Starting phenix.real_space_refine on Mon Jul 22 08:54:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zr5_14883/07_2024/7zr5_14883.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zr5_14883/07_2024/7zr5_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_14883/07_2024/7zr5_14883.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zr5_14883/07_2024/7zr5_14883.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zr5_14883/07_2024/7zr5_14883.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zr5_14883/07_2024/7zr5_14883.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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-dev-5388/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: 9.80, per 1000 atoms: 0.56 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: 6.70 Conformation dependent library (CDL) restraints added in 3.1 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... Secondary structure from input PDB file: 86 helices and 17 sheets defined 48.8% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.08 Creating SS restraints... Processing helix chain 'A' and resid 20 through 31 removed outlier: 3.541A pdb=" N ASN A 30 " --> pdb=" O SER A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 61 removed outlier: 3.904A pdb=" N ARG A 41 " --> pdb=" O GLU A 37 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER A 58 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR A 60 " --> pdb=" O TYR A 56 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASP A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 101 removed outlier: 3.989A pdb=" N ILE A 99 " --> pdb=" O LYS A 95 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASN A 100 " --> pdb=" O ALA A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 115 removed outlier: 3.541A pdb=" N GLU A 115 " --> pdb=" O LYS A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 138 Processing helix chain 'A' and resid 194 through 205 removed outlier: 4.271A pdb=" N VAL A 198 " --> pdb=" O GLU A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 291 removed outlier: 4.137A pdb=" N THR A 290 " --> pdb=" O PRO A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 296 removed outlier: 4.051A pdb=" N ILE A 296 " --> pdb=" O PRO A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 307 Processing helix chain 'A' and resid 399 through 420 removed outlier: 4.253A pdb=" N VAL A 403 " --> pdb=" O LYS A 399 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA A 420 " --> pdb=" O PHE A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 433 removed outlier: 3.767A pdb=" N LYS A 428 " --> pdb=" O GLU A 424 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA A 432 " --> pdb=" O LYS A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 444 removed outlier: 4.343A pdb=" N LEU A 437 " --> pdb=" O PHE A 433 " (cutoff:3.500A) 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 447 through 452 Processing helix chain 'A' and resid 469 through 474 removed outlier: 3.656A pdb=" N SER A 474 " --> pdb=" O SER A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 496 removed outlier: 3.871A pdb=" N ASN A 496 " --> pdb=" O GLU A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 523 removed outlier: 3.673A pdb=" N GLU A 519 " --> pdb=" O GLU A 515 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN A 523 " --> pdb=" O GLU A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 560 removed outlier: 3.791A pdb=" N LYS A 550 " --> pdb=" O ASP A 546 " (cutoff:3.500A) 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) removed outlier: 3.806A pdb=" N PHE A 560 " --> pdb=" O SER A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 572 removed outlier: 3.682A pdb=" N LYS A 565 " --> pdb=" O GLU A 561 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASP A 572 " --> pdb=" O LYS A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 609 Processing helix chain 'A' and resid 613 through 618 removed outlier: 4.628A pdb=" N MET A 617 " --> pdb=" O ASP A 613 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLY A 618 " --> pdb=" O ASN A 614 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 613 through 618' Processing helix chain 'A' and resid 632 through 645 removed outlier: 3.577A pdb=" N GLU A 636 " --> pdb=" O HIS A 632 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ALA A 644 " --> pdb=" O GLN A 640 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP A 645 " --> pdb=" O LYS A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 665 removed outlier: 4.288A pdb=" N LYS A 652 " --> pdb=" O ASP A 648 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP A 653 " --> pdb=" O LYS A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 688 removed outlier: 4.205A pdb=" N HIS A 676 " --> pdb=" O ASP A 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 31 Processing helix chain 'B' and resid 38 through 59 removed outlier: 3.767A pdb=" N LEU B 59 " --> pdb=" O ARG B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 66 Processing helix chain 'B' and resid 94 through 103 Processing helix chain 'B' and resid 108 through 117 removed outlier: 4.186A pdb=" N ALA B 112 " --> pdb=" O SER B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 140 removed outlier: 3.602A pdb=" N VAL B 139 " --> pdb=" O ALA B 136 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ALA B 140 " --> pdb=" O TYR B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 205 removed outlier: 3.566A pdb=" N VAL B 198 " --> pdb=" O GLU B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 307 Processing helix chain 'B' and resid 398 through 420 removed outlier: 3.738A pdb=" N LYS B 402 " --> pdb=" O SER B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 431 Processing helix chain 'B' and resid 433 through 443 removed outlier: 4.193A pdb=" N LEU B 437 " --> pdb=" O PHE B 433 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS B 438 " --> pdb=" O SER B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 453 Processing helix chain 'B' and resid 468 through 475 Processing helix chain 'B' and resid 490 through 496 removed outlier: 3.572A pdb=" N VAL B 494 " --> pdb=" O SER B 490 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ASN B 496 " --> pdb=" O GLU B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 504 removed outlier: 4.513A pdb=" N VAL B 503 " --> pdb=" O PHE B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 507 No H-bonds generated for 'chain 'B' and resid 505 through 507' Processing helix chain 'B' and resid 516 through 525 removed outlier: 4.359A pdb=" N TYR B 520 " --> pdb=" O PRO B 516 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLN B 524 " --> pdb=" O TYR B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 560 removed outlier: 3.656A pdb=" N ALA B 558 " --> pdb=" O GLU B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 571 removed outlier: 3.685A pdb=" N CYS B 564 " --> pdb=" O PHE B 560 " (cutoff:3.500A) 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) removed outlier: 3.639A pdb=" N LEU B 571 " --> pdb=" O MET B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 608 removed outlier: 3.560A pdb=" N ALA B 608 " --> pdb=" O ARG B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 621 removed outlier: 3.990A pdb=" N MET B 620 " --> pdb=" O THR B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 645 removed outlier: 3.620A pdb=" N GLU B 636 " --> pdb=" O HIS B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 666 Processing helix chain 'B' and resid 672 through 688 removed outlier: 4.011A pdb=" N HIS B 676 " --> pdb=" O ASP B 672 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 8 removed outlier: 3.842A pdb=" N ASP C 8 " --> pdb=" O SER C 5 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 72 Processing helix chain 'C' and resid 78 through 112 removed outlier: 3.738A pdb=" N LYS C 107 " --> pdb=" O GLU C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 119 removed outlier: 3.770A pdb=" N LEU C 119 " --> pdb=" O ASN C 115 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 115 through 119' Processing helix chain 'C' and resid 139 through 164 removed outlier: 4.267A pdb=" N MET C 164 " --> pdb=" O LYS C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 182 Processing helix chain 'C' and resid 183 through 201 removed outlier: 3.596A pdb=" N ALA C 187 " --> pdb=" O CYS C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 227 Processing helix chain 'C' and resid 234 through 243 removed outlier: 3.697A pdb=" N THR C 243 " --> pdb=" O THR C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 265 Processing helix chain 'K' and resid 537 through 543 Processing helix chain 'K' and resid 549 through 568 Processing helix chain 'K' and resid 569 through 571 No H-bonds generated for 'chain 'K' and resid 569 through 571' Processing helix chain 'K' and resid 578 through 581 Processing helix chain 'K' and resid 634 through 652 removed outlier: 4.010A pdb=" N ASP K 638 " --> pdb=" O SER K 634 " (cutoff:3.500A) Processing helix chain 'K' and resid 661 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 686 through 697 removed outlier: 3.953A pdb=" N LYS K 690 " --> pdb=" O PRO K 686 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LEU K 697 " --> pdb=" O MET K 693 " (cutoff:3.500A) Processing helix chain 'K' and resid 706 through 719 Processing helix chain 'P' and resid 28 through 30 No H-bonds generated for 'chain 'P' and resid 28 through 30' Processing helix chain 'P' and resid 31 through 36 Processing helix chain 'P' and resid 36 through 41 removed outlier: 4.022A pdb=" N LYS P 40 " --> pdb=" O ASN P 36 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA P 41 " --> pdb=" O ASP P 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 36 through 41' Processing helix chain 'P' and resid 43 through 58 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 61 through 74 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 78 through 91 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 95 through 110 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 113 through 121 Processing helix chain 'P' and resid 133 through 151 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 187 through 200 Processing helix chain 'P' and resid 205 through 221 Processing helix chain 'P' and resid 246 through 258 Processing helix chain 'P' and resid 278 through 293 Processing helix chain 'P' and resid 302 through 305 Processing helix chain 'P' and resid 306 through 311 Processing helix chain 'P' and resid 314 through 323 Processing helix chain 'P' and resid 324 through 336 removed outlier: 3.830A pdb=" N TYR P 328 " --> pdb=" O THR P 324 " (cutoff:3.500A) Processing helix chain 'P' and resid 362 through 368 Processing helix chain 'P' and resid 379 through 387 Processing helix chain 'P' and resid 407 through 419 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=AA1, first strand: chain 'A' and resid 13 through 14 removed outlier: 3.859A pdb=" N GLU A 13 " --> pdb=" O VAL B 167 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL B 167 " --> pdb=" O GLU A 13 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS B 142 " --> pdb=" O HIS B 184 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 18 through 19 removed outlier: 6.591A pdb=" N GLN A 18 " --> pdb=" O ILE B 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, 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=AA4, first strand: chain 'A' and resid 104 through 105 removed outlier: 3.506A pdb=" N ILE A 105 " --> pdb=" O GLN B 18 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, 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: 6.181A pdb=" N LYS A 354 " --> pdb=" O VAL A 381 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N SER A 383 " --> pdb=" O LYS A 354 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N TYR A 356 " --> pdb=" O SER A 383 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 456 through 457 Processing sheet with id=AA7, first strand: chain 'A' and resid 511 through 513 removed outlier: 5.684A pdb=" N ILE A 483 " --> pdb=" O VAL A 534 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 578 through 580 removed outlier: 3.884A pdb=" N THR A 579 " --> pdb=" O LEU A 626 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ILE A 628 " --> pdb=" O THR A 579 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N CYS A 590 " --> pdb=" O GLU A 627 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.964A pdb=" N ILE B 73 " --> pdb=" O THR B 214 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 333 through 335 removed outlier: 3.532A pdb=" N ILE B 335 " --> pdb=" O ALA B 317 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALA B 317 " --> pdb=" O ILE B 335 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N VAL B 318 " --> pdb=" O MET C 128 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 322 through 325 removed outlier: 6.812A pdb=" N SER B 322 " --> pdb=" O GLY C 123 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 458 through 459 removed outlier: 4.466A pdb=" N HIS B 458 " --> pdb=" O TYR B 512 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N TYR B 484 " --> pdb=" O VAL B 511 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N MET B 513 " --> pdb=" O TYR B 484 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ILE B 486 " --> pdb=" O MET B 513 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 575 through 580 removed outlier: 7.790A pdb=" N LEU B 626 " --> pdb=" O GLU B 576 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N VAL B 578 " --> pdb=" O LEU B 626 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N ILE B 628 " --> pdb=" O VAL B 578 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N ILE B 580 " --> pdb=" O ILE B 628 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 535 through 536 removed outlier: 3.601A pdb=" N SER K 535 " --> pdb=" O LEU K 584 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'P' and resid 226 through 229 removed outlier: 6.318A pdb=" N VAL P 227 " --> pdb=" O CYS P 343 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU P 349 " --> pdb=" O TYR P 422 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE P 423 " --> pdb=" O VAL P 443 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N VAL P 445 " --> pdb=" O ILE P 423 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'P' and resid 297 through 299 Processing sheet with id=AB8, first strand: chain 'P' and resid 388 through 389 removed outlier: 6.464A pdb=" N ASP P 388 " --> pdb=" O PHE P 406 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER P 396 " --> pdb=" O GLN P 405 " (cutoff:3.500A) 721 hydrogen bonds defined for protein. 2061 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: 5.14 Time building geometry restraints manager: 7.38 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: 9419 17.86 - 35.72: 1216 35.72 - 53.58: 286 53.58 - 71.44: 61 71.44 - 89.30: 25 Dihedral angle restraints: 11007 sinusoidal: 4702 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 11004 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: 335 2.67 - 3.23: 16490 3.23 - 3.79: 25380 3.79 - 4.34: 32535 4.34 - 4.90: 53677 Nonbonded interactions: 128417 Sorted by model distance: nonbonded pdb=" O LEU A 27 " pdb=" OG1 THR A 31 " model vdw 2.119 2.440 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 nonbonded pdb=" O SER A 307 " pdb=" OG SER A 307 " model vdw 2.206 2.440 ... (remaining 128412 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: 2.100 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: 0.670 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 45.950 Find NCS groups from input model: 0.620 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: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.550 ------------------------------------------------------------------------------- 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= 0.688 Angle : 1.018 106.053 23992 Z= 0.467 Chirality : 0.043 0.361 2610 Planarity : 0.006 0.154 3076 Dihedral : 16.990 89.296 6923 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 % Allowed : 17.00 % Favored : 82.74 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP C 7 HIS 0.016 0.001 HIS K 568 PHE 0.036 0.002 PHE P 331 TYR 0.024 0.001 TYR A 681 ARG 0.006 0.000 ARG C 231 *********************** 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 : 1.981 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: B 80 GLN cc_start: 0.7757 (tt0) cc_final: 0.7459 (mt0) REVERT: B 114 MET cc_start: 0.7055 (tmm) cc_final: 0.6795 (mmm) outliers start: 5 outliers final: 4 residues processed: 328 average time/residue: 0.3476 time to fit residues: 165.1774 Evaluate side-chains 332 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 328 time to evaluate : 1.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 378 ARG Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 632 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 9.9990 chunk 160 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 chunk 85 optimal weight: 0.0770 chunk 166 optimal weight: 0.0170 chunk 64 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 123 optimal weight: 3.9990 chunk 192 optimal weight: 40.0000 overall best weight: 0.5576 ------------------------------------------------------------------------------- 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 ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 46 ASN 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6681 moved from start: 0.0782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 17837 Z= 0.173 Angle : 0.575 14.226 23992 Z= 0.302 Chirality : 0.041 0.198 2610 Planarity : 0.005 0.104 3076 Dihedral : 6.825 75.848 2413 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.47 % Allowed : 8.80 % Favored : 90.73 % Rotamer: Outliers : 2.39 % Allowed : 16.22 % Favored : 81.39 % 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: 0.72 (0.18), residues: 963 sheet: -0.67 (0.36), residues: 231 loop : -2.73 (0.18), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 7 HIS 0.005 0.001 HIS P 352 PHE 0.014 0.001 PHE P 331 TYR 0.022 0.001 TYR C 155 ARG 0.005 0.000 ARG C 231 *********************** 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: 46 poor density : 342 time to evaluate : 1.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 ASN cc_start: 0.7883 (p0) cc_final: 0.7563 (p0) REVERT: A 330 ARG cc_start: 0.7170 (ptp-170) cc_final: 0.6896 (ptp-170) REVERT: B 95 LYS cc_start: 0.7765 (mttm) cc_final: 0.7417 (mmtm) REVERT: B 177 ARG cc_start: 0.7760 (ptt-90) cc_final: 0.7195 (ptt-90) REVERT: C 105 MET cc_start: 0.6990 (tpt) cc_final: 0.6709 (tpt) REVERT: C 249 MET cc_start: 0.5974 (mmm) cc_final: 0.5517 (mmm) REVERT: P 351 MET cc_start: 0.1653 (ptp) cc_final: 0.1352 (ptp) outliers start: 46 outliers final: 28 residues processed: 363 average time/residue: 0.3304 time to fit residues: 175.0000 Evaluate side-chains 361 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 333 time to evaluate : 1.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 423 LYS Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 632 HIS Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain K residue 592 ILE Chi-restraints excluded: chain P residue 33 THR 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: 3.9990 chunk 131 optimal weight: 50.0000 chunk 53 optimal weight: 0.8980 chunk 192 optimal weight: 40.0000 chunk 208 optimal weight: 10.0000 chunk 171 optimal weight: 7.9990 chunk 191 optimal weight: 20.0000 chunk 65 optimal weight: 2.9990 chunk 154 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN A 625 HIS C 20 HIS C 22 ASN ** C 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 145 GLN ** P 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6847 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.081 17837 Z= 0.563 Angle : 0.761 14.530 23992 Z= 0.405 Chirality : 0.050 0.207 2610 Planarity : 0.006 0.087 3076 Dihedral : 7.336 78.770 2409 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.52 % Allowed : 10.55 % Favored : 88.94 % Rotamer: Outliers : 4.21 % Allowed : 17.67 % Favored : 78.12 % 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: -1.74 (0.18), residues: 2124 helix: 0.34 (0.17), residues: 965 sheet: -0.77 (0.36), residues: 228 loop : -2.99 (0.17), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP C 7 HIS 0.017 0.002 HIS K 574 PHE 0.041 0.003 PHE A 32 TYR 0.031 0.002 TYR B 356 ARG 0.007 0.001 ARG A 583 *********************** 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 436 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 355 time to evaluate : 1.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 VAL cc_start: 0.8368 (t) cc_final: 0.7344 (m) REVERT: A 26 SER cc_start: 0.8547 (p) cc_final: 0.8171 (p) REVERT: A 114 MET cc_start: 0.8084 (OUTLIER) cc_final: 0.7457 (mpp) REVERT: A 175 ILE cc_start: 0.8142 (mm) cc_final: 0.7840 (tt) REVERT: A 275 LYS cc_start: 0.7351 (pptt) cc_final: 0.6984 (ptpt) REVERT: A 283 ASN cc_start: 0.7958 (p0) cc_final: 0.7607 (p0) REVERT: A 286 LYS cc_start: 0.8342 (mptt) cc_final: 0.8141 (mmtm) REVERT: A 330 ARG cc_start: 0.7281 (ptp-170) cc_final: 0.7031 (ptp-170) REVERT: B 80 GLN cc_start: 0.7905 (OUTLIER) cc_final: 0.7679 (mt0) REVERT: B 95 LYS cc_start: 0.7807 (mttm) cc_final: 0.7558 (ttmm) REVERT: B 101 ASN cc_start: 0.7509 (m110) cc_final: 0.7283 (m-40) REVERT: B 122 ASP cc_start: 0.7652 (p0) cc_final: 0.7432 (p0) REVERT: B 364 ASP cc_start: 0.7294 (p0) cc_final: 0.6998 (p0) REVERT: B 444 ASP cc_start: 0.7892 (t0) cc_final: 0.7652 (t0) REVERT: B 569 GLU cc_start: 0.7166 (pm20) cc_final: 0.6888 (pm20) REVERT: B 639 ARG cc_start: 0.7741 (ttm170) cc_final: 0.7453 (ttm170) REVERT: C 7 TRP cc_start: 0.8059 (m-90) cc_final: 0.7798 (m-90) REVERT: C 105 MET cc_start: 0.6968 (tpt) cc_final: 0.6480 (tpt) REVERT: C 151 PHE cc_start: 0.4067 (OUTLIER) cc_final: 0.3426 (t80) REVERT: C 249 MET cc_start: 0.6016 (mmm) cc_final: 0.5574 (mmm) REVERT: K 689 MET cc_start: 0.5657 (mtp) cc_final: 0.5450 (mtp) REVERT: P 351 MET cc_start: 0.1752 (ptp) cc_final: 0.1503 (ptp) REVERT: P 425 ARG cc_start: 0.0155 (OUTLIER) cc_final: -0.1195 (tmm160) outliers start: 81 outliers final: 63 residues processed: 404 average time/residue: 0.3291 time to fit residues: 194.0112 Evaluate side-chains 422 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 355 time to evaluate : 1.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 628 ILE Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 80 GLN Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 352 ASN Chi-restraints excluded: chain B residue 434 SER Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 517 ILE Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 613 ASP Chi-restraints excluded: chain B residue 632 HIS Chi-restraints excluded: chain B residue 634 ILE Chi-restraints excluded: chain B residue 640 GLN Chi-restraints excluded: chain B residue 647 ASN Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 122 ASP Chi-restraints excluded: chain C residue 151 PHE Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 216 MET Chi-restraints excluded: chain K residue 536 SER Chi-restraints excluded: chain K residue 546 THR Chi-restraints excluded: chain K residue 560 THR Chi-restraints excluded: chain K residue 567 LEU Chi-restraints excluded: chain K residue 571 SER Chi-restraints excluded: chain K residue 580 ASN Chi-restraints excluded: chain K residue 588 LEU Chi-restraints excluded: chain K residue 592 ILE Chi-restraints excluded: chain K residue 647 TYR Chi-restraints excluded: chain K residue 706 LEU Chi-restraints excluded: chain P residue 33 THR Chi-restraints excluded: chain P residue 425 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 190 optimal weight: 0.7980 chunk 145 optimal weight: 20.0000 chunk 100 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 129 optimal weight: 0.9990 chunk 193 optimal weight: 7.9990 chunk 204 optimal weight: 10.0000 chunk 101 optimal weight: 0.8980 chunk 183 optimal weight: 6.9990 chunk 55 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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** C 146 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6753 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17837 Z= 0.205 Angle : 0.599 11.832 23992 Z= 0.313 Chirality : 0.042 0.195 2610 Planarity : 0.004 0.079 3076 Dihedral : 6.699 61.514 2409 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.38 % Allowed : 9.42 % Favored : 90.21 % Rotamer: Outliers : 3.53 % Allowed : 19.91 % Favored : 76.56 % 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: -1.44 (0.18), residues: 2124 helix: 0.67 (0.17), residues: 960 sheet: -0.79 (0.36), residues: 226 loop : -2.86 (0.18), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 114 HIS 0.010 0.001 HIS K 574 PHE 0.019 0.001 PHE A 32 TYR 0.020 0.001 TYR C 155 ARG 0.006 0.000 ARG K 575 *********************** 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 418 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 350 time to evaluate : 1.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 SER cc_start: 0.8556 (p) cc_final: 0.8249 (p) REVERT: A 275 LYS cc_start: 0.7356 (pptt) cc_final: 0.7002 (ptpt) REVERT: A 283 ASN cc_start: 0.7843 (p0) cc_final: 0.7556 (p0) REVERT: A 330 ARG cc_start: 0.7247 (ptp-170) cc_final: 0.6980 (ptp-170) REVERT: A 385 ASP cc_start: 0.6970 (p0) cc_final: 0.6674 (p0) REVERT: A 401 LEU cc_start: 0.5929 (OUTLIER) cc_final: 0.5712 (mp) REVERT: A 682 ARG cc_start: 0.7111 (ttp-170) cc_final: 0.6832 (tmm-80) REVERT: B 80 GLN cc_start: 0.7815 (OUTLIER) cc_final: 0.7552 (mt0) REVERT: B 95 LYS cc_start: 0.7854 (mttm) cc_final: 0.7527 (ttmm) REVERT: B 101 ASN cc_start: 0.7543 (m110) cc_final: 0.7173 (m-40) REVERT: B 364 ASP cc_start: 0.7290 (p0) cc_final: 0.6954 (p0) REVERT: B 443 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.6797 (pp20) REVERT: B 444 ASP cc_start: 0.7639 (t0) cc_final: 0.7397 (t0) REVERT: B 639 ARG cc_start: 0.7541 (ttm170) cc_final: 0.7221 (ttm170) REVERT: B 641 LYS cc_start: 0.7711 (mmmm) cc_final: 0.7456 (mptt) REVERT: B 674 GLN cc_start: 0.7601 (OUTLIER) cc_final: 0.7383 (mm110) REVERT: C 105 MET cc_start: 0.6938 (tpt) cc_final: 0.6510 (tpt) REVERT: C 151 PHE cc_start: 0.3920 (OUTLIER) cc_final: 0.3265 (t80) REVERT: C 249 MET cc_start: 0.6020 (mmm) cc_final: 0.5571 (mmm) REVERT: P 351 MET cc_start: 0.1680 (ptp) cc_final: 0.1448 (ptp) REVERT: P 425 ARG cc_start: 0.0039 (OUTLIER) cc_final: -0.1198 (tmm160) outliers start: 68 outliers final: 47 residues processed: 385 average time/residue: 0.3263 time to fit residues: 182.6432 Evaluate side-chains 399 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 346 time to evaluate : 3.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain B residue 80 GLN Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 352 ASN Chi-restraints excluded: chain B residue 423 LYS Chi-restraints excluded: chain B residue 434 SER Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 443 GLU Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 632 HIS Chi-restraints excluded: chain B residue 640 GLN Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain B residue 674 GLN Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 151 PHE Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain K residue 536 SER Chi-restraints excluded: chain K residue 537 LEU Chi-restraints excluded: chain K residue 546 THR Chi-restraints excluded: chain K residue 567 LEU Chi-restraints excluded: chain K residue 588 LEU Chi-restraints excluded: chain K residue 592 ILE Chi-restraints excluded: chain P residue 33 THR Chi-restraints excluded: chain P residue 425 ARG 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: 0.6980 chunk 2 optimal weight: 0.0770 chunk 152 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 174 optimal weight: 20.0000 chunk 141 optimal weight: 7.9990 chunk 0 optimal weight: 3.9990 chunk 104 optimal weight: 0.5980 chunk 183 optimal weight: 9.9990 chunk 51 optimal weight: 0.4980 overall best weight: 0.5738 ------------------------------------------------------------------------------- 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** C 211 HIS ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6727 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17837 Z= 0.172 Angle : 0.573 10.766 23992 Z= 0.298 Chirality : 0.040 0.189 2610 Planarity : 0.004 0.068 3076 Dihedral : 6.150 59.340 2409 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.38 % Allowed : 9.23 % Favored : 90.40 % Rotamer: Outliers : 4.00 % Allowed : 19.70 % Favored : 76.30 % 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: -1.25 (0.18), residues: 2124 helix: 0.86 (0.18), residues: 950 sheet: -0.61 (0.37), residues: 223 loop : -2.79 (0.18), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 114 HIS 0.010 0.001 HIS K 574 PHE 0.014 0.001 PHE A 32 TYR 0.018 0.001 TYR C 155 ARG 0.004 0.000 ARG K 575 *********************** 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 422 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 345 time to evaluate : 1.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 SER cc_start: 0.8567 (p) cc_final: 0.8260 (p) REVERT: A 114 MET cc_start: 0.7921 (OUTLIER) cc_final: 0.7288 (mpp) REVERT: A 275 LYS cc_start: 0.7420 (pptt) cc_final: 0.6984 (ptpt) REVERT: A 320 HIS cc_start: 0.7200 (t-170) cc_final: 0.6967 (t-170) REVERT: A 330 ARG cc_start: 0.7216 (ptp-170) cc_final: 0.6925 (ptp-170) REVERT: A 385 ASP cc_start: 0.6977 (p0) cc_final: 0.6541 (p0) REVERT: A 401 LEU cc_start: 0.5761 (OUTLIER) cc_final: 0.5522 (mp) REVERT: A 519 GLU cc_start: 0.7248 (tp30) cc_final: 0.6972 (tp30) REVERT: A 682 ARG cc_start: 0.7048 (ttp-170) cc_final: 0.6821 (tmm-80) REVERT: B 80 GLN cc_start: 0.7765 (OUTLIER) cc_final: 0.7498 (mt0) REVERT: B 95 LYS cc_start: 0.7872 (mttm) cc_final: 0.7478 (ttmm) REVERT: B 101 ASN cc_start: 0.7593 (m110) cc_final: 0.7131 (m-40) REVERT: B 364 ASP cc_start: 0.7287 (p0) cc_final: 0.6945 (p0) REVERT: B 443 GLU cc_start: 0.7365 (OUTLIER) cc_final: 0.6942 (pp20) REVERT: C 105 MET cc_start: 0.6965 (tpt) cc_final: 0.6325 (tpt) REVERT: C 108 LYS cc_start: 0.5274 (OUTLIER) cc_final: 0.4908 (tmtt) REVERT: C 151 PHE cc_start: 0.3963 (OUTLIER) cc_final: 0.3262 (t80) REVERT: C 249 MET cc_start: 0.5997 (mmm) cc_final: 0.5545 (mmm) REVERT: K 693 MET cc_start: 0.7070 (mtm) cc_final: 0.6819 (mtm) REVERT: P 107 MET cc_start: 0.7399 (mmp) cc_final: 0.6575 (mmp) REVERT: P 331 PHE cc_start: 0.0181 (OUTLIER) cc_final: -0.0070 (t80) REVERT: P 425 ARG cc_start: -0.0120 (OUTLIER) cc_final: -0.1155 (tmm160) outliers start: 77 outliers final: 50 residues processed: 390 average time/residue: 0.3215 time to fit residues: 182.5425 Evaluate side-chains 399 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 341 time to evaluate : 1.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 628 ILE Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 80 GLN Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 443 GLU Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 613 ASP Chi-restraints excluded: chain B residue 632 HIS Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 108 LYS Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 151 PHE Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 216 MET Chi-restraints excluded: chain K residue 536 SER Chi-restraints excluded: chain K residue 546 THR Chi-restraints excluded: chain K residue 580 ASN Chi-restraints excluded: chain K residue 588 LEU Chi-restraints excluded: chain K residue 592 ILE Chi-restraints excluded: chain K residue 644 ILE Chi-restraints excluded: chain K residue 648 GLU Chi-restraints excluded: chain K residue 706 LEU Chi-restraints excluded: chain P residue 33 THR Chi-restraints excluded: chain P residue 121 THR Chi-restraints excluded: chain P residue 331 PHE Chi-restraints excluded: chain P residue 425 ARG Chi-restraints excluded: chain P residue 445 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 68 optimal weight: 1.9990 chunk 184 optimal weight: 4.9990 chunk 40 optimal weight: 0.6980 chunk 120 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 205 optimal weight: 4.9990 chunk 170 optimal weight: 40.0000 chunk 94 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 107 optimal weight: 0.7980 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 B 640 GLN B 674 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: 0.6747 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17837 Z= 0.212 Angle : 0.595 10.384 23992 Z= 0.309 Chirality : 0.041 0.184 2610 Planarity : 0.004 0.063 3076 Dihedral : 6.109 64.590 2409 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.33 % Allowed : 9.32 % Favored : 90.35 % Rotamer: Outliers : 4.42 % Allowed : 19.80 % Favored : 75.78 % 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: -1.23 (0.18), residues: 2124 helix: 0.86 (0.17), residues: 961 sheet: -0.54 (0.37), residues: 223 loop : -2.81 (0.18), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 114 HIS 0.009 0.001 HIS K 574 PHE 0.018 0.001 PHE A 32 TYR 0.016 0.001 TYR C 155 ARG 0.003 0.000 ARG K 575 *********************** 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 425 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 340 time to evaluate : 2.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 MET cc_start: 0.8337 (OUTLIER) cc_final: 0.7111 (tmm) REVERT: A 26 SER cc_start: 0.8592 (p) cc_final: 0.8245 (p) REVERT: A 32 PHE cc_start: 0.7579 (OUTLIER) cc_final: 0.7260 (p90) REVERT: A 99 ILE cc_start: 0.8455 (OUTLIER) cc_final: 0.8248 (pt) REVERT: A 114 MET cc_start: 0.7900 (OUTLIER) cc_final: 0.7284 (mpp) REVERT: A 165 PHE cc_start: 0.8730 (OUTLIER) cc_final: 0.8521 (p90) REVERT: A 275 LYS cc_start: 0.7469 (pptt) cc_final: 0.7009 (ptpt) REVERT: A 330 ARG cc_start: 0.7215 (ptp-170) cc_final: 0.7014 (ptm160) REVERT: A 338 ARG cc_start: 0.7779 (ttm110) cc_final: 0.7443 (mtm110) REVERT: A 401 LEU cc_start: 0.5941 (OUTLIER) cc_final: 0.5731 (mp) REVERT: A 466 MET cc_start: 0.7168 (OUTLIER) cc_final: 0.6789 (tpp) REVERT: A 682 ARG cc_start: 0.7085 (ttp-170) cc_final: 0.6819 (tmm-80) REVERT: B 80 GLN cc_start: 0.7788 (OUTLIER) cc_final: 0.7449 (mt0) REVERT: B 95 LYS cc_start: 0.7902 (mttm) cc_final: 0.7546 (ttmm) REVERT: B 101 ASN cc_start: 0.7678 (m-40) cc_final: 0.7287 (m110) REVERT: B 364 ASP cc_start: 0.7309 (p0) cc_final: 0.6917 (p0) REVERT: B 406 LYS cc_start: 0.6796 (OUTLIER) cc_final: 0.6422 (mttm) REVERT: C 105 MET cc_start: 0.6947 (tpt) cc_final: 0.6292 (tpt) REVERT: C 108 LYS cc_start: 0.5268 (OUTLIER) cc_final: 0.4905 (tmtt) REVERT: C 151 PHE cc_start: 0.4018 (OUTLIER) cc_final: 0.3294 (t80) REVERT: C 249 MET cc_start: 0.5982 (mmm) cc_final: 0.5539 (mmm) REVERT: P 107 MET cc_start: 0.7381 (mmp) cc_final: 0.6563 (mmp) REVERT: P 425 ARG cc_start: -0.0178 (OUTLIER) cc_final: -0.1164 (tmm160) outliers start: 85 outliers final: 64 residues processed: 393 average time/residue: 0.3296 time to fit residues: 188.9530 Evaluate side-chains 414 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 338 time to evaluate : 1.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 378 ARG Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 466 MET Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 553 MET Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 628 ILE Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 640 GLN Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 80 GLN Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 352 ASN Chi-restraints excluded: chain B residue 406 LYS Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 613 ASP Chi-restraints excluded: chain B residue 632 HIS Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 108 LYS Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 151 PHE Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain K residue 536 SER Chi-restraints excluded: chain K residue 537 LEU Chi-restraints excluded: chain K residue 546 THR Chi-restraints excluded: chain K residue 567 LEU Chi-restraints excluded: chain K residue 577 LEU Chi-restraints excluded: chain K residue 580 ASN Chi-restraints excluded: chain K residue 588 LEU Chi-restraints excluded: chain K residue 592 ILE Chi-restraints excluded: chain K residue 648 GLU Chi-restraints excluded: chain K residue 706 LEU Chi-restraints excluded: chain P residue 33 THR Chi-restraints excluded: chain P residue 121 THR Chi-restraints excluded: chain P residue 425 ARG Chi-restraints excluded: chain P residue 445 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 197 optimal weight: 40.0000 chunk 23 optimal weight: 0.9980 chunk 116 optimal weight: 0.9990 chunk 149 optimal weight: 0.8980 chunk 172 optimal weight: 8.9990 chunk 114 optimal weight: 0.9990 chunk 204 optimal weight: 20.0000 chunk 127 optimal weight: 0.0060 chunk 124 optimal weight: 0.6980 chunk 94 optimal weight: 1.9990 chunk 126 optimal weight: 0.7980 overall best weight: 0.6796 ------------------------------------------------------------------------------- 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** ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6732 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17837 Z= 0.188 Angle : 0.591 9.979 23992 Z= 0.307 Chirality : 0.041 0.182 2610 Planarity : 0.004 0.060 3076 Dihedral : 5.993 67.515 2409 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.33 % Allowed : 9.04 % Favored : 90.63 % Rotamer: Outliers : 4.37 % Allowed : 20.69 % Favored : 74.95 % 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: -1.15 (0.18), residues: 2124 helix: 0.97 (0.18), residues: 943 sheet: -0.52 (0.37), residues: 221 loop : -2.74 (0.18), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 114 HIS 0.009 0.001 HIS K 574 PHE 0.014 0.001 PHE A 32 TYR 0.018 0.001 TYR C 155 ARG 0.004 0.000 ARG K 575 *********************** 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 422 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 338 time to evaluate : 1.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 MET cc_start: 0.8376 (OUTLIER) cc_final: 0.7177 (tmm) REVERT: A 26 SER cc_start: 0.8591 (p) cc_final: 0.8246 (p) REVERT: A 99 ILE cc_start: 0.8412 (OUTLIER) cc_final: 0.8201 (pt) REVERT: A 114 MET cc_start: 0.7881 (OUTLIER) cc_final: 0.7367 (mpp) REVERT: A 275 LYS cc_start: 0.7503 (pptt) cc_final: 0.7052 (ptpt) REVERT: A 338 ARG cc_start: 0.7766 (ttm110) cc_final: 0.7438 (mtm110) REVERT: A 401 LEU cc_start: 0.5858 (OUTLIER) cc_final: 0.5629 (mp) REVERT: A 466 MET cc_start: 0.7186 (OUTLIER) cc_final: 0.6791 (tpp) REVERT: A 682 ARG cc_start: 0.7105 (ttp-170) cc_final: 0.6823 (tmm-80) REVERT: B 80 GLN cc_start: 0.7726 (OUTLIER) cc_final: 0.7467 (mt0) REVERT: B 95 LYS cc_start: 0.7903 (mttm) cc_final: 0.7557 (ttmm) REVERT: B 101 ASN cc_start: 0.7661 (m-40) cc_final: 0.7227 (m110) REVERT: B 364 ASP cc_start: 0.7303 (p0) cc_final: 0.6911 (p0) REVERT: C 103 GLU cc_start: 0.5110 (pm20) cc_final: 0.4809 (pm20) REVERT: C 105 MET cc_start: 0.6960 (tpt) cc_final: 0.6363 (tpt) REVERT: C 108 LYS cc_start: 0.5314 (OUTLIER) cc_final: 0.4950 (tmtt) REVERT: C 151 PHE cc_start: 0.4035 (OUTLIER) cc_final: 0.3318 (t80) REVERT: C 249 MET cc_start: 0.5972 (mmm) cc_final: 0.5518 (mmm) REVERT: P 107 MET cc_start: 0.7368 (mmp) cc_final: 0.6559 (mmp) REVERT: P 141 LYS cc_start: 0.7369 (mttm) cc_final: 0.7123 (mttm) REVERT: P 425 ARG cc_start: -0.0252 (OUTLIER) cc_final: -0.1238 (tmm160) outliers start: 84 outliers final: 67 residues processed: 386 average time/residue: 0.3179 time to fit residues: 178.5897 Evaluate side-chains 413 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 337 time to evaluate : 1.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 378 ARG Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 466 MET Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 553 MET Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 628 ILE Chi-restraints excluded: chain A residue 640 GLN Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 80 GLN Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 352 ASN Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 517 ILE Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 613 ASP Chi-restraints excluded: chain B residue 632 HIS Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 108 LYS Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 151 PHE Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 216 MET Chi-restraints excluded: chain K residue 537 LEU Chi-restraints excluded: chain K residue 546 THR Chi-restraints excluded: chain K residue 567 LEU Chi-restraints excluded: chain K residue 577 LEU Chi-restraints excluded: chain K residue 580 ASN Chi-restraints excluded: chain K residue 588 LEU Chi-restraints excluded: chain K residue 592 ILE Chi-restraints excluded: chain K residue 644 ILE Chi-restraints excluded: chain K residue 648 GLU Chi-restraints excluded: chain K residue 706 LEU Chi-restraints excluded: chain P residue 33 THR Chi-restraints excluded: chain P residue 121 THR Chi-restraints excluded: chain P residue 425 ARG Chi-restraints excluded: chain P residue 445 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 81 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 129 optimal weight: 0.8980 chunk 139 optimal weight: 0.3980 chunk 101 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 160 optimal weight: 1.9990 chunk 185 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 640 GLN ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 36 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6731 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17837 Z= 0.198 Angle : 0.605 10.210 23992 Z= 0.313 Chirality : 0.041 0.180 2610 Planarity : 0.004 0.056 3076 Dihedral : 5.957 68.013 2409 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.33 % Allowed : 9.27 % Favored : 90.40 % Rotamer: Outliers : 4.73 % Allowed : 20.63 % Favored : 74.64 % 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: -1.13 (0.18), residues: 2124 helix: 0.98 (0.18), residues: 943 sheet: -0.52 (0.37), residues: 223 loop : -2.72 (0.18), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 114 HIS 0.007 0.001 HIS K 574 PHE 0.014 0.001 PHE A 32 TYR 0.017 0.001 TYR C 155 ARG 0.004 0.000 ARG K 575 *********************** 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 428 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 337 time to evaluate : 2.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 MET cc_start: 0.8387 (OUTLIER) cc_final: 0.7200 (tmm) REVERT: A 26 SER cc_start: 0.8589 (p) cc_final: 0.8258 (p) REVERT: A 32 PHE cc_start: 0.7582 (OUTLIER) cc_final: 0.7289 (p90) REVERT: A 99 ILE cc_start: 0.8395 (OUTLIER) cc_final: 0.8191 (pt) REVERT: A 114 MET cc_start: 0.7998 (OUTLIER) cc_final: 0.7291 (mpp) REVERT: A 275 LYS cc_start: 0.7511 (pptt) cc_final: 0.7073 (ptpt) REVERT: A 330 ARG cc_start: 0.7178 (ptm160) cc_final: 0.6928 (ptp-170) REVERT: A 338 ARG cc_start: 0.7760 (ttm110) cc_final: 0.7444 (mtm110) REVERT: A 401 LEU cc_start: 0.5875 (OUTLIER) cc_final: 0.5646 (mp) REVERT: A 606 MET cc_start: 0.7187 (tpp) cc_final: 0.6981 (mmm) REVERT: A 682 ARG cc_start: 0.7072 (ttp-170) cc_final: 0.6797 (tmm-80) REVERT: B 80 GLN cc_start: 0.7723 (OUTLIER) cc_final: 0.7434 (mt0) REVERT: B 95 LYS cc_start: 0.7904 (mttm) cc_final: 0.7543 (ttmm) REVERT: B 101 ASN cc_start: 0.7643 (m-40) cc_final: 0.7198 (m110) REVERT: B 364 ASP cc_start: 0.7292 (p0) cc_final: 0.6906 (p0) REVERT: B 406 LYS cc_start: 0.6757 (OUTLIER) cc_final: 0.6419 (mttm) REVERT: B 444 ASP cc_start: 0.7814 (t0) cc_final: 0.7608 (t0) REVERT: B 447 ASN cc_start: 0.8497 (OUTLIER) cc_final: 0.8284 (p0) REVERT: B 606 MET cc_start: 0.7813 (tpp) cc_final: 0.7306 (mpp) REVERT: C 105 MET cc_start: 0.6967 (tpt) cc_final: 0.6367 (tpt) REVERT: C 108 LYS cc_start: 0.5220 (OUTLIER) cc_final: 0.4883 (tmtt) REVERT: C 151 PHE cc_start: 0.4042 (OUTLIER) cc_final: 0.3315 (t80) REVERT: C 249 MET cc_start: 0.6005 (mmm) cc_final: 0.5544 (mmm) REVERT: K 693 MET cc_start: 0.7094 (mtm) cc_final: 0.6847 (mtm) REVERT: P 107 MET cc_start: 0.7351 (mmp) cc_final: 0.6554 (mmp) REVERT: P 141 LYS cc_start: 0.7376 (mttm) cc_final: 0.7094 (mttm) REVERT: P 425 ARG cc_start: -0.0278 (OUTLIER) cc_final: -0.1223 (tmm160) outliers start: 91 outliers final: 66 residues processed: 391 average time/residue: 0.3155 time to fit residues: 179.6748 Evaluate side-chains 414 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 337 time to evaluate : 2.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 378 ARG Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 553 MET Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 628 ILE Chi-restraints excluded: chain A residue 640 GLN Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 80 GLN Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 352 ASN Chi-restraints excluded: chain B residue 406 LYS Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 447 ASN Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 517 ILE Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 613 ASP Chi-restraints excluded: chain B residue 632 HIS Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 108 LYS Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 151 PHE Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain K residue 536 SER Chi-restraints excluded: chain K residue 537 LEU Chi-restraints excluded: chain K residue 546 THR Chi-restraints excluded: chain K residue 567 LEU Chi-restraints excluded: chain K residue 577 LEU Chi-restraints excluded: chain K residue 580 ASN Chi-restraints excluded: chain K residue 588 LEU Chi-restraints excluded: chain K residue 592 ILE Chi-restraints excluded: chain K residue 648 GLU Chi-restraints excluded: chain K residue 706 LEU Chi-restraints excluded: chain P residue 33 THR Chi-restraints excluded: chain P residue 121 THR Chi-restraints excluded: chain P residue 425 ARG Chi-restraints excluded: chain P residue 445 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 195 optimal weight: 20.0000 chunk 178 optimal weight: 10.0000 chunk 190 optimal weight: 8.9990 chunk 114 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 172 optimal weight: 7.9990 chunk 180 optimal weight: 0.3980 chunk 189 optimal weight: 20.0000 chunk 125 optimal weight: 1.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 253 ASN K 540 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6822 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 17837 Z= 0.396 Angle : 0.714 11.580 23992 Z= 0.374 Chirality : 0.046 0.184 2610 Planarity : 0.005 0.055 3076 Dihedral : 6.599 69.753 2409 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.38 % Allowed : 10.69 % Favored : 88.94 % Rotamer: Outliers : 4.47 % Allowed : 20.69 % Favored : 74.84 % 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: -1.48 (0.18), residues: 2124 helix: 0.58 (0.17), residues: 978 sheet: -0.69 (0.36), residues: 225 loop : -2.91 (0.18), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP K 619 HIS 0.011 0.001 HIS B 320 PHE 0.036 0.002 PHE A 113 TYR 0.025 0.002 TYR B 356 ARG 0.005 0.000 ARG A 639 *********************** 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 441 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 355 time to evaluate : 1.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 SER cc_start: 0.8576 (p) cc_final: 0.8234 (p) REVERT: A 32 PHE cc_start: 0.7655 (OUTLIER) cc_final: 0.7281 (p90) REVERT: A 99 ILE cc_start: 0.8526 (OUTLIER) cc_final: 0.8287 (pt) REVERT: A 114 MET cc_start: 0.8071 (OUTLIER) cc_final: 0.7634 (mpp) REVERT: A 175 ILE cc_start: 0.8117 (mm) cc_final: 0.7814 (tt) REVERT: A 275 LYS cc_start: 0.7618 (pptt) cc_final: 0.7162 (ptpt) REVERT: A 330 ARG cc_start: 0.7243 (ptm160) cc_final: 0.7023 (ptp-170) REVERT: A 338 ARG cc_start: 0.7923 (ttm110) cc_final: 0.7687 (mtm110) REVERT: B 80 GLN cc_start: 0.7809 (OUTLIER) cc_final: 0.7547 (mt0) REVERT: B 95 LYS cc_start: 0.7940 (mttm) cc_final: 0.7670 (ttmm) REVERT: B 101 ASN cc_start: 0.7532 (m-40) cc_final: 0.7006 (m-40) REVERT: B 364 ASP cc_start: 0.7358 (p0) cc_final: 0.6962 (p0) REVERT: B 406 LYS cc_start: 0.6996 (OUTLIER) cc_final: 0.6562 (mttp) REVERT: B 447 ASN cc_start: 0.8547 (OUTLIER) cc_final: 0.8301 (p0) REVERT: B 565 LYS cc_start: 0.8222 (pttm) cc_final: 0.7798 (pttt) REVERT: B 606 MET cc_start: 0.7888 (tpp) cc_final: 0.7334 (mpp) REVERT: C 7 TRP cc_start: 0.7962 (m-90) cc_final: 0.7393 (m-90) REVERT: C 105 MET cc_start: 0.7010 (tpt) cc_final: 0.6310 (tpt) REVERT: C 108 LYS cc_start: 0.5315 (OUTLIER) cc_final: 0.4936 (tmtt) REVERT: C 151 PHE cc_start: 0.4099 (OUTLIER) cc_final: 0.3353 (t80) REVERT: C 249 MET cc_start: 0.6003 (mmm) cc_final: 0.5572 (mmm) REVERT: P 107 MET cc_start: 0.7370 (mmp) cc_final: 0.6581 (mmp) REVERT: P 141 LYS cc_start: 0.7376 (mttm) cc_final: 0.7060 (mttm) REVERT: P 425 ARG cc_start: -0.0150 (OUTLIER) cc_final: -0.0996 (tmm160) outliers start: 86 outliers final: 66 residues processed: 410 average time/residue: 0.3235 time to fit residues: 191.3547 Evaluate side-chains 429 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 354 time to evaluate : 1.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 378 ARG Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 553 MET Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 628 ILE Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 80 GLN Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 406 LYS Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 447 ASN Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 517 ILE Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 552 LYS Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 613 ASP Chi-restraints excluded: chain B residue 632 HIS Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 108 LYS Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 151 PHE Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain K residue 527 ILE Chi-restraints excluded: chain K residue 536 SER Chi-restraints excluded: chain K residue 537 LEU Chi-restraints excluded: chain K residue 540 HIS Chi-restraints excluded: chain K residue 546 THR Chi-restraints excluded: chain K residue 567 LEU Chi-restraints excluded: chain K residue 577 LEU Chi-restraints excluded: chain K residue 588 LEU Chi-restraints excluded: chain K residue 592 ILE Chi-restraints excluded: chain K residue 648 GLU Chi-restraints excluded: chain K residue 706 LEU Chi-restraints excluded: chain P residue 33 THR Chi-restraints excluded: chain P residue 121 THR Chi-restraints excluded: chain P residue 425 ARG Chi-restraints excluded: chain P residue 445 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 201 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 95 optimal weight: 0.8980 chunk 139 optimal weight: 0.0050 chunk 211 optimal weight: 0.0030 chunk 194 optimal weight: 10.0000 chunk 168 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 129 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 133 optimal weight: 20.0000 overall best weight: 0.5404 ------------------------------------------------------------------------------- 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 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 540 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6737 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17837 Z= 0.190 Angle : 0.638 10.549 23992 Z= 0.331 Chirality : 0.041 0.188 2610 Planarity : 0.004 0.057 3076 Dihedral : 6.202 68.195 2409 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.33 % Allowed : 8.47 % Favored : 91.20 % Rotamer: Outliers : 3.33 % Allowed : 22.35 % Favored : 74.32 % 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: -1.29 (0.18), residues: 2124 helix: 0.81 (0.17), residues: 962 sheet: -0.60 (0.37), residues: 221 loop : -2.82 (0.18), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 114 HIS 0.023 0.001 HIS K 540 PHE 0.019 0.001 PHE A 113 TYR 0.019 0.001 TYR B 56 ARG 0.005 0.000 ARG P 113 ********************** 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 404 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 340 time to evaluate : 1.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 SER cc_start: 0.8564 (p) cc_final: 0.8235 (p) REVERT: A 275 LYS cc_start: 0.7554 (pptt) cc_final: 0.7143 (ptpt) REVERT: A 330 ARG cc_start: 0.7267 (ptm160) cc_final: 0.6963 (ptp-170) REVERT: A 338 ARG cc_start: 0.7756 (ttm110) cc_final: 0.7457 (mtm110) REVERT: A 682 ARG cc_start: 0.7058 (ttp-170) cc_final: 0.6795 (tmm-80) REVERT: B 80 GLN cc_start: 0.7724 (OUTLIER) cc_final: 0.7450 (mt0) REVERT: B 95 LYS cc_start: 0.7890 (mttm) cc_final: 0.7512 (ttmm) REVERT: B 101 ASN cc_start: 0.7586 (m-40) cc_final: 0.7079 (m-40) REVERT: B 364 ASP cc_start: 0.7302 (p0) cc_final: 0.6876 (p0) REVERT: B 406 LYS cc_start: 0.6695 (OUTLIER) cc_final: 0.6404 (mttm) REVERT: B 565 LYS cc_start: 0.8172 (pttm) cc_final: 0.7746 (pttt) REVERT: B 582 ASN cc_start: 0.8247 (p0) cc_final: 0.7936 (p0) REVERT: B 606 MET cc_start: 0.7802 (tpp) cc_final: 0.7278 (mpp) REVERT: C 105 MET cc_start: 0.6948 (tpt) cc_final: 0.6214 (tpt) REVERT: C 108 LYS cc_start: 0.5280 (OUTLIER) cc_final: 0.4909 (tmmt) REVERT: C 151 PHE cc_start: 0.4055 (OUTLIER) cc_final: 0.3310 (t80) REVERT: C 249 MET cc_start: 0.5998 (mmm) cc_final: 0.5562 (mmm) REVERT: K 706 LEU cc_start: 0.7157 (OUTLIER) cc_final: 0.6931 (mm) REVERT: P 107 MET cc_start: 0.7330 (mmp) cc_final: 0.6552 (mmp) REVERT: P 141 LYS cc_start: 0.7358 (mttm) cc_final: 0.7042 (mttm) REVERT: P 425 ARG cc_start: -0.0234 (OUTLIER) cc_final: -0.1124 (tmm160) outliers start: 64 outliers final: 46 residues processed: 379 average time/residue: 0.3280 time to fit residues: 179.2278 Evaluate side-chains 389 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 337 time to evaluate : 1.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 378 ARG Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 553 MET Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 628 ILE Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 80 GLN Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 406 LYS Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 517 ILE Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 632 HIS Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 108 LYS Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 151 PHE Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain K residue 536 SER Chi-restraints excluded: chain K residue 546 THR Chi-restraints excluded: chain K residue 567 LEU Chi-restraints excluded: chain K residue 577 LEU Chi-restraints excluded: chain K residue 588 LEU Chi-restraints excluded: chain K residue 648 GLU Chi-restraints excluded: chain K residue 706 LEU Chi-restraints excluded: chain P residue 33 THR Chi-restraints excluded: chain P residue 121 THR Chi-restraints excluded: chain P residue 425 ARG Chi-restraints excluded: chain P residue 445 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 155 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 168 optimal weight: 0.7980 chunk 70 optimal weight: 0.8980 chunk 172 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 147 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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** A 407 ASN B 100 ASN ** B 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 539 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 = 0.4325 r_free = 0.4325 target = 0.193432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.148598 restraints weight = 26684.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.147904 restraints weight = 20937.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.148806 restraints weight = 17406.781| |-----------------------------------------------------------------------------| r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6787 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17837 Z= 0.222 Angle : 0.655 10.565 23992 Z= 0.338 Chirality : 0.042 0.199 2610 Planarity : 0.004 0.058 3076 Dihedral : 6.109 68.220 2409 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.33 % Allowed : 9.32 % Favored : 90.35 % Rotamer: Outliers : 3.43 % Allowed : 22.45 % Favored : 74.12 % 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: -1.24 (0.18), residues: 2124 helix: 0.85 (0.17), residues: 962 sheet: -0.62 (0.36), residues: 223 loop : -2.80 (0.18), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 114 HIS 0.007 0.001 HIS K 574 PHE 0.020 0.001 PHE A 113 TYR 0.020 0.001 TYR B 56 ARG 0.004 0.000 ARG K 575 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4229.77 seconds wall clock time: 76 minutes 3.53 seconds (4563.53 seconds total)