594 through 636)) selection = (chain 'C' and (resid 8 through 29 or (resid 30 through 32 and (name N or name C \ A or name C or name O or name CB )) or resid 33 or (resid 34 and (name N or name \ CA or name C or name O or name CB )) or resid 35 or (resid 36 and (name N or na \ me CA or name C or name O or name CB )) or resid 37 or (resid 38 through 39 and \ (name N or name CA or name C or name O or name CB )) or resid 40 through 47 or ( \ resid 48 through 49 and (name N or name CA or name C or name O or name CB )) or \ resid 50 or (resid 51 through 52 and (name N or name CA or name C or name O or n \ ame CB )) or resid 53 through 54 or (resid 55 and (name N or name CA or name C o \ r name O or name CB )) or resid 56 through 62 or (resid 63 and (name N or name C \ A or name C or name O or name CB )) or resid 64 through 85 or (resid 86 and (nam \ e N or name CA or name C or name O or name CB )) or resid 87 through 93 or (resi \ d 94 and (name N or name CA or name C or name O or name CB )) or resid 95 throug \ h 98 or (resid 99 and (name N or name CA or name C or name O or name CB )) or re \ sid 100 through 103 or (resid 104 and (name N or name CA or name C or name O or \ name CB )) or resid 105 through 122 or (resid 123 and (name N or name CA or name \ C or name O or name CB )) or resid 124 through 132 or (resid 133 through 135 an \ d (name N or name CA or name C or name O or name CB )) or resid 136 through 158 \ or (resid 160 through 161 and (name N or name CA or name C or name O or name CB \ )) or resid 162 through 205 or (resid 206 and (name N or name CA or name C or na \ me O or name CB )) or resid 207 through 218 or (resid 219 and (name N or name CA \ or name C or name O or name CB )) or resid 220 through 234 or (resid 235 and (n \ ame N or name CA or name C or name O or name CB )) or resid 236 through 258 or ( \ resid 259 through 260 and (name N or name CA or name C or name O or name CB )) o \ r resid 261 through 281 or (resid 282 and (name N or name CA or name C or name O \ or name CB )) or resid 284 or (resid 285 and (name N or name CA or name C or na \ me O or name CB )) or resid 286 through 294 or (resid 295 and (name N or name CA \ or name C or name O or name CB )) or resid 296 or (resid 297 and (name N or nam \ e CA or name C or name O or name CB )) or resid 298 through 317 or (resid 318 an \ d (name N or name CA or name C or name O or name CB )) or resid 319 through 341 \ or resid 344 through 362 or (resid 363 through 366 and (name N or name CA or nam \ e C or name O or name CB )) or resid 367 through 407 or (resid 408 and (name N o \ r name CA or name C or name O or name CB )) or resid 409 through 476 or (resid 4 \ 77 through 478 and (name N or name CA or name C or name O or name CB )) or resid \ 479 through 516 or (resid 517 through 518 and (name N or name CA or name C or n \ ame O or name CB )) or resid 519 through 520 or (resid 521 and (name N or name C \ A or name C or name O or name CB )) or resid 522 through 554 or (resid 555 and ( \ name N or name CA or name C or name O or name CB )) or resid 556 through 592 or \ (resid 593 and (name N or name CA or name C or name O or name CB )) or resid 594 \ through 617 or (resid 618 through 619 and (name N or name CA or name C or name \ O or name CB )) or resid 620 through 626 or (resid 627 and (name N or name CA or \ name C or name O or name CB )) or resid 628 through 636)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.200 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: 1.790 Check model and map are aligned: 0.200 Set scattering table: 0.140 Process input model: 34.620 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 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 0.046 14002 Z= 0.190 Angle : 0.606 9.077 19252 Z= 0.334 Chirality : 0.047 0.314 2223 Planarity : 0.005 0.060 2509 Dihedral : 12.334 78.173 4629 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.16 % Allowed : 13.83 % Favored : 86.01 % Rotamer: Outliers : 0.15 % Allowed : 8.75 % Favored : 91.10 % 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: -5.72 (0.15), residues: 1873 helix: -1.79 (0.40), residues: 141 sheet: -3.78 (0.19), residues: 461 loop : -4.35 (0.13), residues: 1271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 474 HIS 0.005 0.001 HIS C 131 PHE 0.024 0.001 PHE A 467 TYR 0.015 0.001 TYR B 465 ARG 0.002 0.000 ARG C 192 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 324 time to evaluate : 1.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 326 average time/residue: 0.2742 time to fit residues: 127.1229 Evaluate side-chains 239 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 237 time to evaluate : 1.269 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1322 time to fit residues: 2.6803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 157 optimal weight: 5.9990 chunk 141 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 48 optimal weight: 7.9990 chunk 95 optimal weight: 8.9990 chunk 75 optimal weight: 0.7980 chunk 146 optimal weight: 0.0870 chunk 56 optimal weight: 0.9990 chunk 89 optimal weight: 8.9990 chunk 109 optimal weight: 0.3980 chunk 169 optimal weight: 10.0000 overall best weight: 1.0562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 HIS A 107 HIS A 282 HIS A 311 HIS A 416 ASN A 445 HIS ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 HIS B 147 GLN B 226 HIS B 410 ASN B 565 HIS C 102 HIS C 131 HIS C 499 GLN C 539 ASN C 597 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14002 Z= 0.173 Angle : 0.599 7.043 19252 Z= 0.301 Chirality : 0.046 0.172 2223 Planarity : 0.005 0.089 2509 Dihedral : 4.519 24.383 1985 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.05 % Allowed : 12.81 % Favored : 87.13 % Rotamer: Outliers : 0.15 % Allowed : 4.95 % Favored : 94.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.98 (0.17), residues: 1873 helix: -1.19 (0.41), residues: 145 sheet: -3.37 (0.20), residues: 466 loop : -3.80 (0.15), residues: 1262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 474 HIS 0.008 0.001 HIS C 131 PHE 0.014 0.001 PHE A 467 TYR 0.017 0.001 TYR C 465 ARG 0.004 0.000 ARG C 192 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 275 time to evaluate : 1.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 277 average time/residue: 0.2336 time to fit residues: 97.4390 Evaluate side-chains 230 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 230 time to evaluate : 1.448 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 94 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 141 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 46 optimal weight: 7.9990 chunk 170 optimal weight: 0.6980 chunk 183 optimal weight: 5.9990 chunk 151 optimal weight: 4.9990 chunk 168 optimal weight: 20.0000 chunk 57 optimal weight: 3.9990 chunk 136 optimal weight: 0.0040 overall best weight: 1.1398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 HIS A 311 HIS A 445 HIS ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 ASN B 503 HIS ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14002 Z= 0.176 Angle : 0.593 7.922 19252 Z= 0.297 Chirality : 0.046 0.166 2223 Planarity : 0.005 0.097 2509 Dihedral : 4.514 24.441 1985 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 12.49 % Favored : 87.45 % Rotamer: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.63 (0.17), residues: 1873 helix: -0.77 (0.44), residues: 143 sheet: -3.20 (0.21), residues: 446 loop : -3.55 (0.15), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 474 HIS 0.003 0.001 HIS B 503 PHE 0.025 0.001 PHE A 60 TYR 0.019 0.001 TYR C 465 ARG 0.004 0.000 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 280 time to evaluate : 1.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 280 average time/residue: 0.2242 time to fit residues: 95.3633 Evaluate side-chains 214 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 214 time to evaluate : 1.628 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 168 optimal weight: 7.9990 chunk 127 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 18 optimal weight: 9.9990 chunk 81 optimal weight: 0.9990 chunk 114 optimal weight: 3.9990 chunk 170 optimal weight: 6.9990 chunk 180 optimal weight: 0.0470 chunk 89 optimal weight: 1.9990 chunk 161 optimal weight: 8.9990 chunk 48 optimal weight: 9.9990 overall best weight: 1.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 HIS ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 ASN ** B 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 27 ASN C 416 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14002 Z= 0.211 Angle : 0.609 8.355 19252 Z= 0.307 Chirality : 0.047 0.174 2223 Planarity : 0.005 0.095 2509 Dihedral : 4.699 23.967 1985 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.05 % Allowed : 14.47 % Favored : 85.48 % Rotamer: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.43 (0.18), residues: 1873 helix: -0.67 (0.45), residues: 143 sheet: -2.77 (0.22), residues: 485 loop : -3.52 (0.16), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 474 HIS 0.005 0.001 HIS B 445 PHE 0.019 0.001 PHE A 101 TYR 0.019 0.002 TYR B 188 ARG 0.004 0.001 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 277 time to evaluate : 1.535 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 277 average time/residue: 0.2288 time to fit residues: 95.4105 Evaluate side-chains 213 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 213 time to evaluate : 1.527 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 150 optimal weight: 0.2980 chunk 102 optimal weight: 0.0870 chunk 2 optimal weight: 5.9990 chunk 134 optimal weight: 5.9990 chunk 74 optimal weight: 0.0570 chunk 154 optimal weight: 3.9990 chunk 124 optimal weight: 0.0000 chunk 0 optimal weight: 10.0000 chunk 92 optimal weight: 1.9990 chunk 162 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 overall best weight: 0.2882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 HIS ** A 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 445 HIS A 483 GLN A 569 ASN B 475 ASN C 226 HIS C 445 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 14002 Z= 0.143 Angle : 0.579 6.901 19252 Z= 0.290 Chirality : 0.046 0.195 2223 Planarity : 0.005 0.103 2509 Dihedral : 4.384 24.100 1985 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.78 % Favored : 89.16 % Rotamer: Outliers : 0.08 % Allowed : 2.48 % Favored : 97.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.05 (0.18), residues: 1873 helix: -0.44 (0.46), residues: 143 sheet: -2.47 (0.23), residues: 466 loop : -3.27 (0.16), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 474 HIS 0.004 0.001 HIS C 226 PHE 0.017 0.001 PHE A 137 TYR 0.015 0.001 TYR C 323 ARG 0.005 0.000 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 276 time to evaluate : 1.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 277 average time/residue: 0.2408 time to fit residues: 99.6609 Evaluate side-chains 209 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 209 time to evaluate : 1.624 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 60 optimal weight: 0.7980 chunk 162 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 106 optimal weight: 0.0980 chunk 44 optimal weight: 4.9990 chunk 180 optimal weight: 6.9990 chunk 150 optimal weight: 20.0000 chunk 83 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 59 optimal weight: 0.0020 chunk 94 optimal weight: 3.9990 overall best weight: 1.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 GLN A 311 HIS ** A 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 445 HIS A 569 ASN B 23 GLN ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14002 Z= 0.188 Angle : 0.592 7.392 19252 Z= 0.297 Chirality : 0.046 0.206 2223 Planarity : 0.005 0.108 2509 Dihedral : 4.463 24.079 1985 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.05 % Allowed : 13.29 % Favored : 86.65 % Rotamer: Outliers : 0.08 % Allowed : 2.63 % Favored : 97.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.02 (0.18), residues: 1873 helix: -0.35 (0.46), residues: 143 sheet: -2.45 (0.23), residues: 475 loop : -3.25 (0.16), residues: 1255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 474 HIS 0.003 0.001 HIS B 445 PHE 0.018 0.001 PHE A 137 TYR 0.020 0.002 TYR B 465 ARG 0.005 0.000 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 263 time to evaluate : 1.549 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 264 average time/residue: 0.2250 time to fit residues: 91.5675 Evaluate side-chains 210 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 210 time to evaluate : 1.590 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 174 optimal weight: 0.0870 chunk 20 optimal weight: 0.9990 chunk 103 optimal weight: 10.0000 chunk 132 optimal weight: 0.4980 chunk 102 optimal weight: 6.9990 chunk 152 optimal weight: 6.9990 chunk 101 optimal weight: 0.9990 chunk 180 optimal weight: 6.9990 chunk 112 optimal weight: 0.0470 chunk 109 optimal weight: 0.9990 chunk 83 optimal weight: 0.6980 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 HIS A 315 ASN A 445 HIS ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 23 GLN B 445 HIS B 483 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 14002 Z= 0.148 Angle : 0.584 7.224 19252 Z= 0.292 Chirality : 0.045 0.172 2223 Planarity : 0.005 0.110 2509 Dihedral : 4.279 23.327 1985 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.73 % Favored : 89.22 % Rotamer: Outliers : 0.08 % Allowed : 1.86 % Favored : 98.07 % 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: -3.77 (0.18), residues: 1873 helix: -0.12 (0.47), residues: 143 sheet: -2.32 (0.24), residues: 423 loop : -3.07 (0.16), residues: 1307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 474 HIS 0.004 0.000 HIS B 80 PHE 0.019 0.001 PHE C 92 TYR 0.016 0.001 TYR A 224 ARG 0.006 0.000 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 265 time to evaluate : 1.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 266 average time/residue: 0.2237 time to fit residues: 91.2099 Evaluate side-chains 212 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 1.498 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 111 optimal weight: 6.9990 chunk 71 optimal weight: 10.0000 chunk 107 optimal weight: 0.0070 chunk 54 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 34 optimal weight: 0.0980 chunk 114 optimal weight: 7.9990 chunk 122 optimal weight: 5.9990 chunk 89 optimal weight: 0.3980 chunk 16 optimal weight: 0.0670 chunk 141 optimal weight: 3.9990 overall best weight: 0.9138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 HIS A 445 HIS ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 499 GLN B 23 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 14002 Z= 0.160 Angle : 0.580 7.404 19252 Z= 0.289 Chirality : 0.046 0.213 2223 Planarity : 0.005 0.113 2509 Dihedral : 4.258 22.894 1985 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.96 % Favored : 87.99 % Rotamer: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % 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: -3.73 (0.18), residues: 1873 helix: -0.11 (0.47), residues: 143 sheet: -2.29 (0.24), residues: 447 loop : -3.04 (0.16), residues: 1283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 474 HIS 0.003 0.001 HIS C 108 PHE 0.016 0.001 PHE C 60 TYR 0.022 0.002 TYR B 465 ARG 0.007 0.000 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 268 time to evaluate : 1.615 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 268 average time/residue: 0.2396 time to fit residues: 96.1955 Evaluate side-chains 218 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 218 time to evaluate : 1.497 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 163 optimal weight: 0.8980 chunk 172 optimal weight: 6.9990 chunk 157 optimal weight: 7.9990 chunk 167 optimal weight: 4.9990 chunk 101 optimal weight: 0.9990 chunk 73 optimal weight: 10.0000 chunk 131 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 151 optimal weight: 2.9990 chunk 158 optimal weight: 9.9990 chunk 110 optimal weight: 6.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 HIS A 445 HIS ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 499 GLN B 23 GLN B 425 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14002 Z= 0.286 Angle : 0.684 7.791 19252 Z= 0.349 Chirality : 0.049 0.217 2223 Planarity : 0.006 0.125 2509 Dihedral : 5.112 25.276 1985 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 16.34 % Favored : 83.61 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.00 (0.18), residues: 1873 helix: -0.45 (0.45), residues: 143 sheet: -2.43 (0.23), residues: 465 loop : -3.23 (0.16), residues: 1265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 474 HIS 0.007 0.001 HIS C 80 PHE 0.022 0.002 PHE B 564 TYR 0.033 0.002 TYR B 465 ARG 0.007 0.001 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 278 time to evaluate : 1.600 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 278 average time/residue: 0.2215 time to fit residues: 93.2021 Evaluate side-chains 212 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 1.605 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 177 optimal weight: 8.9990 chunk 108 optimal weight: 4.9990 chunk 84 optimal weight: 0.0070 chunk 123 optimal weight: 3.9990 chunk 186 optimal weight: 5.9990 chunk 171 optimal weight: 6.9990 chunk 148 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 114 optimal weight: 0.0870 chunk 90 optimal weight: 10.0000 chunk 117 optimal weight: 3.9990 overall best weight: 2.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 HIS ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 499 GLN B 445 HIS ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14002 Z= 0.232 Angle : 0.646 7.781 19252 Z= 0.328 Chirality : 0.048 0.210 2223 Planarity : 0.006 0.122 2509 Dihedral : 4.979 24.916 1985 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.05 % Allowed : 13.35 % Favored : 86.60 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % 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: -3.95 (0.18), residues: 1873 helix: -0.48 (0.44), residues: 145 sheet: -2.57 (0.24), residues: 422 loop : -3.11 (0.16), residues: 1306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 474 HIS 0.006 0.001 HIS C 80 PHE 0.027 0.002 PHE C 467 TYR 0.024 0.002 TYR B 97 ARG 0.007 0.001 ARG A 192 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 266 time to evaluate : 1.636 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 266 average time/residue: 0.2308 time to fit residues: 94.1896 Evaluate side-chains 210 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 210 time to evaluate : 1.533 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 158 optimal weight: 8.9990 chunk 45 optimal weight: 4.9990 chunk 136 optimal weight: 10.0000 chunk 21 optimal weight: 6.9990 chunk 41 optimal weight: 0.0670 chunk 148 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 chunk 152 optimal weight: 7.9990 chunk 18 optimal weight: 10.0000 chunk 27 optimal weight: 0.7980 chunk 130 optimal weight: 2.9990 overall best weight: 3.1724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 HIS A 445 HIS ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 499 GLN B 244 ASN B 439 HIS B 445 HIS C 27 ASN C 107 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.172593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.164715 restraints weight = 17873.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 76)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.154155 restraints weight = 27135.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.151062 restraints weight = 41389.786| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 14002 Z= 0.328 Angle : 0.709 8.007 19252 Z= 0.362 Chirality : 0.050 0.204 2223 Planarity : 0.006 0.127 2509 Dihedral : 5.438 26.394 1985 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.05 % Allowed : 17.62 % Favored : 82.33 % Rotamer: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.18 (0.18), residues: 1873 helix: -0.71 (0.44), residues: 142 sheet: -2.71 (0.22), residues: 478 loop : -3.25 (0.16), residues: 1253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 474 HIS 0.008 0.001 HIS C 80 PHE 0.026 0.002 PHE C 467 TYR 0.040 0.002 TYR B 465 ARG 0.006 0.001 ARG A 192 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2823.26 seconds wall clock time: 52 minutes 3.16 seconds (3123.16 seconds total)