Starting phenix.real_space_refine on Sat Dec 9 08:35:05 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m5u_30093/12_2023/6m5u_30093_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m5u_30093/12_2023/6m5u_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_30093/12_2023/6m5u_30093.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m5u_30093/12_2023/6m5u_30093.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m5u_30093/12_2023/6m5u_30093_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m5u_30093/12_2023/6m5u_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-1.21rc1-5172/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: 6.29, per 1000 atoms: 0.60 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: 2.48 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: 2.85 Time building geometry restraints manager: 4.60 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: 1.500 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: 4.000 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 34.360 Find NCS groups from input model: 0.370 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: 0.010 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.560 ------------------------------------------------------------------------------- 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 : 1.109 Fit side-chains outliers start: 61 outliers final: 41 residues processed: 265 average time/residue: 0.2793 time to fit residues: 99.4241 Evaluate side-chains 199 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 158 time to evaluate : 1.083 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 0 residues processed: 41 average time/residue: 0.1020 time to fit residues: 9.3528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 105 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 chunk 64 optimal weight: 0.4980 chunk 78 optimal weight: 1.9990 chunk 122 optimal weight: 7.9990 overall best weight: 1.2502 ------------------------------------------------------------------------------- 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 165 GLN 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 125 GLN B 210 GLN B 224 ASN B 229 GLN B 237 ASN B 323 GLN B 617 HIS 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: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10776 Z= 0.233 Angle : 0.672 9.915 14643 Z= 0.328 Chirality : 0.041 0.193 1681 Planarity : 0.004 0.046 1892 Dihedral : 6.677 129.710 1501 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.88 % Favored : 91.05 % Rotamer: Outliers : 3.21 % Allowed : 20.99 % Favored : 75.80 % 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: -1.64 (0.23), residues: 1329 helix: 0.21 (0.20), residues: 685 sheet: -1.40 (0.53), residues: 94 loop : -2.78 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 308 HIS 0.007 0.001 HIS B 535 PHE 0.020 0.002 PHE A 372 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 209 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 174 time to evaluate : 1.191 Fit side-chains outliers start: 35 outliers final: 15 residues processed: 197 average time/residue: 0.2430 time to fit residues: 66.9281 Evaluate side-chains 165 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 150 time to evaluate : 1.373 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.0992 time to fit residues: 4.3804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 68 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 122 optimal weight: 9.9990 chunk 132 optimal weight: 10.0000 chunk 109 optimal weight: 0.9980 chunk 121 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 ASN B 224 ASN B 229 GLN B 237 ASN B 624 ASN B 770 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10776 Z= 0.193 Angle : 0.607 10.441 14643 Z= 0.299 Chirality : 0.040 0.200 1681 Planarity : 0.004 0.045 1892 Dihedral : 6.115 127.260 1501 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.43 % Favored : 91.50 % Rotamer: Outliers : 3.67 % Allowed : 21.08 % Favored : 75.25 % 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: -0.98 (0.24), residues: 1329 helix: 0.81 (0.21), residues: 679 sheet: -0.54 (0.66), residues: 64 loop : -2.54 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 658 HIS 0.004 0.001 HIS B 535 PHE 0.019 0.001 PHE A 633 TYR 0.008 0.001 TYR B 721 ARG 0.006 0.000 ARG B 714 *********************** 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 211 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 171 time to evaluate : 1.160 Fit side-chains outliers start: 40 outliers final: 18 residues processed: 198 average time/residue: 0.2308 time to fit residues: 65.0938 Evaluate side-chains 171 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 153 time to evaluate : 1.152 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1027 time to fit residues: 5.0286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 121 optimal weight: 3.9990 chunk 92 optimal weight: 0.5980 chunk 63 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 58 optimal weight: 0.0010 chunk 82 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 116 optimal weight: 2.9990 chunk 35 optimal weight: 9.9990 overall best weight: 1.1192 ------------------------------------------------------------------------------- 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 229 GLN B 237 ASN B 770 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.2225 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= 0.210 Angle : 0.615 8.992 14643 Z= 0.302 Chirality : 0.040 0.208 1681 Planarity : 0.004 0.050 1892 Dihedral : 5.976 128.737 1501 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.95 % Favored : 90.97 % Rotamer: Outliers : 2.29 % Allowed : 24.20 % Favored : 73.51 % 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: -0.74 (0.24), residues: 1329 helix: 1.01 (0.21), residues: 685 sheet: -0.99 (0.56), residues: 86 loop : -2.42 (0.27), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 308 HIS 0.004 0.001 HIS B 617 PHE 0.022 0.001 PHE B 72 TYR 0.007 0.001 TYR B 721 ARG 0.006 0.000 ARG B 714 *********************** 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 182 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 157 time to evaluate : 1.254 Fit side-chains outliers start: 25 outliers final: 9 residues processed: 175 average time/residue: 0.2092 time to fit residues: 53.3174 Evaluate side-chains 162 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 153 time to evaluate : 1.147 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1003 time to fit residues: 3.1958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 108 optimal weight: 0.9980 chunk 74 optimal weight: 0.4980 chunk 1 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 111 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 66 optimal weight: 5.9990 chunk 117 optimal weight: 8.9990 chunk 32 optimal weight: 4.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 ASN B 229 GLN B 237 ASN ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 770 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10776 Z= 0.199 Angle : 0.600 8.965 14643 Z= 0.293 Chirality : 0.040 0.169 1681 Planarity : 0.004 0.050 1892 Dihedral : 5.855 128.966 1501 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.58 % Favored : 91.35 % Rotamer: Outliers : 2.84 % Allowed : 24.56 % Favored : 72.59 % 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: -0.66 (0.24), residues: 1329 helix: 1.08 (0.21), residues: 696 sheet: -0.95 (0.55), residues: 86 loop : -2.46 (0.27), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 308 HIS 0.003 0.001 HIS C 125 PHE 0.023 0.001 PHE B 72 TYR 0.006 0.001 TYR B 721 ARG 0.006 0.000 ARG B 714 *********************** 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 188 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 157 time to evaluate : 1.186 Fit side-chains outliers start: 31 outliers final: 16 residues processed: 180 average time/residue: 0.2288 time to fit residues: 58.7730 Evaluate side-chains 163 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 147 time to evaluate : 1.120 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1003 time to fit residues: 4.6981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 43 optimal weight: 0.0370 chunk 117 optimal weight: 2.9990 chunk 25 optimal weight: 10.0000 chunk 76 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 130 optimal weight: 0.8980 chunk 108 optimal weight: 0.8980 chunk 60 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 68 optimal weight: 0.8980 chunk 125 optimal weight: 8.9990 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 ASN B 229 GLN B 237 ASN B 770 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10776 Z= 0.161 Angle : 0.584 8.665 14643 Z= 0.286 Chirality : 0.039 0.227 1681 Planarity : 0.004 0.051 1892 Dihedral : 5.694 127.540 1501 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 1.56 % Allowed : 25.66 % Favored : 72.78 % 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: -0.40 (0.24), residues: 1329 helix: 1.30 (0.21), residues: 687 sheet: -0.57 (0.57), residues: 76 loop : -2.32 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 658 HIS 0.006 0.001 HIS B 535 PHE 0.024 0.001 PHE B 72 TYR 0.007 0.001 TYR B 132 ARG 0.007 0.000 ARG B 714 *********************** 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 174 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 157 time to evaluate : 1.170 Fit side-chains outliers start: 17 outliers final: 11 residues processed: 166 average time/residue: 0.2318 time to fit residues: 54.9183 Evaluate side-chains 156 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 145 time to evaluate : 1.179 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0985 time to fit residues: 3.5829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 95 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 109 optimal weight: 5.9990 chunk 72 optimal weight: 0.8980 chunk 130 optimal weight: 3.9990 chunk 81 optimal weight: 9.9990 chunk 79 optimal weight: 5.9990 chunk 60 optimal weight: 0.7980 chunk 80 optimal weight: 0.6980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 ASN B 229 GLN B 237 ASN B 770 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10776 Z= 0.218 Angle : 0.600 8.505 14643 Z= 0.293 Chirality : 0.040 0.203 1681 Planarity : 0.004 0.056 1892 Dihedral : 5.698 127.513 1501 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.43 % Favored : 91.50 % Rotamer: Outliers : 1.65 % Allowed : 26.21 % Favored : 72.14 % 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: -0.20 (0.25), residues: 1329 helix: 1.46 (0.21), residues: 678 sheet: -0.65 (0.55), residues: 86 loop : -2.16 (0.27), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 658 HIS 0.005 0.001 HIS B 535 PHE 0.031 0.001 PHE B 72 TYR 0.007 0.001 TYR A 533 ARG 0.008 0.000 ARG B 714 *********************** 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 173 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 155 time to evaluate : 1.209 Fit side-chains outliers start: 18 outliers final: 9 residues processed: 167 average time/residue: 0.2294 time to fit residues: 55.2469 Evaluate side-chains 155 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 146 time to evaluate : 1.214 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1369 time to fit residues: 3.6790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 51 optimal weight: 8.9990 chunk 77 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 25 optimal weight: 10.0000 chunk 82 optimal weight: 6.9990 chunk 88 optimal weight: 6.9990 chunk 64 optimal weight: 0.0980 chunk 12 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 118 optimal weight: 0.2980 chunk 124 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 408 ASN B 144 HIS B 224 ASN B 229 GLN B 237 ASN B 770 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10776 Z= 0.183 Angle : 0.592 8.411 14643 Z= 0.287 Chirality : 0.040 0.234 1681 Planarity : 0.004 0.050 1892 Dihedral : 5.632 126.721 1501 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.13 % Favored : 91.80 % Rotamer: Outliers : 1.37 % Allowed : 26.67 % Favored : 71.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.25), residues: 1329 helix: 1.53 (0.21), residues: 680 sheet: -0.80 (0.53), residues: 94 loop : -2.13 (0.27), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 658 HIS 0.006 0.001 HIS B 535 PHE 0.019 0.001 PHE A 298 TYR 0.007 0.001 TYR A 533 ARG 0.009 0.000 ARG B 714 *********************** REFINEMENT MACRO_CYCLE 8 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 169 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 154 time to evaluate : 1.534 Fit side-chains outliers start: 15 outliers final: 7 residues processed: 163 average time/residue: 0.2408 time to fit residues: 55.5962 Evaluate side-chains 158 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 151 time to evaluate : 1.048 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1000 time to fit residues: 2.8039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 chunk 95 optimal weight: 3.9990 chunk 37 optimal weight: 8.9990 chunk 109 optimal weight: 3.9990 chunk 114 optimal weight: 0.7980 chunk 120 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 ASN B 229 GLN B 237 ASN B 770 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 10776 Z= 0.313 Angle : 0.652 8.604 14643 Z= 0.320 Chirality : 0.042 0.175 1681 Planarity : 0.005 0.060 1892 Dihedral : 5.843 128.773 1501 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.48 % Favored : 90.44 % Rotamer: Outliers : 1.47 % Allowed : 26.95 % Favored : 71.59 % 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: -0.35 (0.24), residues: 1329 helix: 1.35 (0.21), residues: 678 sheet: -0.82 (0.55), residues: 93 loop : -2.23 (0.27), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 658 HIS 0.012 0.001 HIS A 424 PHE 0.021 0.002 PHE A 633 TYR 0.011 0.001 TYR A 533 ARG 0.008 0.000 ARG B 714 *********************** REFINEMENT MACRO_CYCLE 9 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 175 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 159 time to evaluate : 1.160 Fit side-chains outliers start: 16 outliers final: 9 residues processed: 167 average time/residue: 0.2330 time to fit residues: 55.7602 Evaluate side-chains 160 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 151 time to evaluate : 1.230 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1001 time to fit residues: 3.4007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 128 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 89 optimal weight: 0.0370 chunk 134 optimal weight: 0.5980 chunk 123 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 85 optimal weight: 0.7980 overall best weight: 0.6860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN B 770 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10776 Z= 0.176 Angle : 0.613 8.423 14643 Z= 0.300 Chirality : 0.040 0.165 1681 Planarity : 0.004 0.056 1892 Dihedral : 5.703 126.609 1501 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer: Outliers : 0.37 % Allowed : 27.50 % Favored : 72.14 % 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: -0.21 (0.25), residues: 1329 helix: 1.45 (0.21), residues: 686 sheet: -0.75 (0.55), residues: 93 loop : -2.18 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 658 HIS 0.004 0.001 HIS A 424 PHE 0.022 0.001 PHE A 298 TYR 0.011 0.001 TYR B 721 ARG 0.008 0.000 ARG B 646 ********************** REFINEMENT MACRO_CYCLE 10 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 158 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 154 time to evaluate : 1.269 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 154 average time/residue: 0.2262 time to fit residues: 50.5262 Evaluate side-chains 146 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 144 time to evaluate : 1.150 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1040 time to fit residues: 1.9777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 114 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 98 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 chunk 107 optimal weight: 4.9990 chunk 44 optimal weight: 0.3980 chunk 110 optimal weight: 0.0270 chunk 13 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 94 optimal weight: 4.9990 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.134515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.115115 restraints weight = 14942.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.117243 restraints weight = 10426.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.118661 restraints weight = 8097.193| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 10776 Z= 0.172 Angle : 0.609 11.392 14643 Z= 0.293 Chirality : 0.039 0.171 1681 Planarity : 0.004 0.056 1892 Dihedral : 5.495 123.384 1501 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 0.18 % Allowed : 27.96 % Favored : 71.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.25), residues: 1329 helix: 1.48 (0.21), residues: 688 sheet: -0.71 (0.56), residues: 93 loop : -2.07 (0.27), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 658 HIS 0.005 0.001 HIS B 535 PHE 0.021 0.001 PHE A 298 TYR 0.020 0.001 TYR B 721 ARG 0.007 0.000 ARG B 714 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2197.46 seconds wall clock time: 40 minutes 50.67 seconds (2450.67 seconds total)