Starting phenix.real_space_refine (version: 1.21rc1) on Mon Apr 24 12:36:55 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zr5_14883/04_2023/7zr5_14883_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zr5_14883/04_2023/7zr5_14883.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zr5_14883/04_2023/7zr5_14883.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zr5_14883/04_2023/7zr5_14883.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zr5_14883/04_2023/7zr5_14883_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zr5_14883/04_2023/7zr5_14883_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.002 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 7 5.49 5 S 91 5.16 5 C 11078 2.51 5 N 2981 2.21 5 O 3361 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 49": "OD1" <-> "OD2" Residue "A TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 74": "OD1" <-> "OD2" Residue "A ASP 122": "OD1" <-> "OD2" Residue "A ASP 152": "OD1" <-> "OD2" Residue "A GLU 153": "OE1" <-> "OE2" Residue "A ASP 170": "OD1" <-> "OD2" Residue "A TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 294": "OD1" <-> "OD2" Residue "A GLU 299": "OE1" <-> "OE2" Residue "A GLU 313": "OE1" <-> "OE2" Residue "A GLU 328": "OE1" <-> "OE2" Residue "A TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 364": "OD1" <-> "OD2" Residue "A GLU 368": "OE1" <-> "OE2" Residue "A ASP 422": "OD1" <-> "OD2" Residue "A PHE 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 509": "OE1" <-> "OE2" Residue "A GLU 627": "OE1" <-> "OE2" Residue "A GLU 643": "OE1" <-> "OE2" Residue "A ASP 672": "OD1" <-> "OD2" Residue "B GLU 37": "OE1" <-> "OE2" Residue "B ASP 152": "OD1" <-> "OD2" Residue "B PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 324": "OE1" <-> "OE2" Residue "B ASP 364": "OD1" <-> "OD2" Residue "B TYR 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 393": "OE1" <-> "OE2" Residue "B ASP 444": "OD1" <-> "OD2" Residue "B GLU 471": "OE1" <-> "OE2" Residue "B GLU 501": "OE1" <-> "OE2" Residue "B GLU 603": "OE1" <-> "OE2" Residue "C PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 623": "OE1" <-> "OE2" Residue "K PHE 635": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 17518 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 5132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 633, 5132 Classifications: {'peptide': 633} Link IDs: {'PTRANS': 17, 'TRANS': 615} Chain breaks: 1 Chain: "B" Number of atoms: 5112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 631, 5112 Classifications: {'peptide': 631} Link IDs: {'PTRANS': 17, 'TRANS': 613} Chain breaks: 1 Chain: "C" Number of atoms: 2243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2243 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 4, 'TRANS': 261} Chain: "K" Number of atoms: 1503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1503 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 9, 'TRANS': 176} Chain breaks: 1 Chain: "P" Number of atoms: 3466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3466 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 15, 'TRANS': 413} Chain breaks: 1 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.12, per 1000 atoms: 0.52 Number of scatterers: 17518 At special positions: 0 Unit cell: (120.4, 128.14, 191.78, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 91 16.00 P 7 15.00 O 3361 8.00 N 2981 7.00 C 11078 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.98 Conformation dependent library (CDL) restraints added in 2.4 seconds 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4084 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 80 helices and 13 sheets defined 42.1% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.74 Creating SS restraints... Processing helix chain 'A' and resid 21 through 30 removed outlier: 3.541A pdb=" N ASN A 30 " --> pdb=" O SER A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 60 removed outlier: 4.281A pdb=" N GLU A 57 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR A 60 " --> pdb=" O GLU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 98 No H-bonds generated for 'chain 'A' and resid 95 through 98' Processing helix chain 'A' and resid 110 through 114 Processing helix chain 'A' and resid 134 through 138 Processing helix chain 'A' and resid 195 through 204 Processing helix chain 'A' and resid 288 through 290 No H-bonds generated for 'chain 'A' and resid 288 through 290' Processing helix chain 'A' and resid 293 through 295 No H-bonds generated for 'chain 'A' and resid 293 through 295' Processing helix chain 'A' and resid 298 through 306 Processing helix chain 'A' and resid 400 through 421 removed outlier: 3.587A pdb=" N ALA A 420 " --> pdb=" O PHE A 416 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N GLU A 421 " --> pdb=" O SER A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 432 removed outlier: 3.679A pdb=" N ALA A 432 " --> pdb=" O LYS A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 443 removed outlier: 3.812A pdb=" N LYS A 438 " --> pdb=" O SER A 434 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 439 " --> pdb=" O LYS A 435 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY A 440 " --> pdb=" O ASN A 436 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE A 441 " --> pdb=" O LEU A 437 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N HIS A 442 " --> pdb=" O LYS A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 454 removed outlier: 4.496A pdb=" N GLU A 453 " --> pdb=" O ARG A 449 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N LEU A 454 " --> pdb=" O ARG A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 473 Processing helix chain 'A' and resid 491 through 495 Processing helix chain 'A' and resid 516 through 522 Processing helix chain 'A' and resid 547 through 559 removed outlier: 4.062A pdb=" N ALA A 558 " --> pdb=" O GLU A 554 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LYS A 559 " --> pdb=" O GLU A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 571 Processing helix chain 'A' and resid 600 through 608 Processing helix chain 'A' and resid 614 through 619 removed outlier: 4.014A pdb=" N GLY A 618 " --> pdb=" O ASN A 614 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N TYR A 619 " --> pdb=" O SER A 615 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 614 through 619' Processing helix chain 'A' and resid 633 through 644 removed outlier: 4.218A pdb=" N ALA A 644 " --> pdb=" O GLN A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 666 removed outlier: 3.510A pdb=" N ASP A 653 " --> pdb=" O LYS A 649 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER A 666 " --> pdb=" O ALA A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 688 Processing helix chain 'B' and resid 22 through 31 Processing helix chain 'B' and resid 39 through 60 removed outlier: 3.767A pdb=" N LEU B 59 " --> pdb=" O ARG B 55 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N THR B 60 " --> pdb=" O TYR B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 65 Processing helix chain 'B' and resid 95 through 102 Processing helix chain 'B' and resid 109 through 115 Processing helix chain 'B' and resid 134 through 139 removed outlier: 3.602A pdb=" N VAL B 139 " --> pdb=" O ALA B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 204 Processing helix chain 'B' and resid 299 through 306 Processing helix chain 'B' and resid 398 through 420 Processing helix chain 'B' and resid 426 through 430 Processing helix chain 'B' and resid 434 through 442 removed outlier: 3.710A pdb=" N LYS B 438 " --> pdb=" O SER B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 474 Processing helix chain 'B' and resid 500 through 506 removed outlier: 3.575A pdb=" N LYS B 505 " --> pdb=" O GLU B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 524 removed outlier: 3.703A pdb=" N GLN B 524 " --> pdb=" O TYR B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 559 removed outlier: 3.656A pdb=" N ALA B 558 " --> pdb=" O GLU B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 570 removed outlier: 3.923A pdb=" N LYS B 565 " --> pdb=" O GLU B 561 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LYS B 568 " --> pdb=" O CYS B 564 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLU B 569 " --> pdb=" O LYS B 565 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ILE B 570 " --> pdb=" O LEU B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 607 Processing helix chain 'B' and resid 617 through 620 No H-bonds generated for 'chain 'B' and resid 617 through 620' Processing helix chain 'B' and resid 633 through 644 Processing helix chain 'B' and resid 649 through 666 Processing helix chain 'B' and resid 673 through 687 Processing helix chain 'C' and resid 5 through 7 No H-bonds generated for 'chain 'C' and resid 5 through 7' Processing helix chain 'C' and resid 27 through 72 Processing helix chain 'C' and resid 79 through 111 removed outlier: 3.738A pdb=" N LYS C 107 " --> pdb=" O GLU C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 119 No H-bonds generated for 'chain 'C' and resid 116 through 119' Processing helix chain 'C' and resid 140 through 163 Processing helix chain 'C' and resid 168 through 181 Processing helix chain 'C' and resid 184 through 200 Processing helix chain 'C' and resid 203 through 226 Processing helix chain 'C' and resid 235 through 242 Processing helix chain 'C' and resid 246 through 264 Processing helix chain 'K' and resid 537 through 542 Processing helix chain 'K' and resid 550 through 570 removed outlier: 3.705A pdb=" N ALA K 569 " --> pdb=" O ASP K 565 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LYS K 570 " --> pdb=" O TYR K 566 " (cutoff:3.500A) Processing helix chain 'K' and resid 579 through 581 No H-bonds generated for 'chain 'K' and resid 579 through 581' Processing helix chain 'K' and resid 635 through 651 Processing helix chain 'K' and resid 662 through 671 removed outlier: 3.556A pdb=" N ARG K 671 " --> pdb=" O PHE K 667 " (cutoff:3.500A) Processing helix chain 'K' and resid 687 through 696 Processing helix chain 'K' and resid 707 through 720 removed outlier: 3.621A pdb=" N SER K 720 " --> pdb=" O LEU K 716 " (cutoff:3.500A) Processing helix chain 'P' and resid 32 through 40 removed outlier: 3.812A pdb=" N ASP P 37 " --> pdb=" O THR P 33 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N PHE P 39 " --> pdb=" O ALA P 35 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LYS P 40 " --> pdb=" O ASN P 36 " (cutoff:3.500A) Processing helix chain 'P' and resid 44 through 57 removed outlier: 3.793A pdb=" N GLN P 53 " --> pdb=" O LYS P 49 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLU P 56 " --> pdb=" O SER P 52 " (cutoff:3.500A) Processing helix chain 'P' and resid 62 through 73 removed outlier: 4.012A pdb=" N SER P 69 " --> pdb=" O TYR P 65 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU P 70 " --> pdb=" O GLY P 66 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA P 71 " --> pdb=" O ASN P 67 " (cutoff:3.500A) Processing helix chain 'P' and resid 79 through 90 removed outlier: 3.851A pdb=" N GLY P 83 " --> pdb=" O GLY P 79 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N THR P 86 " --> pdb=" O LEU P 82 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARG P 87 " --> pdb=" O GLY P 83 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ALA P 88 " --> pdb=" O ASP P 84 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE P 89 " --> pdb=" O ALA P 85 " (cutoff:3.500A) Processing helix chain 'P' and resid 96 through 109 removed outlier: 4.065A pdb=" N ARG P 101 " --> pdb=" O LYS P 97 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ARG P 102 " --> pdb=" O GLY P 98 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA P 103 " --> pdb=" O TYR P 99 " (cutoff:3.500A) Processing helix chain 'P' and resid 114 through 122 removed outlier: 3.918A pdb=" N VAL P 122 " --> pdb=" O ASP P 118 " (cutoff:3.500A) Processing helix chain 'P' and resid 134 through 150 removed outlier: 4.001A pdb=" N ILE P 142 " --> pdb=" O GLU P 138 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL P 143 " --> pdb=" O CYS P 139 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS P 144 " --> pdb=" O ASN P 140 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N GLN P 145 " --> pdb=" O LYS P 141 " (cutoff:3.500A) Processing helix chain 'P' and resid 188 through 200 Processing helix chain 'P' and resid 206 through 222 removed outlier: 3.918A pdb=" N LYS P 222 " --> pdb=" O GLU P 218 " (cutoff:3.500A) Processing helix chain 'P' and resid 247 through 257 Processing helix chain 'P' and resid 279 through 292 Processing helix chain 'P' and resid 303 through 305 No H-bonds generated for 'chain 'P' and resid 303 through 305' Processing helix chain 'P' and resid 307 through 310 No H-bonds generated for 'chain 'P' and resid 307 through 310' Processing helix chain 'P' and resid 315 through 322 Processing helix chain 'P' and resid 325 through 335 Processing helix chain 'P' and resid 363 through 367 Processing helix chain 'P' and resid 380 through 386 Processing helix chain 'P' and resid 408 through 418 Processing helix chain 'P' and resid 438 through 440 No H-bonds generated for 'chain 'P' and resid 438 through 440' Processing sheet with id= A, first strand: chain 'A' and resid 76 through 78 removed outlier: 3.665A pdb=" N LYS A 142 " --> pdb=" O HIS A 184 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 318 through 324 removed outlier: 3.850A pdb=" N PHE A 321 " --> pdb=" O ALA A 331 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE A 329 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS A 354 " --> pdb=" O GLY A 379 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 533 through 535 removed outlier: 5.684A pdb=" N ILE A 483 " --> pdb=" O VAL A 534 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL A 511 " --> pdb=" O ILE A 486 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 578 through 580 removed outlier: 6.485A pdb=" N LEU A 626 " --> pdb=" O THR A 579 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 72 through 75 removed outlier: 7.539A pdb=" N ILE B 75 " --> pdb=" O PRO B 212 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N THR B 214 " --> pdb=" O ILE B 75 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'B' and resid 76 through 78 Processing sheet with id= G, first strand: chain 'B' and resid 179 through 184 removed outlier: 3.599A pdb=" N LYS B 142 " --> pdb=" O HIS B 184 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 317 through 319 removed outlier: 3.962A pdb=" N ALA B 317 " --> pdb=" O ILE B 335 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE B 335 " --> pdb=" O ALA B 317 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 533 through 535 removed outlier: 5.838A pdb=" N ILE B 483 " --> pdb=" O VAL B 534 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL B 511 " --> pdb=" O ILE B 486 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'B' and resid 578 through 580 removed outlier: 6.405A pdb=" N LEU B 626 " --> pdb=" O THR B 579 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'P' and resid 226 through 229 removed outlier: 7.119A pdb=" N ALA P 341 " --> pdb=" O VAL P 227 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N THR P 229 " --> pdb=" O ALA P 341 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N CYS P 343 " --> pdb=" O THR P 229 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N TYR P 422 " --> pdb=" O LEU P 349 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N MET P 351 " --> pdb=" O TYR P 422 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N ILE P 424 " --> pdb=" O MET P 351 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'P' and resid 472 through 476 removed outlier: 7.948A pdb=" N CYS P 240 " --> pdb=" O PRO P 265 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ILE P 267 " --> pdb=" O CYS P 240 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'P' and resid 434 through 437 610 hydrogen bonds defined for protein. 1653 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: 5.26 Time building geometry restraints manager: 7.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.00 - 1.29: 3013 1.29 - 1.59: 14665 1.59 - 1.89: 158 1.89 - 2.18: 0 2.18 - 2.48: 1 Bond restraints: 17837 Sorted by residual: bond pdb=" CB PRO C 230 " pdb=" CG PRO C 230 " ideal model delta sigma weight residual 1.492 2.480 -0.988 5.00e-02 4.00e+02 3.90e+02 bond pdb=" CG PRO C 230 " pdb=" CD PRO C 230 " ideal model delta sigma weight residual 1.503 0.998 0.505 3.40e-02 8.65e+02 2.21e+02 bond pdb=" N PRO C 230 " pdb=" CA PRO C 230 " ideal model delta sigma weight residual 1.470 1.363 0.107 1.22e-02 6.72e+03 7.70e+01 bond pdb=" N PRO C 230 " pdb=" CD PRO C 230 " ideal model delta sigma weight residual 1.473 1.561 -0.088 1.40e-02 5.10e+03 3.96e+01 bond pdb=" CA PRO C 230 " pdb=" CB PRO C 230 " ideal model delta sigma weight residual 1.535 1.483 0.051 1.72e-02 3.38e+03 8.87e+00 ... (remaining 17832 not shown) Histogram of bond angle deviations from ideal: 0.05 - 29.56: 1 29.56 - 59.08: 0 59.08 - 88.59: 0 88.59 - 118.10: 13473 118.10 - 147.62: 10518 Bond angle restraints: 23992 Sorted by residual: angle pdb=" CB PRO C 230 " pdb=" CG PRO C 230 " pdb=" CD PRO C 230 " ideal model delta sigma weight residual 106.10 0.05 106.05 3.20e+00 9.77e-02 1.10e+03 angle pdb=" CA PRO C 230 " pdb=" N PRO C 230 " pdb=" CD PRO C 230 " ideal model delta sigma weight residual 112.00 89.93 22.07 1.40e+00 5.10e-01 2.48e+02 angle pdb=" N PRO C 230 " pdb=" CA PRO C 230 " pdb=" CB PRO C 230 " ideal model delta sigma weight residual 103.19 89.02 14.17 1.00e+00 1.00e+00 2.01e+02 angle pdb=" CA PRO C 230 " pdb=" CB PRO C 230 " pdb=" CG PRO C 230 " ideal model delta sigma weight residual 104.50 88.59 15.91 1.90e+00 2.77e-01 7.01e+01 angle pdb=" CA PRO B 79 " pdb=" N PRO B 79 " pdb=" CD PRO B 79 " ideal model delta sigma weight residual 112.00 101.69 10.31 1.40e+00 5.10e-01 5.42e+01 ... (remaining 23987 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 9398 17.86 - 35.72: 1196 35.72 - 53.58: 270 53.58 - 71.44: 57 71.44 - 89.30: 24 Dihedral angle restraints: 10945 sinusoidal: 4640 harmonic: 6305 Sorted by residual: dihedral pdb=" CA MET C 112 " pdb=" C MET C 112 " pdb=" N PRO C 113 " pdb=" CA PRO C 113 " ideal model delta harmonic sigma weight residual -180.00 -143.82 -36.18 0 5.00e+00 4.00e-02 5.24e+01 dihedral pdb=" CA THR B 309 " pdb=" C THR B 309 " pdb=" N ASN B 310 " pdb=" CA ASN B 310 " ideal model delta harmonic sigma weight residual 180.00 155.54 24.46 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" N PRO C 230 " pdb=" C PRO C 230 " pdb=" CA PRO C 230 " pdb=" CB PRO C 230 " ideal model delta harmonic sigma weight residual 115.10 103.48 11.62 0 2.50e+00 1.60e-01 2.16e+01 ... (remaining 10942 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 2366 0.072 - 0.144: 231 0.144 - 0.216: 11 0.216 - 0.289: 1 0.289 - 0.361: 1 Chirality restraints: 2610 Sorted by residual: chirality pdb=" CA PRO C 230 " pdb=" N PRO C 230 " pdb=" C PRO C 230 " pdb=" CB PRO C 230 " both_signs ideal model delta sigma weight residual False 2.72 2.36 0.36 2.00e-01 2.50e+01 3.25e+00 chirality pdb=" CB THR B 190 " pdb=" CA THR B 190 " pdb=" OG1 THR B 190 " pdb=" CG2 THR B 190 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.24 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CA PRO K 523 " pdb=" N PRO K 523 " pdb=" C PRO K 523 " pdb=" CB PRO K 523 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 9.95e-01 ... (remaining 2607 not shown) Planarity restraints: 3076 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 61 " 0.103 5.00e-02 4.00e+02 1.54e-01 3.77e+01 pdb=" N PRO A 62 " -0.266 5.00e-02 4.00e+02 pdb=" CA PRO A 62 " 0.086 5.00e-02 4.00e+02 pdb=" CD PRO A 62 " 0.077 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 61 " 0.064 5.00e-02 4.00e+02 9.60e-02 1.48e+01 pdb=" N PRO B 62 " -0.166 5.00e-02 4.00e+02 pdb=" CA PRO B 62 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO B 62 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 78 " -0.064 5.00e-02 4.00e+02 9.04e-02 1.31e+01 pdb=" N PRO B 79 " 0.156 5.00e-02 4.00e+02 pdb=" CA PRO B 79 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO B 79 " -0.048 5.00e-02 4.00e+02 ... (remaining 3073 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 345 2.67 - 3.23: 16545 3.23 - 3.79: 25443 3.79 - 4.34: 32776 4.34 - 4.90: 53752 Nonbonded interactions: 128861 Sorted by model distance: nonbonded pdb=" O LEU A 27 " pdb=" OG1 THR A 31 " model vdw 2.119 2.440 nonbonded pdb=" O ASN C 178 " pdb=" N VAL C 182 " model vdw 2.167 2.520 nonbonded pdb=" O GLY P 66 " pdb=" OG SER P 69 " model vdw 2.177 2.440 nonbonded pdb=" OE2 GLU C 18 " pdb=" NZ LYS K 570 " model vdw 2.204 2.520 nonbonded pdb=" O GLU A 643 " pdb=" NZ LYS A 646 " model vdw 2.204 2.520 ... (remaining 128856 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 10 through 220 or resid 273 through 692 or resid 801)) selection = chain 'B' } 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: 2.040 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: 8.680 Check model and map are aligned: 0.260 Set scattering table: 0.150 Process input model: 43.420 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6702 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 : 0.009 0.988 17837 Z= 0.351 Angle : 1.018 106.053 23992 Z= 0.467 Chirality : 0.043 0.361 2610 Planarity : 0.006 0.154 3076 Dihedral : 16.747 89.296 6861 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.52 % Allowed : 9.13 % Favored : 90.35 % Rotamer Outliers : 0.26 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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: -1.57 (0.18), residues: 2124 helix: 0.38 (0.17), residues: 942 sheet: -0.54 (0.37), residues: 227 loop : -2.75 (0.18), residues: 955 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 327 time to evaluate : 2.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 328 average time/residue: 0.3503 time to fit residues: 165.2341 Evaluate side-chains 333 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 329 time to evaluate : 2.061 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2956 time to fit residues: 4.7877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 10.0000 chunk 160 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 chunk 108 optimal weight: 0.9980 chunk 85 optimal weight: 0.9980 chunk 166 optimal weight: 0.0470 chunk 64 optimal weight: 3.9990 chunk 101 optimal weight: 0.6980 chunk 123 optimal weight: 3.9990 chunk 192 optimal weight: 2.9990 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 GLN C 146 GLN P 67 ASN ** P 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 311 GLN P 342 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6711 moved from start: 0.0516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.061 17837 Z= 0.184 Angle : 0.565 14.401 23992 Z= 0.294 Chirality : 0.041 0.199 2610 Planarity : 0.005 0.104 3076 Dihedral : 4.877 69.568 2342 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.42 % Allowed : 8.95 % Favored : 90.63 % Rotamer Outliers : 2.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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: -1.50 (0.18), residues: 2124 helix: 0.48 (0.18), residues: 943 sheet: -0.67 (0.36), residues: 231 loop : -2.72 (0.18), residues: 950 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 345 time to evaluate : 2.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 30 residues processed: 364 average time/residue: 0.3422 time to fit residues: 181.0169 Evaluate side-chains 360 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 330 time to evaluate : 2.156 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.1788 time to fit residues: 13.0205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 106 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 160 optimal weight: 2.9990 chunk 131 optimal weight: 50.0000 chunk 53 optimal weight: 1.9990 chunk 192 optimal weight: 0.0770 chunk 208 optimal weight: 9.9990 chunk 171 optimal weight: 6.9990 chunk 191 optimal weight: 7.9990 chunk 65 optimal weight: 0.0020 chunk 154 optimal weight: 0.1980 overall best weight: 1.0550 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 640 GLN C 20 HIS C 22 ASN ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6752 moved from start: 0.0930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 17837 Z= 0.239 Angle : 0.581 12.977 23992 Z= 0.304 Chirality : 0.042 0.201 2610 Planarity : 0.005 0.083 3076 Dihedral : 5.004 77.324 2342 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.38 % Allowed : 9.37 % Favored : 90.25 % Rotamer Outliers : 2.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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: -1.47 (0.18), residues: 2124 helix: 0.55 (0.18), residues: 935 sheet: -0.67 (0.36), residues: 231 loop : -2.71 (0.18), residues: 958 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 341 time to evaluate : 1.863 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 outliers start: 41 outliers final: 22 residues processed: 367 average time/residue: 0.3386 time to fit residues: 179.6567 Evaluate side-chains 355 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 333 time to evaluate : 2.126 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.1919 time to fit residues: 10.5613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 190 optimal weight: 10.0000 chunk 145 optimal weight: 20.0000 chunk 100 optimal weight: 1.9990 chunk 21 optimal weight: 0.0470 chunk 92 optimal weight: 0.9980 chunk 129 optimal weight: 1.9990 chunk 193 optimal weight: 7.9990 chunk 204 optimal weight: 9.9990 chunk 101 optimal weight: 1.9990 chunk 183 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 overall best weight: 1.4084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 ASN ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6786 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.048 17837 Z= 0.303 Angle : 0.620 11.860 23992 Z= 0.324 Chirality : 0.043 0.204 2610 Planarity : 0.005 0.077 3076 Dihedral : 5.251 88.728 2342 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.38 % Allowed : 9.70 % Favored : 89.92 % Rotamer Outliers : 1.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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: -1.57 (0.18), residues: 2124 helix: 0.45 (0.17), residues: 934 sheet: -0.69 (0.36), residues: 229 loop : -2.76 (0.18), residues: 961 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 349 time to evaluate : 2.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 21 residues processed: 365 average time/residue: 0.3523 time to fit residues: 185.2052 Evaluate side-chains 359 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 338 time to evaluate : 2.072 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.1738 time to fit residues: 10.1031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 170 optimal weight: 30.0000 chunk 116 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 152 optimal weight: 1.9990 chunk 84 optimal weight: 0.0270 chunk 174 optimal weight: 0.0170 chunk 141 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 183 optimal weight: 6.9990 chunk 51 optimal weight: 0.6980 overall best weight: 0.4676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6729 moved from start: 0.1383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.040 17837 Z= 0.163 Angle : 0.575 11.570 23992 Z= 0.297 Chirality : 0.040 0.178 2610 Planarity : 0.004 0.070 3076 Dihedral : 5.053 89.656 2342 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.85 % Favored : 90.77 % Rotamer Outliers : 1.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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: -1.39 (0.18), residues: 2124 helix: 0.61 (0.18), residues: 938 sheet: -0.58 (0.37), residues: 223 loop : -2.67 (0.18), residues: 963 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 341 time to evaluate : 2.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 16 residues processed: 360 average time/residue: 0.3463 time to fit residues: 181.6311 Evaluate side-chains 351 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 335 time to evaluate : 2.059 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.2329 time to fit residues: 9.7614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 68 optimal weight: 0.0270 chunk 184 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 120 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 chunk 205 optimal weight: 0.8980 chunk 170 optimal weight: 40.0000 chunk 94 optimal weight: 0.0670 chunk 17 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 overall best weight: 0.4976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 326 GLN ** B 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 36 ASN P 140 ASN ** P 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6719 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.061 17837 Z= 0.167 Angle : 0.573 10.641 23992 Z= 0.295 Chirality : 0.040 0.188 2610 Planarity : 0.004 0.062 3076 Dihedral : 4.899 88.915 2342 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.66 % Favored : 90.96 % Rotamer Outliers : 1.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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: -1.30 (0.18), residues: 2124 helix: 0.68 (0.18), residues: 942 sheet: -0.52 (0.37), residues: 225 loop : -2.66 (0.18), residues: 957 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 334 time to evaluate : 1.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 18 residues processed: 348 average time/residue: 0.3424 time to fit residues: 172.4331 Evaluate side-chains 344 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 326 time to evaluate : 2.033 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1631 time to fit residues: 8.4809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 197 optimal weight: 8.9990 chunk 23 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 149 optimal weight: 0.7980 chunk 172 optimal weight: 6.9990 chunk 114 optimal weight: 1.9990 chunk 204 optimal weight: 20.0000 chunk 127 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 94 optimal weight: 0.0870 chunk 126 optimal weight: 1.9990 overall best weight: 1.3764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 326 GLN ** B 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 674 GLN ** C 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 427 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6788 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.040 17837 Z= 0.304 Angle : 0.651 10.195 23992 Z= 0.336 Chirality : 0.043 0.184 2610 Planarity : 0.004 0.058 3076 Dihedral : 5.142 84.467 2342 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.33 % Allowed : 9.98 % Favored : 89.69 % Rotamer Outliers : 1.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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: -1.45 (0.18), residues: 2124 helix: 0.54 (0.17), residues: 943 sheet: -0.50 (0.38), residues: 218 loop : -2.72 (0.18), residues: 963 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 345 time to evaluate : 2.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 19 residues processed: 363 average time/residue: 0.3652 time to fit residues: 192.1066 Evaluate side-chains 356 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 337 time to evaluate : 2.181 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1846 time to fit residues: 9.0924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 81 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 129 optimal weight: 0.5980 chunk 139 optimal weight: 0.3980 chunk 101 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 160 optimal weight: 0.6980 chunk 185 optimal weight: 50.0000 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 GLN ** B 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 217 GLN ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6740 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 17837 Z= 0.187 Angle : 0.618 13.575 23992 Z= 0.316 Chirality : 0.041 0.212 2610 Planarity : 0.004 0.057 3076 Dihedral : 4.996 81.699 2342 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.33 % Allowed : 8.52 % Favored : 91.15 % Rotamer Outliers : 1.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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: -1.37 (0.18), residues: 2124 helix: 0.62 (0.18), residues: 946 sheet: -0.50 (0.37), residues: 223 loop : -2.71 (0.18), residues: 955 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 332 time to evaluate : 2.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 10 residues processed: 341 average time/residue: 0.3536 time to fit residues: 173.6008 Evaluate side-chains 340 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 330 time to evaluate : 2.003 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1798 time to fit residues: 6.4645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 195 optimal weight: 7.9990 chunk 178 optimal weight: 0.0470 chunk 190 optimal weight: 0.6980 chunk 114 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 149 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 172 optimal weight: 0.8980 chunk 180 optimal weight: 20.0000 chunk 189 optimal weight: 10.0000 chunk 125 optimal weight: 2.9990 overall best weight: 1.0680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 HIS ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 GLN ** B 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6770 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.065 17837 Z= 0.258 Angle : 0.648 11.065 23992 Z= 0.333 Chirality : 0.042 0.183 2610 Planarity : 0.004 0.058 3076 Dihedral : 5.093 80.693 2342 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.33 % Allowed : 9.65 % Favored : 90.02 % Rotamer Outliers : 0.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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: -1.47 (0.18), residues: 2124 helix: 0.50 (0.17), residues: 948 sheet: -0.54 (0.37), residues: 223 loop : -2.74 (0.18), residues: 953 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 338 time to evaluate : 2.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 10 residues processed: 346 average time/residue: 0.3513 time to fit residues: 176.4740 Evaluate side-chains 344 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 334 time to evaluate : 2.049 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1687 time to fit residues: 6.3661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 201 optimal weight: 0.6980 chunk 122 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 chunk 139 optimal weight: 0.3980 chunk 211 optimal weight: 40.0000 chunk 194 optimal weight: 10.0000 chunk 168 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 129 optimal weight: 0.6980 chunk 103 optimal weight: 0.4980 chunk 133 optimal weight: 10.0000 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 HIS ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 ASN ** B 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 217 GLN ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6731 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 17837 Z= 0.192 Angle : 0.630 12.000 23992 Z= 0.322 Chirality : 0.041 0.188 2610 Planarity : 0.004 0.057 3076 Dihedral : 4.953 77.442 2342 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.33 % Allowed : 8.15 % Favored : 91.53 % Rotamer Outliers : 0.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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: -1.38 (0.18), residues: 2124 helix: 0.61 (0.18), residues: 946 sheet: -0.61 (0.36), residues: 225 loop : -2.68 (0.18), residues: 953 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 340 time to evaluate : 2.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 342 average time/residue: 0.3570 time to fit residues: 178.1718 Evaluate side-chains 335 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 333 time to evaluate : 2.061 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1670 time to fit residues: 3.8129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 155 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 168 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 172 optimal weight: 0.8980 chunk 21 optimal weight: 0.2980 chunk 31 optimal weight: 0.9990 chunk 147 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.194747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.148353 restraints weight = 26755.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.149737 restraints weight = 17370.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.150992 restraints weight = 13882.911| |-----------------------------------------------------------------------------| r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6769 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.066 17837 Z= 0.223 Angle : 0.648 11.673 23992 Z= 0.332 Chirality : 0.041 0.184 2610 Planarity : 0.004 0.061 3076 Dihedral : 4.939 77.194 2342 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.33 % Allowed : 9.04 % Favored : 90.63 % Rotamer Outliers : 0.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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: -1.39 (0.18), residues: 2124 helix: 0.55 (0.18), residues: 956 sheet: -0.56 (0.36), residues: 225 loop : -2.67 (0.18), residues: 943 =============================================================================== Job complete usr+sys time: 4023.13 seconds wall clock time: 73 minutes 40.03 seconds (4420.03 seconds total)