Starting phenix.real_space_refine on Fri Jan 19 06:01:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m5u_30093/01_2024/6m5u_30093_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m5u_30093/01_2024/6m5u_30093.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m5u_30093/01_2024/6m5u_30093.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m5u_30093/01_2024/6m5u_30093.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m5u_30093/01_2024/6m5u_30093_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m5u_30093/01_2024/6m5u_30093_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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: 9 Type Number sf(0) Gaussians Zn 2 6.06 5 P 2 5.49 5 Mg 1 5.21 5 S 47 5.16 5 Be 1 3.05 5 C 6703 2.51 5 N 1893 2.21 5 O 1897 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 42": "NH1" <-> "NH2" Residue "A ASP 68": "OD1" <-> "OD2" Residue "A ARG 96": "NH1" <-> "NH2" Residue "A TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 154": "NH1" <-> "NH2" Residue "A ASP 162": "OD1" <-> "OD2" Residue "A PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 237": "OE1" <-> "OE2" Residue "A ARG 252": "NH1" <-> "NH2" Residue "A ARG 261": "NH1" <-> "NH2" Residue "A TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 299": "OE1" <-> "OE2" Residue "A GLU 320": "OE1" <-> "OE2" Residue "A ASP 328": "OD1" <-> "OD2" Residue "A PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 356": "OD1" <-> "OD2" Residue "A GLU 357": "OE1" <-> "OE2" Residue "A ARG 362": "NH1" <-> "NH2" Residue "A ASP 364": "OD1" <-> "OD2" Residue "A PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 400": "NH1" <-> "NH2" Residue "A ASP 404": "OD1" <-> "OD2" Residue "A TYR 412": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 420": "NH1" <-> "NH2" Residue "A ARG 485": "NH1" <-> "NH2" Residue "A PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 517": "NH1" <-> "NH2" Residue "A GLU 623": "OE1" <-> "OE2" Residue "B GLU 7": "OE1" <-> "OE2" Residue "B ARG 34": "NH1" <-> "NH2" Residue "B ARG 41": "NH1" <-> "NH2" Residue "B ARG 55": "NH1" <-> "NH2" Residue "B ARG 93": "NH1" <-> "NH2" Residue "B ARG 126": "NH1" <-> "NH2" Residue "B ARG 163": "NH1" <-> "NH2" Residue "B GLU 170": "OE1" <-> "OE2" Residue "B ARG 173": "NH1" <-> "NH2" Residue "B GLU 174": "OE1" <-> "OE2" Residue "B ASP 192": "OD1" <-> "OD2" Residue "B GLU 203": "OE1" <-> "OE2" Residue "B ARG 233": "NH1" <-> "NH2" Residue "B ARG 240": "NH1" <-> "NH2" Residue "B ARG 241": "NH1" <-> "NH2" Residue "B TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 254": "NH1" <-> "NH2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "B GLU 310": "OE1" <-> "OE2" Residue "B ARG 338": "NH1" <-> "NH2" Residue "B ARG 339": "NH1" <-> "NH2" Residue "B ARG 358": "NH1" <-> "NH2" Residue "B PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 389": "OD1" <-> "OD2" Residue "B GLU 416": "OE1" <-> "OE2" Residue "B ARG 425": "NH1" <-> "NH2" Residue "B GLU 498": "OE1" <-> "OE2" Residue "B ARG 501": "NH1" <-> "NH2" Residue "B TYR 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 505": "OD1" <-> "OD2" Residue "B ARG 517": "NH1" <-> "NH2" Residue "B ARG 523": "NH1" <-> "NH2" Residue "B ARG 531": "NH1" <-> "NH2" Residue "B GLU 537": "OE1" <-> "OE2" Residue "B PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 577": "OD1" <-> "OD2" Residue "B ARG 583": "NH1" <-> "NH2" Residue "B PHE 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 613": "OD1" <-> "OD2" Residue "B PHE 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 642": "OE1" <-> "OE2" Residue "B PHE 669": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 687": "NH1" <-> "NH2" Residue "B TYR 700": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 704": "OE1" <-> "OE2" Residue "B GLU 706": "OE1" <-> "OE2" Residue "B ARG 722": "NH1" <-> "NH2" Residue "C ASP 31": "OD1" <-> "OD2" Residue "C TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 54": "OE1" <-> "OE2" Residue "C ARG 111": "NH1" <-> "NH2" Residue "C ARG 113": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 10549 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 4482 Classifications: {'peptide': 585} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 29, 'TRANS': 555} Chain breaks: 7 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 6, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 84 Chain: "B" Number of atoms: 5208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 670, 5208 Classifications: {'peptide': 670} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 33, 'TRANS': 636} Chain breaks: 4 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 825 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 99} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5415 SG CYS B 121 28.952 52.885 52.444 1.00 47.42 S ATOM 10277 SG CYS C 101 27.583 53.204 55.790 1.00 59.52 S ATOM 6010 SG CYS B 197 51.114 57.002 49.253 1.00 43.06 S ATOM 6028 SG CYS B 200 52.928 58.057 52.017 1.00 41.30 S Time building chain proxies: 6.17, per 1000 atoms: 0.58 Number of scatterers: 10549 At special positions: 0 Unit cell: (108.324, 108.324, 118.944, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 2 29.99 S 47 16.00 P 2 15.00 Mg 1 11.99 F 3 9.00 O 1897 8.00 N 1893 7.00 C 6703 6.00 Be 1 4.00 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: 4.32 Conformation dependent library (CDL) restraints added in 1.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 801 " pdb="ZN ZN B 801 " - pdb=" SG CYS B 121 " pdb="ZN ZN B 801 " - pdb=" SG CYS C 101 " pdb=" ZN B 802 " pdb="ZN ZN B 802 " - pdb=" SG CYS B 200 " pdb="ZN ZN B 802 " - pdb=" SG CYS B 197 " 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2566 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 50 helices and 4 sheets defined 47.1% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.15 Creating SS restraints... Processing helix chain 'A' and resid 68 through 71 Processing helix chain 'A' and resid 74 through 80 removed outlier: 4.299A pdb=" N VAL A 79 " --> pdb=" O LEU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 88 removed outlier: 4.817A pdb=" N SER A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LEU A 88 " --> pdb=" O LEU A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 117 Processing helix chain 'A' and resid 130 through 148 Processing helix chain 'A' and resid 151 through 169 removed outlier: 3.741A pdb=" N ASP A 162 " --> pdb=" O HIS A 158 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N THR A 169 " --> pdb=" O GLN A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 220 removed outlier: 4.173A pdb=" N LEU A 209 " --> pdb=" O GLN A 205 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE A 215 " --> pdb=" O HIS A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 235 Processing helix chain 'A' and resid 243 through 250 Processing helix chain 'A' and resid 265 through 277 removed outlier: 3.710A pdb=" N VAL A 269 " --> pdb=" O THR A 265 " (cutoff:3.500A) Proline residue: A 270 - end of helix Processing helix chain 'A' and resid 295 through 308 Processing helix chain 'A' and resid 366 through 374 removed outlier: 4.245A pdb=" N ASN A 374 " --> pdb=" O MET A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 488 Processing helix chain 'A' and resid 497 through 499 No H-bonds generated for 'chain 'A' and resid 497 through 499' Processing helix chain 'A' and resid 550 through 569 Processing helix chain 'A' and resid 586 through 601 Processing helix chain 'A' and resid 639 through 653 Processing helix chain 'A' and resid 673 through 683 removed outlier: 3.974A pdb=" N ASN A 683 " --> pdb=" O GLU A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 718 Processing helix chain 'B' and resid 7 through 32 Processing helix chain 'B' and resid 37 through 40 No H-bonds generated for 'chain 'B' and resid 37 through 40' Processing helix chain 'B' and resid 44 through 57 Processing helix chain 'B' and resid 62 through 69 Processing helix chain 'B' and resid 75 through 100 Processing helix chain 'B' and resid 107 through 114 Processing helix chain 'B' and resid 143 through 157 Processing helix chain 'B' and resid 162 through 179 removed outlier: 3.818A pdb=" N PHE B 175 " --> pdb=" O ARG B 171 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLY B 178 " --> pdb=" O GLU B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 190 No H-bonds generated for 'chain 'B' and resid 188 through 190' Processing helix chain 'B' and resid 198 through 204 removed outlier: 3.577A pdb=" N GLU B 202 " --> pdb=" O ALA B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 216 No H-bonds generated for 'chain 'B' and resid 214 through 216' Processing helix chain 'B' and resid 238 through 243 removed outlier: 3.525A pdb=" N TYR B 242 " --> pdb=" O GLU B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 264 Processing helix chain 'B' and resid 308 through 311 Processing helix chain 'B' and resid 325 through 354 Processing helix chain 'B' and resid 375 through 380 Processing helix chain 'B' and resid 388 through 399 removed outlier: 3.868A pdb=" N ALA B 398 " --> pdb=" O ALA B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 413 Processing helix chain 'B' and resid 415 through 428 Processing helix chain 'B' and resid 486 through 509 removed outlier: 3.557A pdb=" N LEU B 502 " --> pdb=" O GLU B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 530 removed outlier: 3.542A pdb=" N MET B 529 " --> pdb=" O GLU B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 559 removed outlier: 3.741A pdb=" N GLY B 549 " --> pdb=" O ALA B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 586 removed outlier: 3.892A pdb=" N PHE B 581 " --> pdb=" O ASP B 577 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N MET B 582 " --> pdb=" O ALA B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 593 through 607 Proline residue: B 597 - end of helix removed outlier: 4.767A pdb=" N THR B 600 " --> pdb=" O PRO B 597 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N PHE B 603 " --> pdb=" O THR B 600 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N GLU B 605 " --> pdb=" O ARG B 602 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL B 607 " --> pdb=" O PHE B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 632 removed outlier: 3.911A pdb=" N SER B 630 " --> pdb=" O ALA B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 647 removed outlier: 3.643A pdb=" N GLU B 642 " --> pdb=" O PRO B 638 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N GLU B 643 " --> pdb=" O HIS B 639 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU B 644 " --> pdb=" O LEU B 640 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA B 645 " --> pdb=" O LYS B 641 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N PHE B 647 " --> pdb=" O GLU B 643 " (cutoff:3.500A) Processing helix chain 'B' and resid 676 through 699 Processing helix chain 'B' and resid 761 through 771 removed outlier: 3.700A pdb=" N LEU B 769 " --> pdb=" O LEU B 765 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 34 Processing helix chain 'C' and resid 62 through 79 removed outlier: 3.628A pdb=" N LEU C 78 " --> pdb=" O ARG C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 127 removed outlier: 3.739A pdb=" N ALA C 116 " --> pdb=" O GLU C 112 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N HIS C 125 " --> pdb=" O PHE C 121 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 381 through 386 removed outlier: 7.623A pdb=" N THR A 254 " --> pdb=" O PHE A 382 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N SER A 384 " --> pdb=" O THR A 254 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N PHE A 256 " --> pdb=" O SER A 384 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N THR A 386 " --> pdb=" O PHE A 256 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL A 258 " --> pdb=" O THR A 386 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU A 257 " --> pdb=" O ASN A 408 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 314 through 316 Processing sheet with id= C, first strand: chain 'A' and resid 656 through 658 removed outlier: 6.227A pdb=" N TYR A 533 " --> pdb=" O MET A 657 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL A 525 " --> pdb=" O PHE A 536 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LEU A 538 " --> pdb=" O VAL A 523 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N VAL A 523 " --> pdb=" O LEU A 538 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N HIS A 540 " --> pdb=" O THR A 521 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N THR A 521 " --> pdb=" O HIS A 540 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ARG A 528 " --> pdb=" O ASP A 503 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ASP A 503 " --> pdb=" O ARG A 528 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLY A 575 " --> pdb=" O LEU A 504 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N VAL A 506 " --> pdb=" O GLY A 575 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ARG A 577 " --> pdb=" O VAL A 506 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N VAL A 508 " --> pdb=" O ARG A 577 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ALA A 579 " --> pdb=" O VAL A 508 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N GLU A 616 " --> pdb=" O VAL A 576 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N VAL A 578 " --> pdb=" O GLU A 616 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU A 618 " --> pdb=" O VAL A 578 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N VAL A 580 " --> pdb=" O LEU A 618 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 726 through 728 removed outlier: 3.693A pdb=" N VAL B 738 " --> pdb=" O TYR B 728 " (cutoff:3.500A) 426 hydrogen bonds defined for protein. 1248 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.67 Time building geometry restraints manager: 4.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1691 1.30 - 1.43: 2871 1.43 - 1.56: 6133 1.56 - 1.68: 13 1.68 - 1.81: 68 Bond restraints: 10776 Sorted by residual: bond pdb=" BE BEF A 802 " pdb=" F3 BEF A 802 " ideal model delta sigma weight residual 1.476 1.765 -0.289 2.00e-02 2.50e+03 2.08e+02 bond pdb=" BE BEF A 802 " pdb=" F1 BEF A 802 " ideal model delta sigma weight residual 1.476 1.764 -0.288 2.00e-02 2.50e+03 2.08e+02 bond pdb=" BE BEF A 802 " pdb=" F2 BEF A 802 " ideal model delta sigma weight residual 1.476 1.764 -0.288 2.00e-02 2.50e+03 2.08e+02 bond pdb=" C ALA A 482 " pdb=" O ALA A 482 " ideal model delta sigma weight residual 1.237 1.172 0.065 1.17e-02 7.31e+03 3.05e+01 bond pdb=" C4 ADP A 801 " pdb=" C5 ADP A 801 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.00e+01 ... (remaining 10771 not shown) Histogram of bond angle deviations from ideal: 98.57 - 105.65: 253 105.65 - 112.72: 5686 112.72 - 119.80: 3405 119.80 - 126.88: 5165 126.88 - 133.96: 134 Bond angle restraints: 14643 Sorted by residual: angle pdb=" C CYS A 125 " pdb=" N ALA A 126 " pdb=" CA ALA A 126 " ideal model delta sigma weight residual 122.52 130.41 -7.89 1.16e+00 7.43e-01 4.62e+01 angle pdb=" N VAL A 477 " pdb=" CA VAL A 477 " pdb=" C VAL A 477 " ideal model delta sigma weight residual 110.36 115.77 -5.41 1.05e+00 9.07e-01 2.65e+01 angle pdb=" N CYS A 125 " pdb=" CA CYS A 125 " pdb=" C CYS A 125 " ideal model delta sigma weight residual 108.42 116.07 -7.65 1.54e+00 4.22e-01 2.47e+01 angle pdb=" N ARG B 59 " pdb=" CA ARG B 59 " pdb=" C ARG B 59 " ideal model delta sigma weight residual 114.56 108.46 6.10 1.27e+00 6.20e-01 2.31e+01 angle pdb=" N SER A 481 " pdb=" CA SER A 481 " pdb=" C SER A 481 " ideal model delta sigma weight residual 111.07 106.37 4.70 1.07e+00 8.73e-01 1.93e+01 ... (remaining 14638 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.49: 5926 23.49 - 46.98: 417 46.98 - 70.47: 62 70.47 - 93.95: 12 93.95 - 117.44: 2 Dihedral angle restraints: 6419 sinusoidal: 2471 harmonic: 3948 Sorted by residual: dihedral pdb=" O2A ADP A 801 " pdb=" O3A ADP A 801 " pdb=" PA ADP A 801 " pdb=" PB ADP A 801 " ideal model delta sinusoidal sigma weight residual -60.00 57.44 -117.44 1 2.00e+01 2.50e-03 3.51e+01 dihedral pdb=" CA CYS B 223 " pdb=" C CYS B 223 " pdb=" N ASN B 224 " pdb=" CA ASN B 224 " ideal model delta harmonic sigma weight residual 180.00 152.95 27.05 0 5.00e+00 4.00e-02 2.93e+01 dihedral pdb=" C5' ADP A 801 " pdb=" O5' ADP A 801 " pdb=" PA ADP A 801 " pdb=" O2A ADP A 801 " ideal model delta sinusoidal sigma weight residual -60.00 37.48 -97.48 1 2.00e+01 2.50e-03 2.71e+01 ... (remaining 6416 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1474 0.074 - 0.147: 181 0.147 - 0.221: 21 0.221 - 0.294: 4 0.294 - 0.368: 1 Chirality restraints: 1681 Sorted by residual: chirality pdb=" CA VAL A 558 " pdb=" N VAL A 558 " pdb=" C VAL A 558 " pdb=" CB VAL A 558 " both_signs ideal model delta sigma weight residual False 2.44 2.07 0.37 2.00e-01 2.50e+01 3.39e+00 chirality pdb=" CA HIS B 535 " pdb=" N HIS B 535 " pdb=" C HIS B 535 " pdb=" CB HIS B 535 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CA VAL A 663 " pdb=" N VAL A 663 " pdb=" C VAL A 663 " pdb=" CB VAL A 663 " both_signs ideal model delta sigma weight residual False 2.44 2.71 -0.26 2.00e-01 2.50e+01 1.74e+00 ... (remaining 1678 not shown) Planarity restraints: 1892 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR B 242 " -0.016 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" C TYR B 242 " 0.057 2.00e-02 2.50e+03 pdb=" O TYR B 242 " -0.021 2.00e-02 2.50e+03 pdb=" N LEU B 243 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 534 " 0.013 2.00e-02 2.50e+03 2.57e-02 6.60e+00 pdb=" C VAL B 534 " -0.044 2.00e-02 2.50e+03 pdb=" O VAL B 534 " 0.017 2.00e-02 2.50e+03 pdb=" N HIS B 535 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 724 " 0.036 5.00e-02 4.00e+02 5.48e-02 4.81e+00 pdb=" N PRO A 725 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 725 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 725 " 0.030 5.00e-02 4.00e+02 ... (remaining 1889 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1406 2.75 - 3.29: 10649 3.29 - 3.82: 17501 3.82 - 4.36: 20322 4.36 - 4.90: 34879 Nonbonded interactions: 84757 Sorted by model distance: nonbonded pdb=" O CYS B 223 " pdb=" ND1 HIS B 225 " model vdw 2.210 2.520 nonbonded pdb=" O CYS C 101 " pdb=" N GLY C 104 " model vdw 2.224 2.520 nonbonded pdb=" NE2 HIS B 157 " pdb=" O ASN B 608 " model vdw 2.269 2.520 nonbonded pdb=" O SER B 713 " pdb=" OG SER B 713 " model vdw 2.279 2.440 nonbonded pdb=" O GLY A 654 " pdb=" NH1 ARG C 120 " model vdw 2.281 2.520 ... (remaining 84752 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.060 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: 3.980 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 32.770 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.289 10776 Z= 0.496 Angle : 0.862 10.800 14643 Z= 0.537 Chirality : 0.051 0.368 1681 Planarity : 0.005 0.055 1892 Dihedral : 16.072 117.442 3853 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 18.52 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.03 % Favored : 90.82 % Rotamer: Outliers : 5.59 % Allowed : 16.68 % Favored : 77.73 % Cbeta Deviations : 0.08 % 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: -3.03 (0.21), residues: 1329 helix: -1.01 (0.18), residues: 692 sheet: -1.77 (0.52), residues: 92 loop : -3.41 (0.23), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 308 HIS 0.009 0.001 HIS A 540 PHE 0.023 0.002 PHE A 634 TYR 0.019 0.002 TYR A 507 ARG 0.005 0.000 ARG A 528 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 217 time to evaluate : 1.265 Fit side-chains REVERT: A 165 GLN cc_start: 0.8679 (tp-100) cc_final: 0.8454 (tp40) REVERT: A 372 PHE cc_start: 0.7409 (m-80) cc_final: 0.6876 (m-80) REVERT: B 222 ILE cc_start: 0.8481 (OUTLIER) cc_final: 0.8263 (mm) REVERT: B 529 MET cc_start: 0.8908 (tpp) cc_final: 0.8704 (tpt) REVERT: B 617 HIS cc_start: 0.9138 (OUTLIER) cc_final: 0.8910 (m170) REVERT: C 50 MET cc_start: 0.7759 (mtp) cc_final: 0.7558 (mtp) REVERT: C 54 GLU cc_start: 0.8239 (mp0) cc_final: 0.7640 (mp0) outliers start: 61 outliers final: 41 residues processed: 265 average time/residue: 0.2950 time to fit residues: 105.7824 Evaluate side-chains 202 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 159 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 156 CYS Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 617 HIS Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 748 CYS Chi-restraints excluded: chain B residue 761 VAL Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 98 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 0.0570 chunk 102 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 64 optimal weight: 0.4980 chunk 78 optimal weight: 1.9990 chunk 122 optimal weight: 8.9990 overall best weight: 1.0502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 HIS ** A 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 135 ASN A 211 HIS A 224 HIS A 374 ASN A 377 ASN A 583 ASN A 670 GLN B 68 GLN B 124 HIS B 210 GLN B 224 ASN B 229 GLN B 237 ASN B 323 GLN B 621 GLN B 624 ASN B 679 GLN B 770 GLN C 119 ASN C 126 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10776 Z= 0.212 Angle : 0.648 9.341 14643 Z= 0.319 Chirality : 0.041 0.189 1681 Planarity : 0.004 0.045 1892 Dihedral : 8.612 128.630 1564 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.43 % Favored : 91.50 % Rotamer: Outliers : 5.13 % Allowed : 20.81 % Favored : 74.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.23), residues: 1329 helix: 0.24 (0.20), residues: 685 sheet: -1.38 (0.52), residues: 94 loop : -2.77 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 308 HIS 0.006 0.001 HIS B 535 PHE 0.019 0.001 PHE A 633 TYR 0.010 0.001 TYR A 533 ARG 0.004 0.000 ARG A 250 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 173 time to evaluate : 1.160 Fit side-chains REVERT: A 115 ARG cc_start: 0.8399 (mtm-85) cc_final: 0.8057 (mtp85) REVERT: A 149 ARG cc_start: 0.7735 (mtm-85) cc_final: 0.7206 (ptp-110) REVERT: A 165 GLN cc_start: 0.8690 (tp-100) cc_final: 0.8465 (tp40) REVERT: A 240 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8391 (pp) REVERT: A 541 PHE cc_start: 0.7506 (t80) cc_final: 0.7005 (t80) REVERT: A 709 MET cc_start: 0.6728 (OUTLIER) cc_final: 0.6350 (ttp) REVERT: B 521 GLU cc_start: 0.7775 (mt-10) cc_final: 0.7546 (tp30) REVERT: B 582 MET cc_start: 0.8200 (tpp) cc_final: 0.7826 (tpp) REVERT: B 662 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7407 (tm-30) REVERT: B 714 ARG cc_start: 0.8539 (mtp85) cc_final: 0.8273 (mtt-85) REVERT: B 722 ARG cc_start: 0.8682 (ptp90) cc_final: 0.8457 (ptp90) outliers start: 56 outliers final: 32 residues processed: 210 average time/residue: 0.2316 time to fit residues: 68.4713 Evaluate side-chains 189 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 154 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 557 CYS Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain B residue 374 ASP Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 495 ASP Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 535 HIS Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 662 GLU Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 761 VAL Chi-restraints excluded: chain B residue 764 ILE Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 45 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 68 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 chunk 132 optimal weight: 6.9990 chunk 109 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 ASN B 237 ASN ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 624 ASN B 770 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 10776 Z= 0.277 Angle : 0.631 8.649 14643 Z= 0.313 Chirality : 0.041 0.195 1681 Planarity : 0.004 0.047 1892 Dihedral : 7.310 128.050 1527 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.88 % Favored : 91.05 % Rotamer: Outliers : 6.05 % Allowed : 21.26 % Favored : 72.69 % 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: -1.15 (0.24), residues: 1329 helix: 0.66 (0.21), residues: 682 sheet: -1.05 (0.61), residues: 74 loop : -2.59 (0.26), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 308 HIS 0.005 0.001 HIS B 535 PHE 0.022 0.001 PHE A 633 TYR 0.008 0.001 TYR B 503 ARG 0.004 0.000 ARG B 506 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 165 time to evaluate : 1.188 Fit side-chains revert: symmetry clash REVERT: A 115 ARG cc_start: 0.8356 (mtm-85) cc_final: 0.8021 (mtp85) REVERT: A 124 GLU cc_start: 0.7076 (OUTLIER) cc_final: 0.6815 (pm20) REVERT: A 149 ARG cc_start: 0.7673 (mtm-85) cc_final: 0.7193 (ptp-110) REVERT: A 165 GLN cc_start: 0.8641 (tp-100) cc_final: 0.8397 (tp40) REVERT: A 240 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8344 (pp) REVERT: A 525 VAL cc_start: 0.9098 (m) cc_final: 0.8875 (p) REVERT: B 138 MET cc_start: 0.8398 (ptp) cc_final: 0.8194 (pmm) REVERT: B 202 GLU cc_start: 0.8248 (mt-10) cc_final: 0.8047 (mt-10) REVERT: B 582 MET cc_start: 0.8244 (tpp) cc_final: 0.7882 (tpp) REVERT: B 662 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7366 (tm-30) REVERT: B 714 ARG cc_start: 0.8550 (mtp85) cc_final: 0.8224 (mtt-85) outliers start: 66 outliers final: 39 residues processed: 212 average time/residue: 0.2173 time to fit residues: 66.2175 Evaluate side-chains 193 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 151 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 557 CYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 601 HIS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain B residue 374 ASP Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 495 ASP Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 662 GLU Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 761 VAL Chi-restraints excluded: chain B residue 764 ILE Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 98 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 121 optimal weight: 0.9980 chunk 92 optimal weight: 8.9990 chunk 63 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 chunk 58 optimal weight: 0.9990 chunk 82 optimal weight: 7.9990 chunk 123 optimal weight: 0.7980 chunk 130 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 116 optimal weight: 0.5980 chunk 35 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 ASN B 237 ASN B 770 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 10776 Z= 0.189 Angle : 0.587 7.914 14643 Z= 0.291 Chirality : 0.040 0.208 1681 Planarity : 0.004 0.049 1892 Dihedral : 6.925 128.334 1523 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer: Outliers : 5.96 % Allowed : 22.82 % Favored : 71.22 % 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: -0.81 (0.24), residues: 1329 helix: 0.98 (0.21), residues: 681 sheet: -1.11 (0.56), residues: 84 loop : -2.46 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 658 HIS 0.005 0.001 HIS B 535 PHE 0.019 0.001 PHE A 633 TYR 0.008 0.001 TYR B 721 ARG 0.003 0.000 ARG B 722 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 168 time to evaluate : 1.192 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 ARG cc_start: 0.8388 (mtm-85) cc_final: 0.7981 (mtp85) REVERT: A 141 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.7921 (mp) REVERT: A 149 ARG cc_start: 0.7587 (mtm-85) cc_final: 0.7113 (ptp-110) REVERT: A 165 GLN cc_start: 0.8604 (tp-100) cc_final: 0.8385 (tp40) REVERT: A 240 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8315 (pp) REVERT: A 252 ARG cc_start: 0.7853 (ptm160) cc_final: 0.7639 (ptm160) REVERT: A 525 VAL cc_start: 0.9044 (m) cc_final: 0.8826 (p) REVERT: A 541 PHE cc_start: 0.7017 (t80) cc_final: 0.6700 (t80) REVERT: B 72 PHE cc_start: 0.8611 (t80) cc_final: 0.8395 (t80) REVERT: B 582 MET cc_start: 0.8213 (tpp) cc_final: 0.7880 (tpp) REVERT: B 662 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7319 (tm-30) REVERT: B 714 ARG cc_start: 0.8517 (mtp85) cc_final: 0.8065 (mtt-85) outliers start: 65 outliers final: 43 residues processed: 215 average time/residue: 0.2173 time to fit residues: 66.4048 Evaluate side-chains 198 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 152 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 601 HIS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 374 ASP Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 491 GLN Chi-restraints excluded: chain B residue 495 ASP Chi-restraints excluded: chain B residue 535 HIS Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 662 GLU Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 761 VAL Chi-restraints excluded: chain B residue 764 ILE Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 102 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 108 optimal weight: 0.8980 chunk 74 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 66 optimal weight: 0.9990 chunk 117 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 21 GLN B 224 ASN B 237 ASN B 624 ASN B 770 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10776 Z= 0.227 Angle : 0.599 7.875 14643 Z= 0.295 Chirality : 0.040 0.219 1681 Planarity : 0.004 0.051 1892 Dihedral : 6.821 129.075 1521 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer: Outliers : 6.05 % Allowed : 23.65 % Favored : 70.30 % 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: -0.69 (0.24), residues: 1329 helix: 1.09 (0.21), residues: 681 sheet: -1.32 (0.52), residues: 94 loop : -2.37 (0.27), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 308 HIS 0.005 0.001 HIS B 535 PHE 0.019 0.001 PHE A 633 TYR 0.006 0.001 TYR B 503 ARG 0.002 0.000 ARG B 506 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 158 time to evaluate : 1.396 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 ARG cc_start: 0.8420 (mtm-85) cc_final: 0.7994 (mtp85) REVERT: A 149 ARG cc_start: 0.7611 (mtm-85) cc_final: 0.7149 (ptp-110) REVERT: A 165 GLN cc_start: 0.8574 (tp-100) cc_final: 0.8327 (tp40) REVERT: A 240 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8287 (pp) REVERT: B 21 GLN cc_start: 0.8176 (OUTLIER) cc_final: 0.7819 (mt0) REVERT: B 72 PHE cc_start: 0.8605 (t80) cc_final: 0.8342 (t80) REVERT: B 582 MET cc_start: 0.8203 (tpp) cc_final: 0.7888 (tpp) REVERT: B 642 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7752 (pm20) REVERT: B 662 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7292 (tm-30) REVERT: B 714 ARG cc_start: 0.8536 (mtp85) cc_final: 0.8048 (mtt-85) outliers start: 66 outliers final: 53 residues processed: 207 average time/residue: 0.2297 time to fit residues: 68.1340 Evaluate side-chains 207 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 150 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 557 CYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 601 HIS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain B residue 21 GLN Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 195 HIS Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 374 ASP Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 384 GLN Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 491 GLN Chi-restraints excluded: chain B residue 495 ASP Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 642 GLU Chi-restraints excluded: chain B residue 662 GLU Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 761 VAL Chi-restraints excluded: chain B residue 764 ILE Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 102 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 43 optimal weight: 0.3980 chunk 117 optimal weight: 0.0010 chunk 25 optimal weight: 0.9990 chunk 76 optimal weight: 0.0170 chunk 32 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 108 optimal weight: 0.6980 chunk 60 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 125 optimal weight: 0.0980 overall best weight: 0.2424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 ASN B 770 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10776 Z= 0.147 Angle : 0.580 7.820 14643 Z= 0.282 Chirality : 0.039 0.182 1681 Planarity : 0.004 0.051 1892 Dihedral : 6.497 127.566 1520 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 5.41 % Allowed : 25.48 % Favored : 69.11 % 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: -0.57 (0.24), residues: 1329 helix: 1.13 (0.21), residues: 698 sheet: -0.64 (0.59), residues: 76 loop : -2.41 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 658 HIS 0.005 0.001 HIS B 535 PHE 0.018 0.001 PHE A 298 TYR 0.008 0.001 TYR B 721 ARG 0.004 0.000 ARG B 588 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 162 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 141 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7759 (mp) REVERT: A 149 ARG cc_start: 0.7575 (mtm-85) cc_final: 0.7130 (ptp-110) REVERT: A 165 GLN cc_start: 0.8429 (tp-100) cc_final: 0.8195 (tp40) REVERT: A 240 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8276 (pp) REVERT: B 582 MET cc_start: 0.8375 (tpp) cc_final: 0.7694 (tpp) REVERT: B 642 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7740 (pm20) REVERT: B 662 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7349 (tm-30) REVERT: B 714 ARG cc_start: 0.8458 (mtp85) cc_final: 0.8033 (mtt-85) outliers start: 59 outliers final: 41 residues processed: 205 average time/residue: 0.2279 time to fit residues: 66.0828 Evaluate side-chains 194 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 149 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 557 CYS Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 601 HIS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 491 GLN Chi-restraints excluded: chain B residue 495 ASP Chi-restraints excluded: chain B residue 535 HIS Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 642 GLU Chi-restraints excluded: chain B residue 662 GLU Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 761 VAL Chi-restraints excluded: chain B residue 764 ILE Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 98 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 14 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 95 optimal weight: 6.9990 chunk 73 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 130 optimal weight: 0.8980 chunk 81 optimal weight: 0.1980 chunk 79 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 80 optimal weight: 0.1980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 ASN B 624 ASN B 770 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10776 Z= 0.159 Angle : 0.575 7.562 14643 Z= 0.280 Chirality : 0.039 0.239 1681 Planarity : 0.004 0.054 1892 Dihedral : 6.128 126.248 1515 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 5.04 % Allowed : 26.40 % Favored : 68.56 % 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: -0.33 (0.24), residues: 1329 helix: 1.35 (0.21), residues: 688 sheet: -0.75 (0.56), residues: 86 loop : -2.26 (0.27), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 658 HIS 0.005 0.001 HIS B 535 PHE 0.020 0.001 PHE B 72 TYR 0.006 0.001 TYR B 721 ARG 0.007 0.000 ARG A 115 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 161 time to evaluate : 1.474 Fit side-chains REVERT: A 124 GLU cc_start: 0.7051 (OUTLIER) cc_final: 0.6677 (pm20) REVERT: A 149 ARG cc_start: 0.7578 (mtm-85) cc_final: 0.7150 (ptp-110) REVERT: A 165 GLN cc_start: 0.8324 (tp-100) cc_final: 0.8084 (tp40) REVERT: B 582 MET cc_start: 0.8342 (tpp) cc_final: 0.7698 (tpp) REVERT: B 638 PRO cc_start: 0.8865 (Cg_endo) cc_final: 0.8617 (Cg_exo) REVERT: B 642 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7752 (pm20) REVERT: B 662 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7296 (tm-30) REVERT: B 714 ARG cc_start: 0.8265 (mtp85) cc_final: 0.7936 (mtt-85) outliers start: 55 outliers final: 39 residues processed: 201 average time/residue: 0.2284 time to fit residues: 66.3095 Evaluate side-chains 192 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 150 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 264 LYS Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 557 CYS Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 195 HIS Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 491 GLN Chi-restraints excluded: chain B residue 495 ASP Chi-restraints excluded: chain B residue 535 HIS Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 642 GLU Chi-restraints excluded: chain B residue 662 GLU Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 761 VAL Chi-restraints excluded: chain B residue 764 ILE Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 98 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.277 > 50: distance: 78 - 82: 22.080 distance: 82 - 83: 11.347 distance: 83 - 84: 21.303 distance: 83 - 86: 30.379 distance: 84 - 85: 19.084 distance: 84 - 88: 17.488 distance: 86 - 87: 28.128 distance: 88 - 89: 9.706 distance: 89 - 90: 61.338 distance: 90 - 91: 10.440 distance: 90 - 92: 36.542 distance: 92 - 93: 28.325 distance: 93 - 94: 32.550 distance: 93 - 96: 14.672 distance: 94 - 101: 35.651 distance: 96 - 97: 28.786 distance: 97 - 98: 5.099 distance: 98 - 99: 31.329 distance: 101 - 102: 18.474 distance: 102 - 103: 25.948 distance: 102 - 105: 33.922 distance: 103 - 104: 16.905 distance: 103 - 109: 32.851 distance: 105 - 106: 14.949 distance: 106 - 107: 11.977 distance: 106 - 108: 34.075 distance: 109 - 110: 20.751 distance: 110 - 111: 10.407 distance: 110 - 113: 25.022 distance: 111 - 112: 34.770 distance: 111 - 118: 18.279 distance: 113 - 114: 8.082 distance: 114 - 115: 43.327 distance: 115 - 116: 5.212 distance: 115 - 117: 12.800 distance: 118 - 119: 9.064 distance: 119 - 120: 28.032 distance: 119 - 122: 18.661 distance: 120 - 121: 4.220 distance: 120 - 126: 10.072 distance: 122 - 123: 24.670 distance: 123 - 124: 21.110 distance: 123 - 125: 22.160 distance: 126 - 127: 47.495 distance: 127 - 128: 20.057 distance: 127 - 130: 15.173 distance: 128 - 129: 19.830 distance: 128 - 137: 45.243 distance: 130 - 131: 19.723 distance: 132 - 133: 15.484 distance: 133 - 134: 17.530 distance: 134 - 135: 23.817 distance: 134 - 136: 19.051 distance: 137 - 138: 27.903 distance: 138 - 139: 11.891 distance: 138 - 141: 23.367 distance: 139 - 140: 13.087 distance: 139 - 148: 18.224 distance: 141 - 142: 42.221 distance: 142 - 143: 11.138 distance: 143 - 144: 29.534 distance: 144 - 145: 9.724 distance: 145 - 146: 18.240 distance: 145 - 147: 27.711 distance: 148 - 149: 10.684 distance: 148 - 154: 37.572 distance: 149 - 150: 9.741 distance: 149 - 152: 22.835 distance: 150 - 155: 19.253 distance: 152 - 153: 20.011 distance: 155 - 156: 23.212 distance: 156 - 157: 16.383 distance: 156 - 159: 47.811 distance: 157 - 158: 10.839 distance: 157 - 163: 26.173 distance: 159 - 160: 6.754 distance: 160 - 161: 40.576