Starting phenix.real_space_refine on Wed Feb 14 23:38:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m5v_30094/02_2024/6m5v_30094_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m5v_30094/02_2024/6m5v_30094.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m5v_30094/02_2024/6m5v_30094.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m5v_30094/02_2024/6m5v_30094.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m5v_30094/02_2024/6m5v_30094_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m5v_30094/02_2024/6m5v_30094_updated.pdb" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.015 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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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 31.477 46.241 53.912 1.00 47.42 S ATOM 10277 SG CYS C 101 30.191 46.342 57.304 1.00 59.52 S ATOM 6010 SG CYS B 197 52.449 54.153 49.925 1.00 43.06 S ATOM 6028 SG CYS B 200 54.145 55.532 52.620 1.00 41.30 S Time building chain proxies: 5.80, per 1000 atoms: 0.55 Number of scatterers: 10549 At special positions: 0 Unit cell: (108.16, 101.92, 120.64, 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: 4.17 Conformation dependent library (CDL) restraints added in 1.7 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: 2.17 Creating SS restraints... Processing helix chain 'A' and resid 68 through 71 Processing helix chain 'A' and resid 74 through 80 removed outlier: 4.300A 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: 3.975A 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: 3.578A 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: 3.867A 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: 3.891A 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: 3.912A 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: 4.864A pdb=" N GLU B 643 " --> pdb=" O HIS B 639 " (cutoff:3.500A) removed outlier: 3.515A 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: 3.627A pdb=" N LEU C 78 " --> pdb=" O ARG C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 127 removed outlier: 3.740A 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: 6.228A pdb=" N TYR A 533 " --> pdb=" O MET A 657 " (cutoff:3.500A) removed outlier: 6.528A 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: 6.632A pdb=" N GLY A 575 " --> pdb=" O LEU A 504 " (cutoff:3.500A) removed outlier: 7.908A 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: 2.90 Time building geometry restraints manager: 4.52 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: 2872 1.43 - 1.56: 6132 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 2.09e+02 bond pdb=" BE BEF A 802 " pdb=" F1 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=" 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 0.064 1.17e-02 7.31e+03 3.02e+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 3.01e+01 ... (remaining 10771 not shown) Histogram of bond angle deviations from ideal: 98.57 - 105.65: 252 105.65 - 112.73: 5697 112.73 - 119.81: 3416 119.81 - 126.90: 5146 126.90 - 133.98: 132 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 122.52 130.37 -7.85 1.16e+00 7.43e-01 4.58e+01 angle pdb=" N VAL A 477 " pdb=" CA VAL A 477 " pdb=" C VAL A 477 " ideal model delta sigma weight residual 110.36 115.76 -5.40 1.05e+00 9.07e-01 2.64e+01 angle pdb=" N CYS A 125 " pdb=" CA CYS A 125 " pdb=" C CYS A 125 " ideal model delta sigma weight residual 108.42 116.12 -7.70 1.54e+00 4.22e-01 2.50e+01 angle pdb=" N ARG B 59 " pdb=" CA ARG B 59 " pdb=" C ARG B 59 " ideal model delta sigma weight residual 114.56 108.42 6.14 1.27e+00 6.20e-01 2.34e+01 angle pdb=" N SER A 481 " pdb=" CA SER A 481 " pdb=" C SER A 481 " ideal model delta sigma weight residual 111.07 106.34 4.73 1.07e+00 8.73e-01 1.96e+01 ... (remaining 14638 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.48: 5923 23.48 - 46.95: 420 46.95 - 70.43: 62 70.43 - 93.91: 12 93.91 - 117.38: 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 57.38 -117.38 1 2.00e+01 2.50e-03 3.50e+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 180.00 152.99 27.01 0 5.00e+00 4.00e-02 2.92e+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 37.46 -97.45 1 2.00e+01 2.50e-03 2.71e+01 ... (remaining 6416 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1469 0.073 - 0.146: 184 0.146 - 0.219: 22 0.219 - 0.292: 5 0.292 - 0.365: 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 2.08 0.37 2.00e-01 2.50e+01 3.34e+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 1.90e+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 2.70 -0.26 2.00e-01 2.50e+01 1.73e+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 3.26e-02 1.06e+01 pdb=" C TYR B 242 " 0.056 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 2.56e-02 6.54e+00 pdb=" C VAL B 534 " -0.044 2.00e-02 2.50e+03 pdb=" O VAL B 534 " 0.016 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: 1383 2.75 - 3.29: 10665 3.29 - 3.82: 17496 3.82 - 4.36: 20324 4.36 - 4.90: 34888 Nonbonded interactions: 84756 Sorted by model distance: nonbonded pdb=" O CYS B 223 " pdb=" ND1 HIS B 225 " model vdw 2.209 2.520 nonbonded pdb=" O CYS C 101 " pdb=" N GLY C 104 " model vdw 2.225 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 84751 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: 0.280 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: 0.000 Extract box with map and model: 1.810 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 31.680 Find NCS groups from input model: 0.310 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:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5902 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 : 0.865 10.839 14643 Z= 0.538 Chirality : 0.051 0.365 1681 Planarity : 0.005 0.055 1892 Dihedral : 16.072 117.384 3853 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 18.28 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.95 % Favored : 90.90 % Rotamer: Outliers : 5.50 % Allowed : 16.77 % 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: -3.04 (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 0.012 0.002 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 332 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 272 time to evaluate : 1.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 PHE cc_start: 0.6916 (t80) cc_final: 0.6557 (t80) REVERT: A 84 LEU cc_start: 0.8467 (tp) cc_final: 0.8061 (tp) REVERT: A 93 LEU cc_start: 0.8718 (mt) cc_final: 0.8170 (tt) REVERT: A 203 LEU cc_start: 0.8736 (tp) cc_final: 0.8425 (tp) REVERT: A 210 MET cc_start: 0.8690 (mtm) cc_final: 0.8197 (ttm) REVERT: A 213 THR cc_start: 0.8188 (m) cc_final: 0.7815 (p) REVERT: A 241 PHE cc_start: 0.8945 (OUTLIER) cc_final: 0.8679 (m-80) REVERT: A 249 PHE cc_start: 0.7879 (m-10) cc_final: 0.7323 (m-10) REVERT: A 271 LEU cc_start: 0.7751 (tt) cc_final: 0.7409 (tt) REVERT: A 600 MET cc_start: 0.6732 (mmp) cc_final: 0.6011 (tpt) REVERT: B 49 LEU cc_start: 0.7507 (OUTLIER) cc_final: 0.6350 (mt) REVERT: B 143 LEU cc_start: 0.7896 (mt) cc_final: 0.7646 (mt) REVERT: B 156 CYS cc_start: 0.8584 (OUTLIER) cc_final: 0.8210 (m) REVERT: B 601 HIS cc_start: 0.8142 (m-70) cc_final: 0.7790 (m170) REVERT: B 690 ILE cc_start: 0.7997 (mt) cc_final: 0.7684 (tp) REVERT: B 748 CYS cc_start: 0.4796 (OUTLIER) cc_final: 0.4148 (t) REVERT: B 766 TYR cc_start: 0.6760 (t80) cc_final: 0.6452 (t80) REVERT: C 42 ASP cc_start: 0.6139 (t0) cc_final: 0.5889 (t0) REVERT: C 63 ASP cc_start: 0.8344 (m-30) cc_final: 0.7710 (m-30) REVERT: C 77 SER cc_start: 0.8905 (m) cc_final: 0.8335 (p) REVERT: C 79 LEU cc_start: 0.8452 (mt) cc_final: 0.8160 (tp) outliers start: 60 outliers final: 11 residues processed: 319 average time/residue: 0.3148 time to fit residues: 130.9683 Evaluate side-chains 171 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 156 time to evaluate : 1.198 ------------------------------------------------------------------------------- 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: 3.9990 chunk 102 optimal weight: 3.9990 chunk 56 optimal weight: 7.9990 chunk 34 optimal weight: 10.0000 chunk 69 optimal weight: 0.9980 chunk 54 optimal weight: 8.9990 chunk 105 optimal weight: 7.9990 chunk 40 optimal weight: 8.9990 chunk 64 optimal weight: 8.9990 chunk 78 optimal weight: 5.9990 chunk 122 optimal weight: 8.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 67 HIS A 102 HIS A 148 HIS ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 375 GLN A 377 ASN A 670 GLN A 726 HIS B 68 GLN ** B 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 GLN ** B 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 HIS B 210 GLN B 323 GLN ** B 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 491 GLN B 614 HIS ** B 617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 770 GLN C 119 ASN C 126 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6296 moved from start: 0.3819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10776 Z= 0.280 Angle : 0.732 9.951 14643 Z= 0.369 Chirality : 0.043 0.166 1681 Planarity : 0.006 0.069 1892 Dihedral : 6.639 131.928 1501 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 19.57 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.65 % Favored : 91.27 % Rotamer: Outliers : 0.27 % Allowed : 4.86 % Favored : 94.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.23), residues: 1329 helix: 0.12 (0.20), residues: 685 sheet: -1.62 (0.51), residues: 91 loop : -2.60 (0.27), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 308 HIS 0.012 0.001 HIS B 617 PHE 0.028 0.003 PHE A 241 TYR 0.020 0.002 TYR B 123 ARG 0.009 0.001 ARG B 62 *********************** 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 187 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 184 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 PHE cc_start: 0.7827 (t80) cc_final: 0.7108 (t80) REVERT: A 204 PHE cc_start: 0.8076 (p90) cc_final: 0.7737 (p90) REVERT: A 213 THR cc_start: 0.8169 (m) cc_final: 0.7894 (p) REVERT: A 216 LEU cc_start: 0.8324 (mt) cc_final: 0.7954 (mt) REVERT: A 249 PHE cc_start: 0.7713 (m-10) cc_final: 0.7332 (m-10) REVERT: A 335 VAL cc_start: 0.7927 (m) cc_final: 0.7681 (p) REVERT: A 360 PHE cc_start: 0.6047 (m-80) cc_final: 0.5766 (m-80) REVERT: A 600 MET cc_start: 0.7836 (mmp) cc_final: 0.6464 (tpt) REVERT: B 232 VAL cc_start: 0.8509 (p) cc_final: 0.8083 (p) REVERT: B 419 ASP cc_start: 0.7617 (p0) cc_final: 0.7371 (p0) REVERT: B 629 TYR cc_start: 0.8063 (m-80) cc_final: 0.7728 (m-10) REVERT: B 690 ILE cc_start: 0.8475 (mt) cc_final: 0.8201 (tp) REVERT: C 63 ASP cc_start: 0.8280 (m-30) cc_final: 0.7879 (m-30) REVERT: C 75 LEU cc_start: 0.7451 (tp) cc_final: 0.6932 (tp) outliers start: 3 outliers final: 2 residues processed: 187 average time/residue: 0.2649 time to fit residues: 66.9326 Evaluate side-chains 121 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 119 time to evaluate : 1.093 ------------------------------------------------------------------------------- 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: 6.9990 chunk 38 optimal weight: 5.9990 chunk 102 optimal weight: 7.9990 chunk 83 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 chunk 122 optimal weight: 20.0000 chunk 132 optimal weight: 0.2980 chunk 109 optimal weight: 10.0000 chunk 121 optimal weight: 5.9990 chunk 41 optimal weight: 50.0000 chunk 98 optimal weight: 6.9990 overall best weight: 5.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 142 ASN ** A 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 HIS ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 HIS B 342 GLN B 491 GLN ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 119 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6475 moved from start: 0.4911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10776 Z= 0.275 Angle : 0.722 9.906 14643 Z= 0.363 Chirality : 0.042 0.156 1681 Planarity : 0.005 0.046 1892 Dihedral : 6.545 141.040 1501 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 22.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.26 % Favored : 90.74 % Rotamer: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % 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: -1.08 (0.24), residues: 1329 helix: 0.58 (0.20), residues: 681 sheet: -1.41 (0.51), residues: 87 loop : -2.29 (0.27), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 308 HIS 0.009 0.001 HIS B 617 PHE 0.025 0.002 PHE A 354 TYR 0.015 0.002 TYR B 400 ARG 0.019 0.001 ARG B 60 *********************** 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 146 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 1.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 LEU cc_start: 0.9042 (tp) cc_final: 0.8721 (tp) REVERT: A 204 PHE cc_start: 0.7919 (p90) cc_final: 0.7672 (p90) REVERT: A 210 MET cc_start: 0.8362 (ttm) cc_final: 0.7667 (ttm) REVERT: A 335 VAL cc_start: 0.8086 (m) cc_final: 0.7725 (p) REVERT: A 600 MET cc_start: 0.7939 (mmp) cc_final: 0.6569 (tpt) REVERT: B 158 LEU cc_start: 0.8421 (pt) cc_final: 0.8219 (pt) REVERT: B 232 VAL cc_start: 0.8390 (p) cc_final: 0.7978 (p) REVERT: B 543 PHE cc_start: 0.7593 (t80) cc_final: 0.7369 (t80) REVERT: B 690 ILE cc_start: 0.9104 (mt) cc_final: 0.8604 (tp) REVERT: C 45 VAL cc_start: 0.5273 (t) cc_final: 0.5000 (t) REVERT: C 63 ASP cc_start: 0.7660 (m-30) cc_final: 0.7253 (m-30) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.2587 time to fit residues: 52.9249 Evaluate side-chains 103 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 1.235 ------------------------------------------------------------------------------- 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: 20.0000 chunk 92 optimal weight: 7.9990 chunk 63 optimal weight: 3.9990 chunk 13 optimal weight: 9.9990 chunk 58 optimal weight: 6.9990 chunk 82 optimal weight: 20.0000 chunk 123 optimal weight: 10.0000 chunk 130 optimal weight: 8.9990 chunk 64 optimal weight: 10.0000 chunk 116 optimal weight: 7.9990 chunk 35 optimal weight: 0.0070 overall best weight: 5.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 GLN ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 491 GLN ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 119 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6586 moved from start: 0.5619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10776 Z= 0.280 Angle : 0.708 10.416 14643 Z= 0.359 Chirality : 0.041 0.157 1681 Planarity : 0.005 0.070 1892 Dihedral : 6.434 131.989 1501 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 23.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.88 % Favored : 91.12 % Rotamer: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.24), residues: 1329 helix: 0.77 (0.20), residues: 666 sheet: -1.81 (0.47), residues: 104 loop : -2.07 (0.27), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 308 HIS 0.008 0.001 HIS B 157 PHE 0.021 0.002 PHE A 350 TYR 0.014 0.002 TYR B 400 ARG 0.009 0.001 ARG B 60 *********************** 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 135 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 1.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 LEU cc_start: 0.8877 (tp) cc_final: 0.8620 (tp) REVERT: A 204 PHE cc_start: 0.8364 (p90) cc_final: 0.7948 (p90) REVERT: A 205 GLN cc_start: 0.8460 (mm-40) cc_final: 0.8034 (tp-100) REVERT: A 207 MET cc_start: 0.8272 (mtp) cc_final: 0.7882 (mtm) REVERT: A 216 LEU cc_start: 0.7864 (mp) cc_final: 0.7615 (mt) REVERT: A 600 MET cc_start: 0.7563 (mmp) cc_final: 0.6364 (tpt) REVERT: B 158 LEU cc_start: 0.8599 (pt) cc_final: 0.8301 (pp) REVERT: B 232 VAL cc_start: 0.7913 (p) cc_final: 0.7544 (p) REVERT: B 419 ASP cc_start: 0.7548 (p0) cc_final: 0.6947 (p0) REVERT: B 690 ILE cc_start: 0.9234 (mt) cc_final: 0.8786 (tp) REVERT: C 45 VAL cc_start: 0.6217 (t) cc_final: 0.5759 (t) REVERT: C 63 ASP cc_start: 0.7692 (m-30) cc_final: 0.7303 (m-30) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.2500 time to fit residues: 47.1726 Evaluate side-chains 94 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 1.054 ------------------------------------------------------------------------------- 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: 8.9990 chunk 1 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 40.0000 chunk 111 optimal weight: 9.9990 chunk 90 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 66 optimal weight: 7.9990 chunk 117 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 HIS ** B 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 491 GLN ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 617 HIS C 103 HIS C 119 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6461 moved from start: 0.5818 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= 0.177 Angle : 0.651 10.288 14643 Z= 0.320 Chirality : 0.041 0.142 1681 Planarity : 0.005 0.057 1892 Dihedral : 6.210 127.455 1501 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 18.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.80 % Favored : 91.20 % Rotamer: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % 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: 0.91 (0.20), residues: 674 sheet: -1.45 (0.52), residues: 88 loop : -2.13 (0.27), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 308 HIS 0.008 0.001 HIS B 157 PHE 0.021 0.002 PHE B 543 TYR 0.020 0.001 TYR A 397 ARG 0.005 0.000 ARG B 523 *********************** 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 127 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 1.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 PHE cc_start: 0.8134 (p90) cc_final: 0.7872 (p90) REVERT: A 360 PHE cc_start: 0.7709 (m-80) cc_final: 0.7458 (m-80) REVERT: A 600 MET cc_start: 0.7479 (mmp) cc_final: 0.6254 (tpt) REVERT: B 158 LEU cc_start: 0.8297 (pt) cc_final: 0.7940 (pp) REVERT: B 232 VAL cc_start: 0.8164 (p) cc_final: 0.7768 (p) REVERT: B 687 ARG cc_start: 0.8504 (ttp80) cc_final: 0.8188 (ttp80) REVERT: B 690 ILE cc_start: 0.9138 (mt) cc_final: 0.8705 (tp) REVERT: B 764 ILE cc_start: 0.8952 (mm) cc_final: 0.8749 (mm) REVERT: C 45 VAL cc_start: 0.6005 (t) cc_final: 0.5363 (t) REVERT: C 50 MET cc_start: 0.5621 (mmt) cc_final: 0.4986 (mmp) REVERT: C 63 ASP cc_start: 0.7682 (m-30) cc_final: 0.7275 (m-30) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.2402 time to fit residues: 43.1186 Evaluate side-chains 98 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 1.228 ------------------------------------------------------------------------------- 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: 7.9990 chunk 117 optimal weight: 7.9990 chunk 25 optimal weight: 9.9990 chunk 76 optimal weight: 9.9990 chunk 32 optimal weight: 20.0000 chunk 130 optimal weight: 9.9990 chunk 108 optimal weight: 10.0000 chunk 60 optimal weight: 1.9990 chunk 10 optimal weight: 20.0000 chunk 68 optimal weight: 7.9990 chunk 125 optimal weight: 8.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 211 HIS A 597 HIS ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 491 GLN ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 771 HIS ** C 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 119 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6755 moved from start: 0.6757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 10776 Z= 0.354 Angle : 0.821 11.665 14643 Z= 0.415 Chirality : 0.045 0.197 1681 Planarity : 0.006 0.068 1892 Dihedral : 6.586 125.202 1501 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 28.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % Rotamer: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % 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: -1.16 (0.23), residues: 1329 helix: 0.50 (0.20), residues: 675 sheet: -1.32 (0.57), residues: 76 loop : -2.29 (0.26), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP A 308 HIS 0.011 0.002 HIS B 614 PHE 0.022 0.003 PHE A 354 TYR 0.027 0.003 TYR A 397 ARG 0.006 0.001 ARG C 74 *********************** 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 118 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 1.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 PHE cc_start: 0.8700 (p90) cc_final: 0.8302 (p90) REVERT: A 205 GLN cc_start: 0.8507 (mm-40) cc_final: 0.7917 (tp-100) REVERT: A 207 MET cc_start: 0.8477 (mtp) cc_final: 0.6611 (mtp) REVERT: A 210 MET cc_start: 0.8025 (ttp) cc_final: 0.6435 (ppp) REVERT: A 299 GLU cc_start: 0.8162 (tp30) cc_final: 0.7723 (tp30) REVERT: A 600 MET cc_start: 0.7719 (mmp) cc_final: 0.6422 (tpt) REVERT: B 232 VAL cc_start: 0.7714 (p) cc_final: 0.7418 (p) REVERT: B 419 ASP cc_start: 0.7878 (p0) cc_final: 0.7172 (p0) REVERT: B 629 TYR cc_start: 0.8102 (m-80) cc_final: 0.7725 (m-10) REVERT: B 690 ILE cc_start: 0.9340 (mt) cc_final: 0.8810 (tp) REVERT: B 764 ILE cc_start: 0.8946 (mm) cc_final: 0.8736 (mm) REVERT: C 63 ASP cc_start: 0.7809 (m-30) cc_final: 0.7268 (m-30) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.2316 time to fit residues: 38.9857 Evaluate side-chains 91 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 1.192 ------------------------------------------------------------------------------- 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: 5.9990 chunk 95 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 109 optimal weight: 9.9990 chunk 72 optimal weight: 0.9980 chunk 130 optimal weight: 7.9990 chunk 81 optimal weight: 10.0000 chunk 79 optimal weight: 0.0050 chunk 60 optimal weight: 0.9980 chunk 80 optimal weight: 8.9990 overall best weight: 1.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 289 HIS A 646 HIS ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 GLN ** B 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 HIS B 491 GLN ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 119 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6576 moved from start: 0.6752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10776 Z= 0.188 Angle : 0.687 11.560 14643 Z= 0.336 Chirality : 0.042 0.226 1681 Planarity : 0.005 0.062 1892 Dihedral : 6.242 126.704 1501 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 20.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % 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: 0.87 (0.20), residues: 673 sheet: -1.52 (0.53), residues: 90 loop : -2.17 (0.27), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 308 HIS 0.006 0.001 HIS B 614 PHE 0.017 0.002 PHE A 249 TYR 0.013 0.002 TYR A 397 ARG 0.005 0.000 ARG A 96 *********************** 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 129 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 MET cc_start: 0.8451 (mtp) cc_final: 0.6693 (mtp) REVERT: A 210 MET cc_start: 0.7949 (ttp) cc_final: 0.6388 (ppp) REVERT: A 324 PHE cc_start: 0.5643 (t80) cc_final: 0.4978 (t80) REVERT: A 600 MET cc_start: 0.7601 (mmp) cc_final: 0.6457 (tpt) REVERT: B 155 TYR cc_start: 0.7574 (t80) cc_final: 0.7150 (t80) REVERT: B 158 LEU cc_start: 0.8489 (pt) cc_final: 0.8159 (pp) REVERT: B 529 MET cc_start: 0.8573 (ppp) cc_final: 0.8332 (ppp) REVERT: B 690 ILE cc_start: 0.9284 (mt) cc_final: 0.8786 (tp) REVERT: C 45 VAL cc_start: 0.6380 (t) cc_final: 0.5916 (t) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.2393 time to fit residues: 43.3516 Evaluate side-chains 100 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 1.079 ------------------------------------------------------------------------------- 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: 8.9990 chunk 39 optimal weight: 8.9990 chunk 25 optimal weight: 0.0270 chunk 82 optimal weight: 7.9990 chunk 88 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 12 optimal weight: 9.9990 chunk 102 optimal weight: 9.9990 chunk 118 optimal weight: 1.9990 chunk 124 optimal weight: 6.9990 overall best weight: 2.6044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 142 ASN ** A 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 GLN ** B 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 491 GLN ** C 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 GLN C 119 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6592 moved from start: 0.6951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10776 Z= 0.201 Angle : 0.682 10.981 14643 Z= 0.336 Chirality : 0.041 0.143 1681 Planarity : 0.004 0.042 1892 Dihedral : 6.119 123.169 1501 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 20.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.48 % Favored : 90.52 % Rotamer: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % 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: -0.70 (0.24), residues: 1329 helix: 0.90 (0.20), residues: 683 sheet: -1.36 (0.56), residues: 78 loop : -2.10 (0.27), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 308 HIS 0.010 0.001 HIS A 158 PHE 0.018 0.002 PHE A 249 TYR 0.030 0.002 TYR A 198 ARG 0.004 0.000 ARG A 96 *********************** 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 128 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 1.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 PHE cc_start: 0.8460 (p90) cc_final: 0.8096 (p90) REVERT: A 205 GLN cc_start: 0.8422 (mm-40) cc_final: 0.8023 (tp-100) REVERT: A 210 MET cc_start: 0.8039 (ttp) cc_final: 0.7022 (tmm) REVERT: A 324 PHE cc_start: 0.5708 (t80) cc_final: 0.5410 (t80) REVERT: A 600 MET cc_start: 0.7598 (mmp) cc_final: 0.6425 (tpt) REVERT: B 155 TYR cc_start: 0.7598 (t80) cc_final: 0.7125 (t80) REVERT: B 158 LEU cc_start: 0.8547 (pt) cc_final: 0.8229 (pp) REVERT: B 419 ASP cc_start: 0.7723 (p0) cc_final: 0.7423 (p0) REVERT: B 529 MET cc_start: 0.8418 (ppp) cc_final: 0.8204 (ppp) REVERT: B 690 ILE cc_start: 0.9372 (mt) cc_final: 0.8840 (tp) REVERT: B 694 THR cc_start: 0.9290 (p) cc_final: 0.9050 (p) REVERT: B 764 ILE cc_start: 0.8809 (mm) cc_final: 0.8582 (mm) REVERT: C 45 VAL cc_start: 0.6406 (t) cc_final: 0.5986 (t) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.2443 time to fit residues: 45.4079 Evaluate side-chains 103 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 1.164 ------------------------------------------------------------------------------- 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: 0.9980 chunk 121 optimal weight: 6.9990 chunk 124 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 52 optimal weight: 10.0000 chunk 95 optimal weight: 7.9990 chunk 37 optimal weight: 20.0000 chunk 109 optimal weight: 8.9990 chunk 114 optimal weight: 9.9990 chunk 120 optimal weight: 7.9990 chunk 79 optimal weight: 0.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 491 GLN ** C 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 119 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6649 moved from start: 0.7250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10776 Z= 0.232 Angle : 0.703 11.414 14643 Z= 0.347 Chirality : 0.042 0.197 1681 Planarity : 0.005 0.045 1892 Dihedral : 6.167 123.209 1501 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 22.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.41 % Favored : 90.59 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % 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: -0.67 (0.24), residues: 1329 helix: 0.91 (0.20), residues: 679 sheet: -1.47 (0.56), residues: 78 loop : -2.02 (0.27), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 308 HIS 0.007 0.001 HIS B 617 PHE 0.027 0.002 PHE A 231 TYR 0.014 0.002 TYR A 286 ARG 0.008 0.001 ARG B 531 *********************** 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 125 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 LEU cc_start: 0.8713 (mt) cc_final: 0.8373 (mt) REVERT: A 204 PHE cc_start: 0.8026 (p90) cc_final: 0.6566 (p90) REVERT: A 205 GLN cc_start: 0.8359 (mm-40) cc_final: 0.7881 (mm-40) REVERT: A 210 MET cc_start: 0.8097 (ttp) cc_final: 0.7105 (tmm) REVERT: A 272 ILE cc_start: 0.8158 (mm) cc_final: 0.7887 (mm) REVERT: A 324 PHE cc_start: 0.5846 (t80) cc_final: 0.5557 (t80) REVERT: A 600 MET cc_start: 0.7661 (mmp) cc_final: 0.6462 (tpt) REVERT: B 155 TYR cc_start: 0.7669 (t80) cc_final: 0.7168 (t80) REVERT: B 158 LEU cc_start: 0.8431 (pt) cc_final: 0.8114 (pp) REVERT: B 375 MET cc_start: 0.3400 (mmp) cc_final: 0.2937 (mmp) REVERT: B 419 ASP cc_start: 0.7762 (p0) cc_final: 0.7370 (p0) REVERT: B 690 ILE cc_start: 0.9342 (mt) cc_final: 0.8769 (tp) REVERT: B 694 THR cc_start: 0.9303 (p) cc_final: 0.9068 (p) REVERT: B 764 ILE cc_start: 0.8858 (mm) cc_final: 0.8609 (mm) REVERT: C 45 VAL cc_start: 0.6467 (t) cc_final: 0.6181 (t) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.2360 time to fit residues: 41.7477 Evaluate side-chains 99 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 1.194 ------------------------------------------------------------------------------- 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: 10.0000 chunk 78 optimal weight: 7.9990 chunk 60 optimal weight: 5.9990 chunk 89 optimal weight: 9.9990 chunk 134 optimal weight: 7.9990 chunk 123 optimal weight: 10.0000 chunk 107 optimal weight: 10.0000 chunk 11 optimal weight: 6.9990 chunk 82 optimal weight: 0.0170 chunk 65 optimal weight: 3.9990 chunk 85 optimal weight: 8.9990 overall best weight: 5.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 491 GLN ** C 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 119 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6722 moved from start: 0.7642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10776 Z= 0.271 Angle : 0.734 10.730 14643 Z= 0.365 Chirality : 0.043 0.336 1681 Planarity : 0.005 0.059 1892 Dihedral : 6.318 123.463 1501 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 25.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.78 % Favored : 90.22 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.24), residues: 1329 helix: 0.90 (0.20), residues: 671 sheet: -1.64 (0.56), residues: 78 loop : -1.97 (0.27), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 308 HIS 0.009 0.001 HIS B 157 PHE 0.061 0.002 PHE A 241 TYR 0.016 0.002 TYR A 198 ARG 0.008 0.001 ARG B 531 ********************** 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 125 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 1.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 PHE cc_start: 0.8677 (p90) cc_final: 0.8115 (p90) REVERT: A 205 GLN cc_start: 0.8300 (mm-40) cc_final: 0.8025 (tp40) REVERT: A 210 MET cc_start: 0.8386 (ttp) cc_final: 0.7383 (tmm) REVERT: A 237 GLU cc_start: 0.7730 (pm20) cc_final: 0.7211 (pp20) REVERT: A 299 GLU cc_start: 0.8171 (tp30) cc_final: 0.7705 (tp30) REVERT: A 324 PHE cc_start: 0.5958 (t80) cc_final: 0.5674 (t80) REVERT: A 600 MET cc_start: 0.7758 (mmp) cc_final: 0.6472 (tpt) REVERT: B 155 TYR cc_start: 0.7739 (t80) cc_final: 0.7239 (t80) REVERT: B 158 LEU cc_start: 0.8576 (pt) cc_final: 0.8227 (pp) REVERT: B 329 PHE cc_start: 0.6274 (t80) cc_final: 0.6067 (t80) REVERT: B 375 MET cc_start: 0.2853 (mmp) cc_final: 0.2487 (mmt) REVERT: B 419 ASP cc_start: 0.7727 (p0) cc_final: 0.7410 (p0) REVERT: B 690 ILE cc_start: 0.9323 (mt) cc_final: 0.8910 (tp) REVERT: B 694 THR cc_start: 0.9312 (p) cc_final: 0.9067 (p) REVERT: B 764 ILE cc_start: 0.8731 (mm) cc_final: 0.8508 (mm) REVERT: C 45 VAL cc_start: 0.6733 (t) cc_final: 0.6302 (t) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.2499 time to fit residues: 44.1975 Evaluate side-chains 97 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 1.264 ------------------------------------------------------------------------------- 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: 10.0000 chunk 32 optimal weight: 20.0000 chunk 98 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 107 optimal weight: 0.0370 chunk 44 optimal weight: 20.0000 chunk 110 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 94 optimal weight: 0.0020 overall best weight: 2.4072 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 491 GLN ** C 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 119 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.078030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.064723 restraints weight = 62261.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.066219 restraints weight = 43727.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.067292 restraints weight = 33149.664| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.7687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10776 Z= 0.199 Angle : 0.694 12.380 14643 Z= 0.337 Chirality : 0.042 0.183 1681 Planarity : 0.004 0.053 1892 Dihedral : 6.129 122.359 1501 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 20.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.63 % Favored : 90.37 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % 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: -0.48 (0.24), residues: 1329 helix: 1.02 (0.20), residues: 681 sheet: -1.51 (0.56), residues: 78 loop : -1.85 (0.28), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP A 308 HIS 0.007 0.001 HIS B 614 PHE 0.033 0.002 PHE A 241 TYR 0.012 0.001 TYR A 286 ARG 0.005 0.000 ARG B 531 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1974.36 seconds wall clock time: 37 minutes 9.65 seconds (2229.65 seconds total)