Starting phenix.real_space_refine (version: 1.21rc1) on Sun Jul 9 19:25:34 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7egm_31136/07_2023/7egm_31136.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7egm_31136/07_2023/7egm_31136.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7egm_31136/07_2023/7egm_31136.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7egm_31136/07_2023/7egm_31136.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7egm_31136/07_2023/7egm_31136.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7egm_31136/07_2023/7egm_31136.pdb" } resolution = 3.6 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= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 63 5.16 5 C 12656 2.51 5 N 3382 2.21 5 O 3718 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 526": "NH1" <-> "NH2" Residue "A ARG 546": "NH1" <-> "NH2" Residue "A PHE 567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 572": "NH1" <-> "NH2" Residue "B PHE 696": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 772": "NH1" <-> "NH2" Residue "B TYR 777": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 881": "NH1" <-> "NH2" Residue "B ARG 926": "NH1" <-> "NH2" Residue "B PHE 1025": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1028": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1102": "NH1" <-> "NH2" Residue "B PHE 1183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1256": "OE1" <-> "OE2" Residue "B TYR 1299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 435": "NH1" <-> "NH2" Residue "C PHE 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 561": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 615": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 640": "NH1" <-> "NH2" Residue "C ARG 662": "NH1" <-> "NH2" Residue "C PHE 730": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 417": "OD1" <-> "OD2" Residue "D PHE 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 525": "OE1" <-> "OE2" Residue "D ARG 564": "NH1" <-> "NH2" Residue "D PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 635": "OE1" <-> "OE2" Residue "D TYR 666": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 667": "NH1" <-> "NH2" Residue "D PHE 671": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 681": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 685": "OE1" <-> "OE2" Residue "D ASP 695": "OD1" <-> "OD2" Residue "D GLU 711": "OE1" <-> "OE2" Residue "D PHE 729": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 761": "OE1" <-> "OE2" Residue "H PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 163": "NH1" <-> "NH2" Residue "H PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 299": "NH1" <-> "NH2" Residue "H ARG 428": "NH1" <-> "NH2" Residue "H ASP 510": "OD1" <-> "OD2" Residue "H TYR 535": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 538": "OD1" <-> "OD2" Residue "H ARG 541": "NH1" <-> "NH2" Residue "I ARG 77": "NH1" <-> "NH2" Residue "I ARG 84": "NH1" <-> "NH2" Residue "I PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 135": "NH1" <-> "NH2" Residue "I ARG 143": "NH1" <-> "NH2" Residue "J ARG 241": "NH1" <-> "NH2" Residue "J PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 319": "NH1" <-> "NH2" Residue "J ARG 322": "NH1" <-> "NH2" Residue "J GLU 470": "OE1" <-> "OE2" Residue "J PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 566": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 345": "NH1" <-> "NH2" Residue "E ARG 347": "NH1" <-> "NH2" Residue "E PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 368": "NH1" <-> "NH2" Residue "E PHE 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 459": "OE1" <-> "OE2" Residue "E GLU 525": "OE1" <-> "OE2" Residue "E TYR 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 600": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 666": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 667": "NH1" <-> "NH2" Residue "E PHE 681": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 688": "NH1" <-> "NH2" Residue "E PHE 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 729": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 19819 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 877 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 3, 'TRANS': 105} Chain: "B" Number of atoms: 4098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 4098 Classifications: {'peptide': 507} Link IDs: {'PTRANS': 25, 'TRANS': 481} Chain breaks: 8 Chain: "C" Number of atoms: 2747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2747 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 15, 'TRANS': 321} Chain breaks: 1 Chain: "D" Number of atoms: 3250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3250 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 22, 'TRANS': 372} Chain breaks: 4 Chain: "H" Number of atoms: 3145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3145 Classifications: {'peptide': 388} Link IDs: {'PTRANS': 16, 'TRANS': 371} Chain breaks: 5 Chain: "I" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 888 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 3, 'TRANS': 102} Chain breaks: 1 Chain: "J" Number of atoms: 1360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1360 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 12, 'TRANS': 154} Chain breaks: 3 Chain: "E" Number of atoms: 3454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3454 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 24, 'TRANS': 397} Chain breaks: 3 Time building chain proxies: 9.38, per 1000 atoms: 0.47 Number of scatterers: 19819 At special positions: 0 Unit cell: (148.24, 226.656, 108.494, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 63 16.00 O 3718 8.00 N 3382 7.00 C 12656 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: 7.35 Conformation dependent library (CDL) restraints added in 3.0 seconds 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4714 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 9 sheets defined 55.4% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 489 through 494 Processing helix chain 'A' and resid 494 through 518 removed outlier: 3.665A pdb=" N LEU A 500 " --> pdb=" O ILE A 496 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASP A 514 " --> pdb=" O ASN A 510 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LEU A 516 " --> pdb=" O CYS A 512 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN A 518 " --> pdb=" O ASP A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 538 Processing helix chain 'A' and resid 538 through 557 removed outlier: 3.884A pdb=" N ASN A 557 " --> pdb=" O GLU A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 588 removed outlier: 3.982A pdb=" N ALA A 579 " --> pdb=" O ASN A 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 692 removed outlier: 3.931A pdb=" N LYS B 688 " --> pdb=" O LYS B 684 " (cutoff:3.500A) Processing helix chain 'B' and resid 707 through 714 Processing helix chain 'B' and resid 719 through 734 removed outlier: 3.541A pdb=" N ALA B 725 " --> pdb=" O GLU B 721 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR B 732 " --> pdb=" O THR B 728 " (cutoff:3.500A) Processing helix chain 'B' and resid 747 through 765 removed outlier: 3.576A pdb=" N ASN B 762 " --> pdb=" O ASN B 758 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER B 764 " --> pdb=" O LEU B 760 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN B 765 " --> pdb=" O SER B 761 " (cutoff:3.500A) Processing helix chain 'B' and resid 793 through 800 Processing helix chain 'B' and resid 883 through 896 Processing helix chain 'B' and resid 909 through 929 removed outlier: 3.560A pdb=" N THR B 920 " --> pdb=" O ASP B 916 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N SER B 929 " --> pdb=" O LEU B 925 " (cutoff:3.500A) Processing helix chain 'B' and resid 933 through 938 Processing helix chain 'B' and resid 942 through 957 removed outlier: 3.982A pdb=" N TRP B 953 " --> pdb=" O SER B 949 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU B 954 " --> pdb=" O ASP B 950 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU B 956 " --> pdb=" O LEU B 952 " (cutoff:3.500A) Processing helix chain 'B' and resid 965 through 983 removed outlier: 3.806A pdb=" N LEU B 969 " --> pdb=" O ASN B 965 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS B 972 " --> pdb=" O ILE B 968 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ILE B 977 " --> pdb=" O LYS B 973 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE B 982 " --> pdb=" O VAL B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 990 through 1003 removed outlier: 3.703A pdb=" N LEU B 998 " --> pdb=" O CYS B 994 " (cutoff:3.500A) Processing helix chain 'B' and resid 1033 through 1037 removed outlier: 4.417A pdb=" N GLN B1036 " --> pdb=" O GLY B1033 " (cutoff:3.500A) Processing helix chain 'B' and resid 1038 through 1046 removed outlier: 3.587A pdb=" N ALA B1044 " --> pdb=" O VAL B1040 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1063 removed outlier: 3.620A pdb=" N PHE B1057 " --> pdb=" O ASN B1053 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASN B1063 " --> pdb=" O SER B1059 " (cutoff:3.500A) Processing helix chain 'B' and resid 1080 through 1091 removed outlier: 4.092A pdb=" N ASN B1090 " --> pdb=" O ARG B1086 " (cutoff:3.500A) Processing helix chain 'B' and resid 1103 through 1115 removed outlier: 3.578A pdb=" N ASN B1107 " --> pdb=" O HIS B1103 " (cutoff:3.500A) Processing helix chain 'B' and resid 1118 through 1125 removed outlier: 3.739A pdb=" N GLN B1125 " --> pdb=" O GLN B1121 " (cutoff:3.500A) Processing helix chain 'B' and resid 1130 through 1154 Proline residue: B1138 - end of helix Processing helix chain 'B' and resid 1188 through 1195 Processing helix chain 'B' and resid 1199 through 1213 Processing helix chain 'B' and resid 1233 through 1260 removed outlier: 3.713A pdb=" N ILE B1239 " --> pdb=" O PRO B1235 " (cutoff:3.500A) Processing helix chain 'B' and resid 1265 through 1271 Processing helix chain 'B' and resid 1278 through 1286 removed outlier: 3.537A pdb=" N ILE B1282 " --> pdb=" O THR B1278 " (cutoff:3.500A) Processing helix chain 'B' and resid 1292 through 1314 removed outlier: 4.090A pdb=" N ILE B1296 " --> pdb=" O ASP B1292 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLU B1314 " --> pdb=" O LEU B1310 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 400 removed outlier: 3.817A pdb=" N SER C 375 " --> pdb=" O LYS C 371 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU C 377 " --> pdb=" O TYR C 373 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N TYR C 383 " --> pdb=" O HIS C 379 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP C 386 " --> pdb=" O LYS C 382 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N THR C 398 " --> pdb=" O SER C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 443 through 450 Processing helix chain 'C' and resid 487 through 499 Processing helix chain 'C' and resid 509 through 523 removed outlier: 4.078A pdb=" N ILE C 513 " --> pdb=" O HIS C 509 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN C 522 " --> pdb=" O GLN C 518 " (cutoff:3.500A) Processing helix chain 'C' and resid 571 through 584 Processing helix chain 'C' and resid 589 through 610 removed outlier: 3.724A pdb=" N ALA C 594 " --> pdb=" O VAL C 590 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N HIS C 595 " --> pdb=" O THR C 591 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER C 607 " --> pdb=" O MET C 603 " (cutoff:3.500A) Processing helix chain 'C' and resid 635 through 639 removed outlier: 3.623A pdb=" N VAL C 638 " --> pdb=" O LEU C 635 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N TYR C 639 " --> pdb=" O ASP C 636 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 635 through 639' Processing helix chain 'C' and resid 641 through 646 Processing helix chain 'C' and resid 656 through 663 Processing helix chain 'D' and resid 308 through 312 removed outlier: 3.789A pdb=" N LYS D 312 " --> pdb=" O SER D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 327 removed outlier: 3.801A pdb=" N VAL D 324 " --> pdb=" O HIS D 320 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLN D 325 " --> pdb=" O SER D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 331 removed outlier: 3.702A pdb=" N PHE D 331 " --> pdb=" O PRO D 328 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 328 through 331' Processing helix chain 'D' and resid 343 through 355 removed outlier: 3.642A pdb=" N PHE D 349 " --> pdb=" O ARG D 345 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ASN D 352 " --> pdb=" O ASN D 348 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER D 353 " --> pdb=" O PHE D 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 388 removed outlier: 3.567A pdb=" N TRP D 388 " --> pdb=" O PHE D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 444 Processing helix chain 'D' and resid 451 through 468 removed outlier: 3.746A pdb=" N LYS D 455 " --> pdb=" O SER D 451 " (cutoff:3.500A) Processing helix chain 'D' and resid 518 through 522 removed outlier: 3.534A pdb=" N GLU D 521 " --> pdb=" O LYS D 518 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLN D 522 " --> pdb=" O ILE D 519 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 518 through 522' Processing helix chain 'D' and resid 528 through 542 Processing helix chain 'D' and resid 545 through 554 Processing helix chain 'D' and resid 557 through 567 Processing helix chain 'D' and resid 589 through 594 removed outlier: 3.751A pdb=" N LEU D 592 " --> pdb=" O LEU D 589 " (cutoff:3.500A) Processing helix chain 'D' and resid 605 through 615 removed outlier: 3.638A pdb=" N SER D 609 " --> pdb=" O ASN D 605 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR D 610 " --> pdb=" O PRO D 606 " (cutoff:3.500A) Processing helix chain 'D' and resid 619 through 640 removed outlier: 3.564A pdb=" N GLN D 640 " --> pdb=" O SER D 636 " (cutoff:3.500A) Processing helix chain 'D' and resid 673 through 741 removed outlier: 3.511A pdb=" N ARG D 677 " --> pdb=" O THR D 673 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER D 741 " --> pdb=" O VAL D 737 " (cutoff:3.500A) Processing helix chain 'D' and resid 762 through 776 removed outlier: 3.703A pdb=" N LYS D 776 " --> pdb=" O SER D 772 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 60 removed outlier: 3.856A pdb=" N MET H 59 " --> pdb=" O PRO H 56 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL H 60 " --> pdb=" O SER H 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 56 through 60' Processing helix chain 'H' and resid 70 through 106 removed outlier: 4.050A pdb=" N SER H 74 " --> pdb=" O PRO H 70 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU H 78 " --> pdb=" O SER H 74 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU H 85 " --> pdb=" O SER H 81 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N HIS H 87 " --> pdb=" O LYS H 83 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL H 100 " --> pdb=" O MET H 96 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA H 101 " --> pdb=" O LYS H 97 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG H 105 " --> pdb=" O ALA H 101 " (cutoff:3.500A) Processing helix chain 'H' and resid 313 through 319 removed outlier: 3.636A pdb=" N ILE H 317 " --> pdb=" O GLN H 313 " (cutoff:3.500A) Processing helix chain 'H' and resid 324 through 338 removed outlier: 4.557A pdb=" N ILE H 332 " --> pdb=" O ALA H 328 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N TYR H 333 " --> pdb=" O ILE H 329 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N HIS H 337 " --> pdb=" O TYR H 333 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU H 338 " --> pdb=" O LYS H 334 " (cutoff:3.500A) Processing helix chain 'H' and resid 382 through 387 removed outlier: 4.262A pdb=" N THR H 387 " --> pdb=" O THR H 383 " (cutoff:3.500A) Processing helix chain 'H' and resid 403 through 408 Processing helix chain 'H' and resid 457 through 510 removed outlier: 4.120A pdb=" N ALA H 463 " --> pdb=" O SER H 459 " (cutoff:3.500A) Proline residue: H 478 - end of helix removed outlier: 3.623A pdb=" N GLU H 486 " --> pdb=" O LEU H 482 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASN H 493 " --> pdb=" O SER H 489 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE H 507 " --> pdb=" O PHE H 503 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER H 508 " --> pdb=" O PHE H 504 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP H 510 " --> pdb=" O LYS H 506 " (cutoff:3.500A) Processing helix chain 'H' and resid 513 through 521 removed outlier: 4.452A pdb=" N ILE H 519 " --> pdb=" O LEU H 515 " (cutoff:3.500A) Processing helix chain 'H' and resid 522 through 531 removed outlier: 3.757A pdb=" N LEU H 529 " --> pdb=" O ALA H 525 " (cutoff:3.500A) Processing helix chain 'H' and resid 544 through 549 Processing helix chain 'H' and resid 549 through 564 removed outlier: 3.904A pdb=" N LEU H 553 " --> pdb=" O ASN H 549 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG H 554 " --> pdb=" O GLU H 550 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU H 555 " --> pdb=" O ALA H 551 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU H 558 " --> pdb=" O ARG H 554 " (cutoff:3.500A) Processing helix chain 'I' and resid 68 through 81 removed outlier: 3.884A pdb=" N LYS I 75 " --> pdb=" O GLN I 71 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLN I 76 " --> pdb=" O GLN I 72 " (cutoff:3.500A) Processing helix chain 'I' and resid 102 through 122 removed outlier: 3.607A pdb=" N ALA I 117 " --> pdb=" O SER I 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 140 through 151 removed outlier: 3.621A pdb=" N MET I 146 " --> pdb=" O ILE I 142 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN I 149 " --> pdb=" O LEU I 145 " (cutoff:3.500A) Processing helix chain 'I' and resid 152 through 154 No H-bonds generated for 'chain 'I' and resid 152 through 154' Processing helix chain 'J' and resid 230 through 241 removed outlier: 3.787A pdb=" N SER J 235 " --> pdb=" O THR J 231 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LYS J 236 " --> pdb=" O ASN J 232 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N SER J 238 " --> pdb=" O ILE J 234 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU J 239 " --> pdb=" O SER J 235 " (cutoff:3.500A) Processing helix chain 'J' and resid 284 through 294 Processing helix chain 'J' and resid 329 through 335 Processing helix chain 'J' and resid 450 through 458 removed outlier: 3.555A pdb=" N LEU J 454 " --> pdb=" O GLU J 450 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU J 455 " --> pdb=" O LYS J 451 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU J 456 " --> pdb=" O ASN J 452 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG J 457 " --> pdb=" O THR J 453 " (cutoff:3.500A) Processing helix chain 'J' and resid 465 through 500 removed outlier: 3.657A pdb=" N HIS J 471 " --> pdb=" O LYS J 467 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N VAL J 485 " --> pdb=" O GLY J 481 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS J 495 " --> pdb=" O LYS J 491 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN J 498 " --> pdb=" O LYS J 494 " (cutoff:3.500A) Processing helix chain 'E' and resid 310 through 312 No H-bonds generated for 'chain 'E' and resid 310 through 312' Processing helix chain 'E' and resid 320 through 327 Processing helix chain 'E' and resid 328 through 331 Processing helix chain 'E' and resid 339 through 355 Processing helix chain 'E' and resid 363 through 371 removed outlier: 3.800A pdb=" N ALA E 367 " --> pdb=" O SER E 363 " (cutoff:3.500A) Processing helix chain 'E' and resid 374 through 388 Processing helix chain 'E' and resid 433 through 444 Processing helix chain 'E' and resid 447 through 468 Processing helix chain 'E' and resid 514 through 524 removed outlier: 3.926A pdb=" N ASP E 524 " --> pdb=" O LEU E 520 " (cutoff:3.500A) Processing helix chain 'E' and resid 528 through 542 Processing helix chain 'E' and resid 545 through 554 removed outlier: 3.640A pdb=" N VAL E 549 " --> pdb=" O ASP E 545 " (cutoff:3.500A) Processing helix chain 'E' and resid 557 through 566 Processing helix chain 'E' and resid 591 through 595 removed outlier: 3.566A pdb=" N ALA E 595 " --> pdb=" O LEU E 592 " (cutoff:3.500A) Processing helix chain 'E' and resid 605 through 616 Processing helix chain 'E' and resid 619 through 627 removed outlier: 3.510A pdb=" N VAL E 623 " --> pdb=" O ASN E 619 " (cutoff:3.500A) Processing helix chain 'E' and resid 637 through 644 Processing helix chain 'E' and resid 648 through 747 removed outlier: 3.697A pdb=" N HIS E 652 " --> pdb=" O LYS E 648 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE E 653 " --> pdb=" O PRO E 649 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA E 696 " --> pdb=" O GLU E 692 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LYS E 697 " --> pdb=" O LYS E 693 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N LYS E 702 " --> pdb=" O LEU E 698 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N LYS E 703 " --> pdb=" O ASN E 699 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LEU E 704 " --> pdb=" O HIS E 700 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N MET E 708 " --> pdb=" O LEU E 704 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU E 709 " --> pdb=" O GLU E 705 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASN E 732 " --> pdb=" O ASN E 728 " (cutoff:3.500A) Processing helix chain 'E' and resid 763 through 776 removed outlier: 4.737A pdb=" N LYS E 776 " --> pdb=" O SER E 772 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 705 through 706 removed outlier: 5.953A pdb=" N ILE B 705 " --> pdb=" O ILE C 427 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 1006 through 1007 removed outlier: 4.740A pdb=" N GLN B1006 " --> pdb=" O ASN B1026 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 457 through 461 Processing sheet with id=AA4, first strand: chain 'C' and resid 543 through 552 Processing sheet with id=AA5, first strand: chain 'D' and resid 414 through 417 Processing sheet with id=AA6, first strand: chain 'H' and resid 281 through 283 removed outlier: 3.595A pdb=" N ILE H 442 " --> pdb=" O LEU H 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 184 through 189 removed outlier: 3.816A pdb=" N SER H 184 " --> pdb=" O LEU H 298 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER H 296 " --> pdb=" O VAL H 186 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N VAL H 291 " --> pdb=" O VAL H 427 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR H 425 " --> pdb=" O CYS H 293 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 308 through 309 Processing sheet with id=AA9, first strand: chain 'H' and resid 378 through 379 909 hydrogen bonds defined for protein. 2691 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: 5.29 Time building geometry restraints manager: 8.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5814 1.34 - 1.45: 3112 1.45 - 1.57: 11168 1.57 - 1.69: 0 1.69 - 1.81: 108 Bond restraints: 20202 Sorted by residual: bond pdb=" N ARG C 435 " pdb=" CA ARG C 435 " ideal model delta sigma weight residual 1.456 1.491 -0.034 1.21e-02 6.83e+03 8.08e+00 bond pdb=" N VAL A 545 " pdb=" CA VAL A 545 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.19e-02 7.06e+03 7.76e+00 bond pdb=" N ARG B 905 " pdb=" CA ARG B 905 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.29e-02 6.01e+03 7.58e+00 bond pdb=" N ASN C 434 " pdb=" CA ASN C 434 " ideal model delta sigma weight residual 1.458 1.490 -0.031 1.14e-02 7.69e+03 7.53e+00 bond pdb=" N VAL D 432 " pdb=" CA VAL D 432 " ideal model delta sigma weight residual 1.461 1.493 -0.033 1.19e-02 7.06e+03 7.52e+00 ... (remaining 20197 not shown) Histogram of bond angle deviations from ideal: 99.73 - 106.98: 632 106.98 - 114.23: 11816 114.23 - 121.47: 10392 121.47 - 128.72: 4309 128.72 - 135.97: 130 Bond angle restraints: 27279 Sorted by residual: angle pdb=" C SER D 397 " pdb=" N LYS D 398 " pdb=" CA LYS D 398 " ideal model delta sigma weight residual 121.54 132.24 -10.70 1.91e+00 2.74e-01 3.14e+01 angle pdb=" C ILE I 94 " pdb=" N HIS I 95 " pdb=" CA HIS I 95 " ideal model delta sigma weight residual 121.54 131.79 -10.25 1.91e+00 2.74e-01 2.88e+01 angle pdb=" C ILE C 625 " pdb=" N ARG C 626 " pdb=" CA ARG C 626 " ideal model delta sigma weight residual 121.54 130.97 -9.43 1.91e+00 2.74e-01 2.44e+01 angle pdb=" C GLN C 508 " pdb=" N HIS C 509 " pdb=" CA HIS C 509 " ideal model delta sigma weight residual 121.31 128.21 -6.90 1.49e+00 4.50e-01 2.14e+01 angle pdb=" C ASP D 524 " pdb=" N GLU D 525 " pdb=" CA GLU D 525 " ideal model delta sigma weight residual 120.38 126.90 -6.52 1.46e+00 4.69e-01 2.00e+01 ... (remaining 27274 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 11146 17.79 - 35.58: 915 35.58 - 53.37: 296 53.37 - 71.16: 78 71.16 - 88.95: 15 Dihedral angle restraints: 12450 sinusoidal: 5252 harmonic: 7198 Sorted by residual: dihedral pdb=" CA GLN C 508 " pdb=" C GLN C 508 " pdb=" N HIS C 509 " pdb=" CA HIS C 509 " ideal model delta harmonic sigma weight residual -180.00 -150.27 -29.73 0 5.00e+00 4.00e-02 3.54e+01 dihedral pdb=" CA LEU H 418 " pdb=" C LEU H 418 " pdb=" N GLN H 419 " pdb=" CA GLN H 419 " ideal model delta harmonic sigma weight residual -180.00 -151.27 -28.73 0 5.00e+00 4.00e-02 3.30e+01 dihedral pdb=" CA ILE I 38 " pdb=" C ILE I 38 " pdb=" N PRO I 39 " pdb=" CA PRO I 39 " ideal model delta harmonic sigma weight residual -180.00 -151.62 -28.38 0 5.00e+00 4.00e-02 3.22e+01 ... (remaining 12447 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 2571 0.063 - 0.126: 443 0.126 - 0.190: 50 0.190 - 0.253: 6 0.253 - 0.316: 1 Chirality restraints: 3071 Sorted by residual: chirality pdb=" CA VAL C 432 " pdb=" N VAL C 432 " pdb=" C VAL C 432 " pdb=" CB VAL C 432 " both_signs ideal model delta sigma weight residual False 2.44 2.76 -0.32 2.00e-01 2.50e+01 2.50e+00 chirality pdb=" CA LEU H 388 " pdb=" N LEU H 388 " pdb=" C LEU H 388 " pdb=" CB LEU H 388 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CB ILE B 868 " pdb=" CA ILE B 868 " pdb=" CG1 ILE B 868 " pdb=" CG2 ILE B 868 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 3068 not shown) Planarity restraints: 3491 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 430 " 0.020 2.00e-02 2.50e+03 4.10e-02 1.68e+01 pdb=" C VAL C 430 " -0.071 2.00e-02 2.50e+03 pdb=" O VAL C 430 " 0.027 2.00e-02 2.50e+03 pdb=" N GLU C 431 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR J 462 " -0.039 5.00e-02 4.00e+02 5.93e-02 5.63e+00 pdb=" N PRO J 463 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO J 463 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO J 463 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B1155 " 0.037 5.00e-02 4.00e+02 5.57e-02 4.96e+00 pdb=" N PRO B1156 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO B1156 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B1156 " 0.033 5.00e-02 4.00e+02 ... (remaining 3488 not shown) Histogram of nonbonded interaction distances: 1.44 - 2.13: 11 2.13 - 2.82: 6078 2.82 - 3.52: 25956 3.52 - 4.21: 44583 4.21 - 4.90: 78305 Nonbonded interactions: 154933 Sorted by model distance: nonbonded pdb=" NH1 ARG C 435 " pdb=" OH TYR E 361 " model vdw 1.440 2.520 nonbonded pdb=" NH1 ARG C 435 " pdb=" CZ TYR E 361 " model vdw 1.486 3.340 nonbonded pdb=" NH2 ARG C 435 " pdb=" CE2 TYR E 361 " model vdw 1.539 3.420 nonbonded pdb=" O ASN B 941 " pdb=" N TYR B 943 " model vdw 1.891 2.520 nonbonded pdb=" O PRO B 867 " pdb=" OD2 ASP B 950 " model vdw 1.957 3.040 ... (remaining 154928 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 'D' and (resid 299 through 742 or resid 762 through 781)) selection = (chain 'E' and (resid 299 through 468 or resid 514 through 640 or resid 666 thro \ ugh 742 or resid 762 through 781)) } 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=0.00 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: 2.770 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: 0.030 Extract box with map and model: 14.260 Check model and map are aligned: 0.280 Set scattering table: 0.170 Process input model: 45.970 Find NCS groups from input model: 0.750 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 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 : 0.005 0.055 20202 Z= 0.291 Angle : 0.813 10.968 27279 Z= 0.480 Chirality : 0.048 0.316 3071 Planarity : 0.006 0.059 3491 Dihedral : 15.456 88.952 7736 Min Nonbonded Distance : 1.440 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.30 % Favored : 93.40 % Rotamer Outliers : 8.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.86 (0.13), residues: 2365 helix: -2.23 (0.11), residues: 1298 sheet: -1.57 (0.59), residues: 68 loop : -3.00 (0.16), residues: 999 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 2265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 323 time to evaluate : 2.280 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: 195 outliers final: 49 residues processed: 489 average time/residue: 0.3127 time to fit residues: 234.5590 Evaluate side-chains 246 residues out of total 2265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 197 time to evaluate : 2.267 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 0 residues processed: 49 average time/residue: 0.2185 time to fit residues: 21.4725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 200 optimal weight: 1.9990 chunk 180 optimal weight: 6.9990 chunk 100 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 96 optimal weight: 0.4980 chunk 186 optimal weight: 0.0270 chunk 72 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 138 optimal weight: 0.0870 chunk 216 optimal weight: 2.9990 overall best weight: 0.9220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 564 HIS A 575 ASN A 584 GLN B 708 HIS B 718 ASN B 765 GLN ** B 915 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 941 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1107 ASN B1120 GLN B1135 GLN B1142 GLN B1199 ASN B1213 ASN B1294 GLN B1307 ASN C 509 HIS ** C 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 581 GLN C 651 ASN D 416 HIS D 533 GLN D 560 GLN D 766 GLN D 785 ASN ** H 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 460 GLN H 563 ASN I 48 ASN I 49 ASN ** I 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 110 ASN I 119 ASN J 280 GLN E 359 ASN E 394 GLN E 567 GLN E 587 ASN E 597 HIS E 680 ASN E 690 GLN ** E 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 20202 Z= 0.225 Angle : 0.600 9.349 27279 Z= 0.306 Chirality : 0.041 0.174 3071 Planarity : 0.005 0.045 3491 Dihedral : 5.209 25.954 2595 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.26 % Favored : 93.53 % Rotamer Outliers : 3.36 % 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: -1.91 (0.16), residues: 2365 helix: -0.24 (0.14), residues: 1334 sheet: -1.43 (0.57), residues: 76 loop : -2.77 (0.18), residues: 955 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 214 time to evaluate : 2.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 76 outliers final: 34 residues processed: 272 average time/residue: 0.3093 time to fit residues: 132.1116 Evaluate side-chains 210 residues out of total 2265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 176 time to evaluate : 2.433 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.2092 time to fit residues: 16.0934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 120 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 179 optimal weight: 2.9990 chunk 147 optimal weight: 9.9990 chunk 59 optimal weight: 0.6980 chunk 216 optimal weight: 0.9990 chunk 233 optimal weight: 2.9990 chunk 192 optimal weight: 0.9980 chunk 214 optimal weight: 0.7980 chunk 73 optimal weight: 0.1980 chunk 173 optimal weight: 0.5980 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 537 GLN ** B 915 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 941 ASN ** B1199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 95 HIS ** I 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 110 ASN E 700 HIS ** E 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 20202 Z= 0.171 Angle : 0.551 8.911 27279 Z= 0.278 Chirality : 0.040 0.219 3071 Planarity : 0.004 0.043 3491 Dihedral : 4.815 25.236 2595 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.81 % Favored : 93.11 % Rotamer Outliers : 1.37 % 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: -0.96 (0.17), residues: 2365 helix: 0.59 (0.14), residues: 1340 sheet: -1.39 (0.55), residues: 88 loop : -2.46 (0.19), residues: 937 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 200 time to evaluate : 2.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 11 residues processed: 225 average time/residue: 0.3062 time to fit residues: 109.9425 Evaluate side-chains 190 residues out of total 2265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 179 time to evaluate : 2.346 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1867 time to fit residues: 7.0218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 213 optimal weight: 8.9990 chunk 162 optimal weight: 2.9990 chunk 112 optimal weight: 0.6980 chunk 23 optimal weight: 0.0970 chunk 103 optimal weight: 4.9990 chunk 145 optimal weight: 0.8980 chunk 217 optimal weight: 0.8980 chunk 230 optimal weight: 0.6980 chunk 113 optimal weight: 3.9990 chunk 205 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 537 GLN A 557 ASN B1142 GLN ** B1199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 93 ASN ** I 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 110 ASN J 473 HIS ** E 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 20202 Z= 0.175 Angle : 0.538 8.615 27279 Z= 0.270 Chirality : 0.040 0.194 3071 Planarity : 0.004 0.041 3491 Dihedral : 4.608 24.098 2595 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.10 % Favored : 92.85 % Rotamer Outliers : 1.55 % 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: -0.43 (0.18), residues: 2365 helix: 1.05 (0.15), residues: 1345 sheet: -1.14 (0.61), residues: 80 loop : -2.29 (0.19), residues: 940 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 199 time to evaluate : 2.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 19 residues processed: 226 average time/residue: 0.3038 time to fit residues: 109.3816 Evaluate side-chains 196 residues out of total 2265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 177 time to evaluate : 2.543 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.2163 time to fit residues: 10.3670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 191 optimal weight: 0.6980 chunk 130 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 171 optimal weight: 0.0570 chunk 94 optimal weight: 0.5980 chunk 196 optimal weight: 0.9990 chunk 159 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 117 optimal weight: 0.7980 chunk 206 optimal weight: 3.9990 chunk 58 optimal weight: 0.0270 overall best weight: 0.4356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1238 ASN ** C 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 690 GLN ** D 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 326 HIS ** I 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 110 ASN ** E 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.039 20202 Z= 0.148 Angle : 0.534 8.297 27279 Z= 0.267 Chirality : 0.040 0.219 3071 Planarity : 0.003 0.048 3491 Dihedral : 4.437 25.238 2595 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.47 % Favored : 93.49 % Rotamer Outliers : 1.24 % 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: -0.10 (0.18), residues: 2365 helix: 1.30 (0.15), residues: 1356 sheet: -0.84 (0.62), residues: 80 loop : -2.16 (0.20), residues: 929 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 197 time to evaluate : 2.175 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 6 residues processed: 220 average time/residue: 0.3081 time to fit residues: 108.2944 Evaluate side-chains 176 residues out of total 2265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 170 time to evaluate : 2.368 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1941 time to fit residues: 5.4501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 77 optimal weight: 0.5980 chunk 207 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 56 optimal weight: 0.0670 chunk 230 optimal weight: 0.6980 chunk 191 optimal weight: 0.9980 chunk 106 optimal weight: 0.8980 chunk 19 optimal weight: 0.0670 chunk 76 optimal weight: 0.9980 chunk 120 optimal weight: 1.9990 overall best weight: 0.4656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 557 ASN ** B1199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 769 HIS ** I 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 110 ASN ** E 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 20202 Z= 0.150 Angle : 0.543 14.685 27279 Z= 0.268 Chirality : 0.039 0.196 3071 Planarity : 0.004 0.043 3491 Dihedral : 4.326 23.062 2595 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.51 % Favored : 93.45 % Rotamer Outliers : 1.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.18), residues: 2365 helix: 1.52 (0.15), residues: 1356 sheet: -1.17 (0.57), residues: 92 loop : -2.06 (0.20), residues: 917 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 190 time to evaluate : 2.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 14 residues processed: 211 average time/residue: 0.3031 time to fit residues: 103.1078 Evaluate side-chains 190 residues out of total 2265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 176 time to evaluate : 2.337 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1856 time to fit residues: 8.0304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 222 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 131 optimal weight: 1.9990 chunk 168 optimal weight: 0.5980 chunk 130 optimal weight: 0.6980 chunk 193 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 229 optimal weight: 0.9980 chunk 143 optimal weight: 4.9990 chunk 139 optimal weight: 7.9990 chunk 105 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 941 ASN ** B1199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 769 HIS ** I 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 110 ASN ** E 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 20202 Z= 0.189 Angle : 0.556 14.397 27279 Z= 0.276 Chirality : 0.040 0.199 3071 Planarity : 0.004 0.043 3491 Dihedral : 4.357 23.835 2595 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.85 % Favored : 93.11 % Rotamer Outliers : 0.88 % 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: 0.23 (0.18), residues: 2365 helix: 1.59 (0.15), residues: 1355 sheet: -1.17 (0.56), residues: 92 loop : -2.00 (0.20), residues: 918 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 187 time to evaluate : 2.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 13 residues processed: 202 average time/residue: 0.3024 time to fit residues: 98.9528 Evaluate side-chains 195 residues out of total 2265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 182 time to evaluate : 2.433 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2344 time to fit residues: 8.5834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 141 optimal weight: 0.4980 chunk 91 optimal weight: 0.5980 chunk 137 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 chunk 45 optimal weight: 0.1980 chunk 44 optimal weight: 0.9980 chunk 145 optimal weight: 3.9990 chunk 156 optimal weight: 2.9990 chunk 113 optimal weight: 0.0000 chunk 21 optimal weight: 5.9990 chunk 180 optimal weight: 4.9990 overall best weight: 0.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 941 ASN ** B1199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 567 GLN D 730 ASN D 769 HIS ** I 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 730 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 20202 Z= 0.142 Angle : 0.534 14.868 27279 Z= 0.264 Chirality : 0.039 0.193 3071 Planarity : 0.004 0.042 3491 Dihedral : 4.198 23.059 2595 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.26 % Favored : 93.70 % Rotamer Outliers : 0.84 % 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: 0.41 (0.18), residues: 2365 helix: 1.77 (0.15), residues: 1343 sheet: -1.08 (0.57), residues: 92 loop : -1.94 (0.20), residues: 930 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 198 time to evaluate : 2.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 12 residues processed: 206 average time/residue: 0.3063 time to fit residues: 100.8022 Evaluate side-chains 196 residues out of total 2265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 184 time to evaluate : 2.583 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1948 time to fit residues: 7.8099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 208 optimal weight: 4.9990 chunk 219 optimal weight: 3.9990 chunk 200 optimal weight: 0.0770 chunk 213 optimal weight: 8.9990 chunk 128 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 167 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 193 optimal weight: 0.9980 chunk 202 optimal weight: 1.9990 chunk 140 optimal weight: 0.8980 overall best weight: 0.9740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 491 HIS B 941 ASN ** B1199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 769 HIS ** I 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 20202 Z= 0.226 Angle : 0.594 15.609 27279 Z= 0.295 Chirality : 0.041 0.198 3071 Planarity : 0.004 0.045 3491 Dihedral : 4.358 24.650 2595 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.19 % Favored : 92.77 % Rotamer Outliers : 0.40 % 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: 0.37 (0.18), residues: 2365 helix: 1.68 (0.15), residues: 1354 sheet: -1.21 (0.56), residues: 92 loop : -1.89 (0.21), residues: 919 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 189 time to evaluate : 2.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 3 residues processed: 195 average time/residue: 0.2994 time to fit residues: 94.6194 Evaluate side-chains 179 residues out of total 2265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 176 time to evaluate : 2.360 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1914 time to fit residues: 4.2684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 226 optimal weight: 0.3980 chunk 137 optimal weight: 0.6980 chunk 107 optimal weight: 0.0670 chunk 157 optimal weight: 4.9990 chunk 237 optimal weight: 2.9990 chunk 218 optimal weight: 2.9990 chunk 188 optimal weight: 7.9990 chunk 19 optimal weight: 0.0070 chunk 145 optimal weight: 3.9990 chunk 115 optimal weight: 0.9990 chunk 149 optimal weight: 6.9990 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 941 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 769 HIS ** I 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.054 20202 Z= 0.155 Angle : 0.571 15.585 27279 Z= 0.282 Chirality : 0.040 0.205 3071 Planarity : 0.004 0.043 3491 Dihedral : 4.225 23.964 2595 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.17 % Favored : 93.78 % Rotamer Outliers : 0.31 % 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 (0.18), residues: 2365 helix: 1.79 (0.15), residues: 1355 sheet: -1.09 (0.56), residues: 92 loop : -1.89 (0.20), residues: 918 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 187 time to evaluate : 2.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 191 average time/residue: 0.3021 time to fit residues: 93.2922 Evaluate side-chains 186 residues out of total 2265 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 180 time to evaluate : 2.379 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2112 time to fit residues: 5.6286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 201 optimal weight: 1.9990 chunk 57 optimal weight: 0.2980 chunk 174 optimal weight: 0.2980 chunk 27 optimal weight: 1.9990 chunk 52 optimal weight: 0.0000 chunk 189 optimal weight: 5.9990 chunk 79 optimal weight: 0.3980 chunk 194 optimal weight: 0.8980 chunk 23 optimal weight: 0.0670 chunk 34 optimal weight: 0.0570 chunk 166 optimal weight: 0.6980 overall best weight: 0.1440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 557 ASN A 584 GLN ** B 941 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 769 HIS ** I 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.108543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.086517 restraints weight = 58177.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.089122 restraints weight = 29759.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.089517 restraints weight = 18645.197| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 20202 Z= 0.134 Angle : 0.551 15.103 27279 Z= 0.273 Chirality : 0.039 0.203 3071 Planarity : 0.003 0.044 3491 Dihedral : 3.965 24.246 2595 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.92 % Favored : 94.04 % Rotamer Outliers : 0.44 % 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: 0.67 (0.19), residues: 2365 helix: 1.94 (0.15), residues: 1357 sheet: -0.84 (0.56), residues: 96 loop : -1.84 (0.20), residues: 912 =============================================================================== Job complete usr+sys time: 3604.46 seconds wall clock time: 66 minutes 54.15 seconds (4014.15 seconds total)