Starting phenix.real_space_refine on Thu May 9 18:49:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ugb_42220/05_2024/8ugb_42220_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ugb_42220/05_2024/8ugb_42220.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ugb_42220/05_2024/8ugb_42220_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ugb_42220/05_2024/8ugb_42220_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ugb_42220/05_2024/8ugb_42220_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ugb_42220/05_2024/8ugb_42220.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ugb_42220/05_2024/8ugb_42220.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ugb_42220/05_2024/8ugb_42220_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ugb_42220/05_2024/8ugb_42220_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.030 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 2 5.49 5 Mg 2 5.21 5 S 98 5.16 5 C 8771 2.51 5 N 2308 2.21 5 O 2543 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 187": "OD1" <-> "OD2" Residue "A ASP 320": "OD1" <-> "OD2" Residue "A TYR 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 416": "OD1" <-> "OD2" Residue "A GLU 438": "OE1" <-> "OE2" Residue "A GLU 642": "OE1" <-> "OE2" Residue "A GLU 656": "OE1" <-> "OE2" Residue "A ASP 663": "OD1" <-> "OD2" Residue "A TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 691": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 31": "OD1" <-> "OD2" Residue "B PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 307": "OD1" <-> "OD2" Residue "B GLU 370": "OE1" <-> "OE2" Residue "B ASP 436": "OD1" <-> "OD2" Residue "B GLU 442": "OE1" <-> "OE2" Residue "B GLU 654": "OE1" <-> "OE2" Residue "D PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 13726 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 811, 6645 Classifications: {'peptide': 811} Link IDs: {'PTRANS': 31, 'TRANS': 779} Chain: "B" Number of atoms: 6596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 811, 6596 Classifications: {'peptide': 811} Link IDs: {'PTRANS': 32, 'TRANS': 778} Chain: "C" Number of atoms: 187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 187 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 4, 'TRANS': 19} Chain: "D" Number of atoms: 176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 176 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 4, 'TRANS': 18} Chain: "A" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 61 Unusual residues: {' MG': 1, ' ZN': 1, 'PCG': 1, 'ZUD': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 61 Unusual residues: {' MG': 1, ' ZN': 1, 'PCG': 1, 'ZUD': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 7.51, per 1000 atoms: 0.55 Number of scatterers: 13726 At special positions: 0 Unit cell: (78.6, 120.52, 168.99, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 98 16.00 P 2 15.00 Mg 2 11.99 O 2543 8.00 N 2308 7.00 C 8771 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.48 Conformation dependent library (CDL) restraints added in 2.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 902 " pdb="ZN ZN A 902 " - pdb=" NE2 HIS A 563 " pdb="ZN ZN A 902 " - pdb=" NE2 HIS A 599 " pdb=" ZN B 902 " pdb="ZN ZN B 902 " - pdb=" NE2 HIS B 597 " pdb="ZN ZN B 902 " - pdb=" NE2 HIS B 561 " 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3188 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 77 helices and 4 sheets defined 54.1% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.02 Creating SS restraints... Processing helix chain 'A' and resid 8 through 15 Processing helix chain 'A' and resid 17 through 27 removed outlier: 3.685A pdb=" N GLN A 22 " --> pdb=" O SER A 18 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TYR A 23 " --> pdb=" O PHE A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 37 Processing helix chain 'A' and resid 54 through 67 removed outlier: 3.605A pdb=" N ASP A 67 " --> pdb=" O ASP A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 89 Processing helix chain 'A' and resid 121 through 124 No H-bonds generated for 'chain 'A' and resid 121 through 124' Processing helix chain 'A' and resid 128 through 130 No H-bonds generated for 'chain 'A' and resid 128 through 130' Processing helix chain 'A' and resid 140 through 147 Processing helix chain 'A' and resid 165 through 169 Processing helix chain 'A' and resid 205 through 250 removed outlier: 3.987A pdb=" N ASN A 216 " --> pdb=" O LEU A 212 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N PHE A 217 " --> pdb=" O LYS A 213 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ALA A 218 " --> pdb=" O TYR A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 270 removed outlier: 5.268A pdb=" N ALA A 268 " --> pdb=" O TYR A 264 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N PHE A 269 " --> pdb=" O THR A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 295 Proline residue: A 293 - end of helix Processing helix chain 'A' and resid 346 through 353 Processing helix chain 'A' and resid 362 through 364 No H-bonds generated for 'chain 'A' and resid 362 through 364' Processing helix chain 'A' and resid 414 through 458 removed outlier: 4.990A pdb=" N LEU A 432 " --> pdb=" O GLY A 428 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N ASN A 433 " --> pdb=" O TRP A 429 " (cutoff:3.500A) Proline residue: A 434 - end of helix Processing helix chain 'A' and resid 462 through 467 removed outlier: 3.733A pdb=" N GLN A 466 " --> pdb=" O ASN A 462 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N THR A 467 " --> pdb=" O GLU A 463 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 462 through 467' Processing helix chain 'A' and resid 471 through 474 No H-bonds generated for 'chain 'A' and resid 471 through 474' Processing helix chain 'A' and resid 484 through 494 removed outlier: 3.517A pdb=" N GLY A 493 " --> pdb=" O GLU A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 501 No H-bonds generated for 'chain 'A' and resid 498 through 501' Processing helix chain 'A' and resid 515 through 528 Processing helix chain 'A' and resid 539 through 552 Processing helix chain 'A' and resid 561 through 576 Processing helix chain 'A' and resid 580 through 583 removed outlier: 3.562A pdb=" N TYR A 583 " --> pdb=" O LEU A 580 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 580 through 583' Processing helix chain 'A' and resid 586 through 597 Processing helix chain 'A' and resid 608 through 614 Processing helix chain 'A' and resid 617 through 621 Processing helix chain 'A' and resid 627 through 640 Processing helix chain 'A' and resid 646 through 649 removed outlier: 4.117A pdb=" N ASN A 649 " --> pdb=" O ILE A 646 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 646 through 649' Processing helix chain 'A' and resid 652 through 669 removed outlier: 3.575A pdb=" N THR A 669 " --> pdb=" O ALA A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 690 removed outlier: 3.573A pdb=" N LYS A 676 " --> pdb=" O ALA A 672 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N THR A 679 " --> pdb=" O PHE A 675 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N MET A 680 " --> pdb=" O LYS A 676 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LYS A 689 " --> pdb=" O VAL A 685 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N THR A 690 " --> pdb=" O ASP A 686 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 703 removed outlier: 3.901A pdb=" N LEU A 703 " --> pdb=" O GLN A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 720 Processing helix chain 'A' and resid 722 through 725 Processing helix chain 'A' and resid 728 through 734 removed outlier: 3.683A pdb=" N LYS A 733 " --> pdb=" O GLU A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 753 Processing helix chain 'A' and resid 766 through 777 Proline residue: A 770 - end of helix Processing helix chain 'A' and resid 781 through 791 Processing helix chain 'A' and resid 793 through 816 Proline residue: A 797 - end of helix removed outlier: 3.532A pdb=" N ILE A 802 " --> pdb=" O LEU A 799 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR A 803 " --> pdb=" O ASP A 800 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TRP A 809 " --> pdb=" O ARG A 806 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 14 removed outlier: 3.545A pdb=" N LEU B 12 " --> pdb=" O HIS B 9 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASP B 13 " --> pdb=" O ARG B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 24 Processing helix chain 'B' and resid 48 through 67 removed outlier: 3.761A pdb=" N GLN B 67 " --> pdb=" O VAL B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 83 Processing helix chain 'B' and resid 119 through 121 No H-bonds generated for 'chain 'B' and resid 119 through 121' Processing helix chain 'B' and resid 126 through 128 No H-bonds generated for 'chain 'B' and resid 126 through 128' Processing helix chain 'B' and resid 137 through 145 removed outlier: 3.544A pdb=" N HIS B 141 " --> pdb=" O GLY B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 168 Processing helix chain 'B' and resid 203 through 246 removed outlier: 3.715A pdb=" N LEU B 210 " --> pdb=" O GLU B 206 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N PHE B 215 " --> pdb=" O LYS B 211 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N GLY B 216 " --> pdb=" O TYR B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 268 removed outlier: 3.542A pdb=" N ARG B 265 " --> pdb=" O PHE B 261 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N ALA B 266 " --> pdb=" O TYR B 262 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N TYR B 267 " --> pdb=" O THR B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 293 Proline residue: B 291 - end of helix Processing helix chain 'B' and resid 338 through 341 No H-bonds generated for 'chain 'B' and resid 338 through 341' Processing helix chain 'B' and resid 344 through 351 Processing helix chain 'B' and resid 360 through 362 No H-bonds generated for 'chain 'B' and resid 360 through 362' Processing helix chain 'B' and resid 412 through 456 removed outlier: 3.678A pdb=" N VAL B 429 " --> pdb=" O LEU B 425 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N LEU B 430 " --> pdb=" O GLY B 426 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N ASN B 431 " --> pdb=" O TRP B 427 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N THR B 432 " --> pdb=" O SER B 428 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N HIS B 455 " --> pdb=" O MET B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 465 Processing helix chain 'B' and resid 469 through 472 No H-bonds generated for 'chain 'B' and resid 469 through 472' Processing helix chain 'B' and resid 477 through 479 No H-bonds generated for 'chain 'B' and resid 477 through 479' Processing helix chain 'B' and resid 482 through 492 Processing helix chain 'B' and resid 513 through 527 Processing helix chain 'B' and resid 529 through 533 Processing helix chain 'B' and resid 537 through 550 Processing helix chain 'B' and resid 559 through 574 Processing helix chain 'B' and resid 578 through 581 Processing helix chain 'B' and resid 584 through 595 Processing helix chain 'B' and resid 606 through 612 Processing helix chain 'B' and resid 615 through 619 Processing helix chain 'B' and resid 627 through 638 Processing helix chain 'B' and resid 640 through 642 No H-bonds generated for 'chain 'B' and resid 640 through 642' Processing helix chain 'B' and resid 650 through 667 removed outlier: 3.534A pdb=" N THR B 667 " --> pdb=" O ALA B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 674 Processing helix chain 'B' and resid 676 through 687 Processing helix chain 'B' and resid 692 through 699 Processing helix chain 'B' and resid 703 through 718 removed outlier: 3.671A pdb=" N THR B 715 " --> pdb=" O ALA B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 726 through 749 removed outlier: 3.640A pdb=" N LYS B 731 " --> pdb=" O GLU B 727 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU B 734 " --> pdb=" O SER B 730 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 759 No H-bonds generated for 'chain 'B' and resid 757 through 759' Processing helix chain 'B' and resid 764 through 777 Proline residue: B 768 - end of helix Processing helix chain 'B' and resid 779 through 789 Processing helix chain 'B' and resid 793 through 816 removed outlier: 3.527A pdb=" N TRP B 807 " --> pdb=" O ARG B 804 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 133 through 135 removed outlier: 6.610A pdb=" N LEU A 96 " --> pdb=" O ARG A 111 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG A 93 " --> pdb=" O VAL A 195 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N VAL A 189 " --> pdb=" O TYR A 99 " (cutoff:3.500A) removed outlier: 11.572A pdb=" N ALA A 101 " --> pdb=" O ASP A 187 " (cutoff:3.500A) removed outlier: 13.939A pdb=" N ASP A 187 " --> pdb=" O ALA A 101 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASP A 187 " --> pdb=" O ASN A 184 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE A 182 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ILE A 191 " --> pdb=" O SER A 180 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N SER A 180 " --> pdb=" O ILE A 191 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N MET A 193 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N LEU A 178 " --> pdb=" O MET A 193 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 328 through 333 removed outlier: 6.936A pdb=" N LEU A 279 " --> pdb=" O TYR A 316 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N VAL A 318 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N VAL A 277 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N ASP A 320 " --> pdb=" O TYR A 275 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N TYR A 275 " --> pdb=" O ASP A 320 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N VAL A 398 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE A 390 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N VAL A 400 " --> pdb=" O MET A 388 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N MET A 388 " --> pdb=" O VAL A 400 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N THR A 402 " --> pdb=" O LEU A 386 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LEU A 386 " --> pdb=" O THR A 402 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 131 through 133 removed outlier: 6.589A pdb=" N LEU B 94 " --> pdb=" O ARG B 109 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N VAL B 187 " --> pdb=" O TYR B 97 " (cutoff:3.500A) removed outlier: 11.650A pdb=" N GLN B 99 " --> pdb=" O ASP B 185 " (cutoff:3.500A) removed outlier: 13.900A pdb=" N ASP B 185 " --> pdb=" O GLN B 99 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE B 180 " --> pdb=" O VAL B 187 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N VAL B 189 " --> pdb=" O THR B 178 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N THR B 178 " --> pdb=" O VAL B 189 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N MET B 191 " --> pdb=" O LEU B 176 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LEU B 176 " --> pdb=" O MET B 191 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 326 through 330 removed outlier: 6.849A pdb=" N LEU B 277 " --> pdb=" O TYR B 314 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N VAL B 316 " --> pdb=" O VAL B 275 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL B 275 " --> pdb=" O VAL B 316 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N ASP B 318 " --> pdb=" O TYR B 273 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N TYR B 273 " --> pdb=" O ASP B 318 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL B 396 " --> pdb=" O LEU B 278 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ILE B 388 " --> pdb=" O VAL B 396 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N VAL B 398 " --> pdb=" O MET B 386 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N MET B 386 " --> pdb=" O VAL B 398 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N THR B 400 " --> pdb=" O LEU B 384 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LEU B 384 " --> pdb=" O THR B 400 " (cutoff:3.500A) 627 hydrogen bonds defined for protein. 1683 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: 4.32 Time building geometry restraints manager: 5.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2321 1.31 - 1.44: 3700 1.44 - 1.57: 7842 1.57 - 1.69: 17 1.69 - 1.82: 164 Bond restraints: 14044 Sorted by residual: bond pdb=" C3' PCG B 901 " pdb=" C4' PCG B 901 " ideal model delta sigma weight residual 1.808 1.366 0.442 2.00e-02 2.50e+03 4.88e+02 bond pdb=" C3' PCG A 901 " pdb=" C4' PCG A 901 " ideal model delta sigma weight residual 1.808 1.369 0.439 2.00e-02 2.50e+03 4.83e+02 bond pdb=" C20 ZUD B 904 " pdb=" N6 ZUD B 904 " ideal model delta sigma weight residual 1.647 1.238 0.409 2.00e-02 2.50e+03 4.19e+02 bond pdb=" C20 ZUD A 904 " pdb=" N6 ZUD A 904 " ideal model delta sigma weight residual 1.647 1.239 0.408 2.00e-02 2.50e+03 4.16e+02 bond pdb=" C17 ZUD A 904 " pdb=" C18 ZUD A 904 " ideal model delta sigma weight residual 1.607 1.268 0.339 2.00e-02 2.50e+03 2.88e+02 ... (remaining 14039 not shown) Histogram of bond angle deviations from ideal: 96.96 - 104.70: 236 104.70 - 112.44: 7056 112.44 - 120.19: 5697 120.19 - 127.93: 5895 127.93 - 135.67: 118 Bond angle restraints: 19002 Sorted by residual: angle pdb=" C3 ZUD B 904 " pdb=" C4 ZUD B 904 " pdb=" N1 ZUD B 904 " ideal model delta sigma weight residual 98.62 126.27 -27.65 3.00e+00 1.11e-01 8.50e+01 angle pdb=" C3 ZUD A 904 " pdb=" C4 ZUD A 904 " pdb=" N1 ZUD A 904 " ideal model delta sigma weight residual 98.62 126.21 -27.59 3.00e+00 1.11e-01 8.46e+01 angle pdb=" CA PRO B 179 " pdb=" N PRO B 179 " pdb=" CD PRO B 179 " ideal model delta sigma weight residual 112.00 100.48 11.52 1.40e+00 5.10e-01 6.77e+01 angle pdb=" C3 ZUD A 904 " pdb=" C4 ZUD A 904 " pdb=" C6 ZUD A 904 " ideal model delta sigma weight residual 149.61 126.73 22.88 3.00e+00 1.11e-01 5.82e+01 angle pdb=" C3 ZUD B 904 " pdb=" C4 ZUD B 904 " pdb=" C6 ZUD B 904 " ideal model delta sigma weight residual 149.61 126.82 22.79 3.00e+00 1.11e-01 5.77e+01 ... (remaining 18997 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.16: 7591 22.16 - 44.32: 753 44.32 - 66.48: 116 66.48 - 88.64: 9 88.64 - 110.80: 5 Dihedral angle restraints: 8474 sinusoidal: 3560 harmonic: 4914 Sorted by residual: dihedral pdb=" CA LEU B 467 " pdb=" C LEU B 467 " pdb=" N PRO B 468 " pdb=" CA PRO B 468 " ideal model delta harmonic sigma weight residual -180.00 -154.27 -25.73 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" CA ASP B 600 " pdb=" C ASP B 600 " pdb=" N HIS B 601 " pdb=" CA HIS B 601 " ideal model delta harmonic sigma weight residual 180.00 155.19 24.81 0 5.00e+00 4.00e-02 2.46e+01 dihedral pdb=" CA ASP B 598 " pdb=" C ASP B 598 " pdb=" N ILE B 599 " pdb=" CA ILE B 599 " ideal model delta harmonic sigma weight residual -180.00 -156.73 -23.27 0 5.00e+00 4.00e-02 2.17e+01 ... (remaining 8471 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 1969 0.095 - 0.191: 82 0.191 - 0.286: 2 0.286 - 0.381: 2 0.381 - 0.476: 3 Chirality restraints: 2058 Sorted by residual: chirality pdb=" PA PCG A 901 " pdb=" O2A PCG A 901 " pdb=" O3' PCG A 901 " pdb=" O5' PCG A 901 " both_signs ideal model delta sigma weight residual True 3.19 2.71 0.48 2.00e-01 2.50e+01 5.67e+00 chirality pdb=" PA PCG B 901 " pdb=" O2A PCG B 901 " pdb=" O3' PCG B 901 " pdb=" O5' PCG B 901 " both_signs ideal model delta sigma weight residual True 3.19 2.74 0.45 2.00e-01 2.50e+01 5.15e+00 chirality pdb=" C4' PCG B 901 " pdb=" C3' PCG B 901 " pdb=" C5' PCG B 901 " pdb=" O4' PCG B 901 " both_signs ideal model delta sigma weight residual False -2.40 -2.82 0.42 2.00e-01 2.50e+01 4.35e+00 ... (remaining 2055 not shown) Planarity restraints: 2441 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 467 " 0.073 5.00e-02 4.00e+02 1.10e-01 1.94e+01 pdb=" N PRO B 468 " -0.191 5.00e-02 4.00e+02 pdb=" CA PRO B 468 " 0.058 5.00e-02 4.00e+02 pdb=" CD PRO B 468 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 38 " 0.073 5.00e-02 4.00e+02 1.10e-01 1.93e+01 pdb=" N PRO A 39 " -0.190 5.00e-02 4.00e+02 pdb=" CA PRO A 39 " 0.059 5.00e-02 4.00e+02 pdb=" CD PRO A 39 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 178 " -0.057 5.00e-02 4.00e+02 7.97e-02 1.02e+01 pdb=" N PRO B 179 " 0.137 5.00e-02 4.00e+02 pdb=" CA PRO B 179 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 179 " -0.044 5.00e-02 4.00e+02 ... (remaining 2438 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 79 2.47 - 3.08: 9522 3.08 - 3.68: 20925 3.68 - 4.29: 31463 4.29 - 4.90: 52771 Nonbonded interactions: 114760 Sorted by model distance: nonbonded pdb=" OD1 ASP A 600 " pdb="MG MG A 903 " model vdw 1.862 2.170 nonbonded pdb=" OD1 ASP A 720 " pdb="ZN ZN A 902 " model vdw 2.015 2.230 nonbonded pdb=" OD2 ASP A 600 " pdb="ZN ZN A 902 " model vdw 2.025 2.230 nonbonded pdb=" OH TYR B 551 " pdb=" O LEU B 595 " model vdw 2.114 2.440 nonbonded pdb=" OD2 ASP B 598 " pdb="ZN ZN B 902 " model vdw 2.152 2.230 ... (remaining 114755 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 'C' and resid 12 through 34) selection = chain 'D' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.280 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 40.320 Find NCS groups from input model: 0.500 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:13.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 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 : 0.015 0.442 14044 Z= 0.987 Angle : 0.825 27.652 19002 Z= 0.373 Chirality : 0.046 0.476 2058 Planarity : 0.005 0.110 2441 Dihedral : 16.729 110.796 5286 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.12 % Favored : 94.58 % Rotamer: Outliers : 1.27 % Allowed : 19.95 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.21), residues: 1661 helix: 1.18 (0.17), residues: 913 sheet: 0.52 (0.43), residues: 142 loop : -0.40 (0.26), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 380 HIS 0.008 0.001 HIS B 629 PHE 0.013 0.001 PHE B 209 TYR 0.014 0.001 TYR A 316 ARG 0.015 0.001 ARG B 531 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 106 time to evaluate : 1.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LEU cc_start: 0.9427 (mt) cc_final: 0.9176 (mp) REVERT: B 181 MET cc_start: 0.8745 (mmm) cc_final: 0.8508 (mmm) REVERT: B 282 LYS cc_start: 0.8299 (mppt) cc_final: 0.7956 (mmmt) REVERT: B 386 MET cc_start: 0.9465 (mtm) cc_final: 0.8884 (mpp) REVERT: B 442 GLU cc_start: 0.9016 (tp30) cc_final: 0.8449 (tm-30) REVERT: B 651 ARG cc_start: 0.8083 (tmm160) cc_final: 0.7848 (tmm-80) outliers start: 19 outliers final: 13 residues processed: 124 average time/residue: 1.4763 time to fit residues: 199.2610 Evaluate side-chains 110 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 97 time to evaluate : 1.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain B residue 13 ASP Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 544 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 0.5980 chunk 125 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 84 optimal weight: 20.0000 chunk 67 optimal weight: 0.9980 chunk 130 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 chunk 96 optimal weight: 5.9990 chunk 150 optimal weight: 0.0070 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 466 GLN B 322 HIS B 729 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.0803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 14044 Z= 0.197 Angle : 0.566 8.817 19002 Z= 0.289 Chirality : 0.041 0.193 2058 Planarity : 0.005 0.109 2441 Dihedral : 7.724 87.910 1878 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.24 % Favored : 94.46 % Rotamer: Outliers : 2.74 % Allowed : 18.15 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.21), residues: 1661 helix: 1.41 (0.17), residues: 924 sheet: 0.52 (0.44), residues: 142 loop : -0.36 (0.26), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 561 HIS 0.009 0.001 HIS B 322 PHE 0.012 0.001 PHE A 565 TYR 0.011 0.001 TYR B 97 ARG 0.004 0.000 ARG B 650 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 105 time to evaluate : 1.658 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 LEU cc_start: 0.9517 (mt) cc_final: 0.9279 (mp) REVERT: A 137 ASP cc_start: 0.9036 (OUTLIER) cc_final: 0.8294 (p0) REVERT: A 183 MET cc_start: 0.8485 (mmm) cc_final: 0.8149 (mmm) REVERT: A 733 LYS cc_start: 0.9237 (OUTLIER) cc_final: 0.8960 (mmtm) REVERT: B 181 MET cc_start: 0.8775 (mmm) cc_final: 0.8537 (mmm) REVERT: B 282 LYS cc_start: 0.8274 (mppt) cc_final: 0.7874 (mmmt) REVERT: B 442 GLU cc_start: 0.8968 (tp30) cc_final: 0.8453 (tm-30) REVERT: B 531 ARG cc_start: 0.8050 (tmm-80) cc_final: 0.7752 (tmm-80) REVERT: B 640 GLU cc_start: 0.8369 (tp30) cc_final: 0.8164 (tp30) REVERT: B 651 ARG cc_start: 0.8013 (tmm160) cc_final: 0.7761 (tmm-80) REVERT: D 29 LYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7716 (tmtt) REVERT: D 30 PHE cc_start: 0.8696 (m-10) cc_final: 0.8493 (m-10) outliers start: 41 outliers final: 14 residues processed: 139 average time/residue: 1.5517 time to fit residues: 234.4052 Evaluate side-chains 119 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 102 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain B residue 13 ASP Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 159 HIS Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 386 MET Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 580 SER Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain D residue 29 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 83 optimal weight: 30.0000 chunk 46 optimal weight: 0.6980 chunk 125 optimal weight: 2.9990 chunk 102 optimal weight: 0.5980 chunk 41 optimal weight: 3.9990 chunk 151 optimal weight: 0.5980 chunk 163 optimal weight: 2.9990 chunk 134 optimal weight: 0.6980 chunk 149 optimal weight: 3.9990 chunk 51 optimal weight: 0.5980 chunk 121 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 219 ASN B 322 HIS ** B 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.1023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14044 Z= 0.183 Angle : 0.538 6.954 19002 Z= 0.272 Chirality : 0.040 0.178 2058 Planarity : 0.004 0.108 2441 Dihedral : 7.228 91.725 1867 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.18 % Favored : 94.52 % Rotamer: Outliers : 2.47 % Allowed : 18.68 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.21), residues: 1661 helix: 1.47 (0.18), residues: 918 sheet: 0.52 (0.44), residues: 144 loop : -0.29 (0.26), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 561 HIS 0.009 0.001 HIS B 322 PHE 0.012 0.001 PHE A 565 TYR 0.015 0.001 TYR A 674 ARG 0.005 0.000 ARG A 750 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 109 time to evaluate : 1.615 Fit side-chains revert: symmetry clash REVERT: A 26 LEU cc_start: 0.9518 (mt) cc_final: 0.9279 (mp) REVERT: A 183 MET cc_start: 0.8438 (mmm) cc_final: 0.8232 (mmm) REVERT: A 733 LYS cc_start: 0.9226 (OUTLIER) cc_final: 0.8955 (mmtm) REVERT: B 181 MET cc_start: 0.8741 (mmm) cc_final: 0.8479 (mmm) REVERT: B 282 LYS cc_start: 0.8307 (mppt) cc_final: 0.7908 (mmmt) REVERT: B 531 ARG cc_start: 0.8030 (tmm-80) cc_final: 0.7753 (tmm-80) REVERT: B 640 GLU cc_start: 0.8442 (tp30) cc_final: 0.8126 (tp30) REVERT: D 29 LYS cc_start: 0.8166 (OUTLIER) cc_final: 0.7716 (tmtt) REVERT: D 30 PHE cc_start: 0.8671 (m-10) cc_final: 0.8449 (m-10) outliers start: 37 outliers final: 15 residues processed: 138 average time/residue: 1.4462 time to fit residues: 217.7038 Evaluate side-chains 120 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 103 time to evaluate : 1.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 159 HIS Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 548 SER Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 33 ARG Chi-restraints excluded: chain D residue 29 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 149 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 16 optimal weight: 4.9990 chunk 72 optimal weight: 0.9990 chunk 101 optimal weight: 0.7980 chunk 151 optimal weight: 0.6980 chunk 160 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 143 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 322 HIS B 653 HIS ** B 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14044 Z= 0.190 Angle : 0.530 7.556 19002 Z= 0.269 Chirality : 0.041 0.182 2058 Planarity : 0.004 0.108 2441 Dihedral : 6.746 91.747 1864 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.24 % Favored : 94.46 % Rotamer: Outliers : 2.67 % Allowed : 19.01 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.21), residues: 1661 helix: 1.47 (0.18), residues: 923 sheet: 0.44 (0.44), residues: 146 loop : -0.25 (0.27), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 561 HIS 0.011 0.001 HIS B 322 PHE 0.012 0.001 PHE A 565 TYR 0.012 0.001 TYR B 97 ARG 0.006 0.000 ARG A 27 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 106 time to evaluate : 1.628 Fit side-chains revert: symmetry clash REVERT: A 26 LEU cc_start: 0.9504 (mt) cc_final: 0.9246 (mp) REVERT: A 183 MET cc_start: 0.8469 (mmm) cc_final: 0.8212 (mmm) REVERT: A 500 LYS cc_start: 0.9244 (OUTLIER) cc_final: 0.8986 (tmmt) REVERT: A 733 LYS cc_start: 0.9226 (OUTLIER) cc_final: 0.8963 (mmtm) REVERT: B 181 MET cc_start: 0.8733 (mmm) cc_final: 0.8482 (mmm) REVERT: B 282 LYS cc_start: 0.8249 (mppt) cc_final: 0.7895 (mmmt) REVERT: B 442 GLU cc_start: 0.8932 (tp30) cc_final: 0.8263 (tm-30) REVERT: B 640 GLU cc_start: 0.8414 (tp30) cc_final: 0.8086 (tp30) REVERT: D 29 LYS cc_start: 0.8145 (OUTLIER) cc_final: 0.7642 (tmtt) REVERT: D 30 PHE cc_start: 0.8663 (m-10) cc_final: 0.8434 (m-10) outliers start: 40 outliers final: 17 residues processed: 138 average time/residue: 1.4082 time to fit residues: 212.3969 Evaluate side-chains 120 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 100 time to evaluate : 1.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 500 LYS Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 159 HIS Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 548 SER Chi-restraints excluded: chain B residue 580 SER Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 710 MET Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 33 ARG Chi-restraints excluded: chain D residue 29 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 133 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 119 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 chunk 136 optimal weight: 0.6980 chunk 110 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 81 optimal weight: 0.0980 chunk 144 optimal weight: 0.5980 chunk 40 optimal weight: 0.3980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14044 Z= 0.165 Angle : 0.517 7.140 19002 Z= 0.262 Chirality : 0.040 0.176 2058 Planarity : 0.004 0.108 2441 Dihedral : 6.467 92.328 1862 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.88 % Favored : 94.82 % Rotamer: Outliers : 2.20 % Allowed : 19.55 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.22), residues: 1661 helix: 1.53 (0.18), residues: 924 sheet: 0.54 (0.44), residues: 146 loop : -0.26 (0.27), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 561 HIS 0.010 0.001 HIS B 322 PHE 0.012 0.001 PHE B 215 TYR 0.014 0.001 TYR A 674 ARG 0.010 0.000 ARG B 531 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 103 time to evaluate : 1.598 Fit side-chains REVERT: A 26 LEU cc_start: 0.9494 (mt) cc_final: 0.9236 (mp) REVERT: A 183 MET cc_start: 0.8412 (mmm) cc_final: 0.8182 (mmm) REVERT: A 733 LYS cc_start: 0.9198 (OUTLIER) cc_final: 0.8943 (mmtm) REVERT: B 181 MET cc_start: 0.8716 (mmm) cc_final: 0.8470 (mmm) REVERT: B 282 LYS cc_start: 0.8212 (mppt) cc_final: 0.7874 (mmmt) REVERT: B 640 GLU cc_start: 0.8389 (tp30) cc_final: 0.8058 (tp30) REVERT: D 29 LYS cc_start: 0.8136 (OUTLIER) cc_final: 0.7618 (tmtt) REVERT: D 30 PHE cc_start: 0.8668 (m-10) cc_final: 0.8439 (m-10) outliers start: 33 outliers final: 14 residues processed: 130 average time/residue: 1.5150 time to fit residues: 214.5145 Evaluate side-chains 118 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 102 time to evaluate : 1.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 159 HIS Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 548 SER Chi-restraints excluded: chain B residue 710 MET Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 33 ARG Chi-restraints excluded: chain D residue 29 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 53 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 160 optimal weight: 0.8980 chunk 133 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 84 optimal weight: 30.0000 chunk 154 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 466 GLN B 14 GLN ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 14044 Z= 0.338 Angle : 0.605 9.844 19002 Z= 0.305 Chirality : 0.043 0.214 2058 Planarity : 0.005 0.111 2441 Dihedral : 6.535 92.211 1862 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.06 % Favored : 94.64 % Rotamer: Outliers : 2.20 % Allowed : 19.61 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.21), residues: 1661 helix: 1.47 (0.18), residues: 924 sheet: 0.39 (0.44), residues: 146 loop : -0.40 (0.27), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 380 HIS 0.008 0.001 HIS B 629 PHE 0.018 0.002 PHE A 12 TYR 0.016 0.002 TYR A 316 ARG 0.005 0.000 ARG B 650 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 102 time to evaluate : 1.674 Fit side-chains REVERT: A 26 LEU cc_start: 0.9510 (mt) cc_final: 0.9244 (mp) REVERT: A 183 MET cc_start: 0.8712 (mmm) cc_final: 0.8316 (mmm) REVERT: A 285 GLN cc_start: 0.8720 (tp40) cc_final: 0.8493 (tm-30) REVERT: A 733 LYS cc_start: 0.9190 (OUTLIER) cc_final: 0.8808 (mmtm) REVERT: B 282 LYS cc_start: 0.8200 (mppt) cc_final: 0.7901 (mmmt) REVERT: B 442 GLU cc_start: 0.8959 (tp30) cc_final: 0.8277 (tm-30) REVERT: D 29 LYS cc_start: 0.8380 (OUTLIER) cc_final: 0.7946 (tmtt) REVERT: D 30 PHE cc_start: 0.8697 (m-10) cc_final: 0.8482 (m-10) outliers start: 33 outliers final: 14 residues processed: 129 average time/residue: 1.5793 time to fit residues: 221.8605 Evaluate side-chains 113 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 97 time to evaluate : 1.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 159 HIS Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 548 SER Chi-restraints excluded: chain B residue 580 SER Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 33 ARG Chi-restraints excluded: chain D residue 29 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 18 optimal weight: 0.9980 chunk 91 optimal weight: 0.5980 chunk 117 optimal weight: 6.9990 chunk 90 optimal weight: 0.9990 chunk 135 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 466 GLN B 141 HIS B 322 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14044 Z= 0.238 Angle : 0.558 7.821 19002 Z= 0.284 Chirality : 0.042 0.193 2058 Planarity : 0.004 0.110 2441 Dihedral : 6.326 91.686 1858 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.24 % Favored : 94.46 % Rotamer: Outliers : 2.20 % Allowed : 19.75 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.22), residues: 1661 helix: 1.47 (0.18), residues: 924 sheet: 0.56 (0.44), residues: 143 loop : -0.37 (0.27), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 561 HIS 0.006 0.001 HIS B 322 PHE 0.012 0.001 PHE A 565 TYR 0.012 0.001 TYR B 97 ARG 0.012 0.000 ARG B 531 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 99 time to evaluate : 1.639 Fit side-chains REVERT: A 26 LEU cc_start: 0.9496 (mt) cc_final: 0.9232 (mp) REVERT: A 183 MET cc_start: 0.8736 (mmm) cc_final: 0.8326 (mmm) REVERT: A 733 LYS cc_start: 0.9231 (OUTLIER) cc_final: 0.8933 (mmtm) REVERT: B 282 LYS cc_start: 0.8194 (mppt) cc_final: 0.7910 (mmmt) REVERT: B 412 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.7777 (tp30) REVERT: B 442 GLU cc_start: 0.8943 (tp30) cc_final: 0.8397 (tm-30) REVERT: D 29 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.8008 (tmtt) outliers start: 33 outliers final: 18 residues processed: 124 average time/residue: 1.5305 time to fit residues: 207.3676 Evaluate side-chains 120 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 99 time to evaluate : 1.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 702 MET Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 159 HIS Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 412 GLU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 548 SER Chi-restraints excluded: chain B residue 580 SER Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 33 ARG Chi-restraints excluded: chain D residue 29 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 63 optimal weight: 0.8980 chunk 95 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 101 optimal weight: 0.8980 chunk 109 optimal weight: 0.9980 chunk 79 optimal weight: 0.0670 chunk 14 optimal weight: 6.9990 chunk 125 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 overall best weight: 0.7720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 322 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14044 Z= 0.198 Angle : 0.557 11.360 19002 Z= 0.282 Chirality : 0.041 0.183 2058 Planarity : 0.004 0.109 2441 Dihedral : 6.257 91.958 1858 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.24 % Favored : 94.46 % Rotamer: Outliers : 1.73 % Allowed : 20.28 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.22), residues: 1661 helix: 1.51 (0.18), residues: 925 sheet: 0.65 (0.45), residues: 143 loop : -0.34 (0.27), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 561 HIS 0.006 0.001 HIS B 322 PHE 0.020 0.001 PHE D 30 TYR 0.015 0.001 TYR A 674 ARG 0.003 0.000 ARG B 650 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 101 time to evaluate : 1.605 Fit side-chains REVERT: A 26 LEU cc_start: 0.9483 (mt) cc_final: 0.9222 (mp) REVERT: A 183 MET cc_start: 0.8715 (mmm) cc_final: 0.8320 (mmm) REVERT: A 733 LYS cc_start: 0.9220 (OUTLIER) cc_final: 0.8935 (mmtm) REVERT: B 282 LYS cc_start: 0.8181 (mppt) cc_final: 0.7905 (mmmt) REVERT: B 412 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.7774 (tp30) REVERT: B 442 GLU cc_start: 0.8914 (tp30) cc_final: 0.8236 (tm-30) REVERT: D 29 LYS cc_start: 0.8338 (OUTLIER) cc_final: 0.7947 (tmtt) outliers start: 26 outliers final: 16 residues processed: 122 average time/residue: 1.5221 time to fit residues: 202.6087 Evaluate side-chains 116 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 97 time to evaluate : 1.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 159 HIS Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 412 GLU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 548 SER Chi-restraints excluded: chain B residue 580 SER Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 33 ARG Chi-restraints excluded: chain D residue 29 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 153 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 149 optimal weight: 0.7980 chunk 89 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 117 optimal weight: 0.8980 chunk 45 optimal weight: 0.0670 chunk 134 optimal weight: 0.8980 chunk 141 optimal weight: 1.9990 chunk 148 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 GLN A 616 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14044 Z= 0.189 Angle : 0.554 11.431 19002 Z= 0.280 Chirality : 0.041 0.179 2058 Planarity : 0.004 0.108 2441 Dihedral : 6.231 92.149 1858 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.12 % Favored : 94.58 % Rotamer: Outliers : 1.53 % Allowed : 20.41 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.22), residues: 1661 helix: 1.51 (0.18), residues: 927 sheet: 0.68 (0.45), residues: 143 loop : -0.33 (0.27), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 561 HIS 0.004 0.001 HIS B 322 PHE 0.020 0.001 PHE D 30 TYR 0.020 0.001 TYR A 674 ARG 0.015 0.000 ARG B 531 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 97 time to evaluate : 1.573 Fit side-chains REVERT: A 26 LEU cc_start: 0.9482 (mt) cc_final: 0.9227 (mp) REVERT: A 183 MET cc_start: 0.8698 (mmm) cc_final: 0.8316 (mmm) REVERT: A 733 LYS cc_start: 0.9236 (OUTLIER) cc_final: 0.8960 (mmtm) REVERT: B 282 LYS cc_start: 0.8177 (mppt) cc_final: 0.7898 (mmmt) REVERT: B 412 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.7775 (tp30) REVERT: D 29 LYS cc_start: 0.8337 (OUTLIER) cc_final: 0.7882 (tmtt) outliers start: 23 outliers final: 17 residues processed: 116 average time/residue: 1.4792 time to fit residues: 187.3446 Evaluate side-chains 118 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 98 time to evaluate : 1.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 159 HIS Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 412 GLU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 548 SER Chi-restraints excluded: chain B residue 580 SER Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 33 ARG Chi-restraints excluded: chain D residue 29 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 157 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 109 optimal weight: 0.8980 chunk 165 optimal weight: 0.9990 chunk 152 optimal weight: 0.0060 chunk 131 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 chunk 80 optimal weight: 0.7980 chunk 104 optimal weight: 0.6980 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14044 Z= 0.182 Angle : 0.555 11.742 19002 Z= 0.280 Chirality : 0.041 0.177 2058 Planarity : 0.004 0.108 2441 Dihedral : 6.225 92.323 1858 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.12 % Favored : 94.58 % Rotamer: Outliers : 1.40 % Allowed : 20.61 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.22), residues: 1661 helix: 1.55 (0.18), residues: 921 sheet: 0.71 (0.45), residues: 143 loop : -0.30 (0.27), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 561 HIS 0.005 0.001 HIS B 322 PHE 0.012 0.001 PHE D 30 TYR 0.017 0.001 TYR A 674 ARG 0.012 0.000 ARG B 531 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 100 time to evaluate : 1.636 Fit side-chains REVERT: A 26 LEU cc_start: 0.9479 (mt) cc_final: 0.9225 (mp) REVERT: A 183 MET cc_start: 0.8691 (mmm) cc_final: 0.8326 (mmm) REVERT: A 714 MET cc_start: 0.9057 (OUTLIER) cc_final: 0.7891 (mmp) REVERT: A 733 LYS cc_start: 0.9226 (OUTLIER) cc_final: 0.8956 (mmtm) REVERT: B 282 LYS cc_start: 0.8176 (mppt) cc_final: 0.7897 (mmmt) REVERT: B 412 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.7775 (tp30) REVERT: B 442 GLU cc_start: 0.8917 (tp30) cc_final: 0.8360 (tm-30) REVERT: D 29 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.7738 (tmtt) outliers start: 21 outliers final: 17 residues processed: 118 average time/residue: 1.4961 time to fit residues: 192.7851 Evaluate side-chains 118 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 97 time to evaluate : 1.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 714 MET Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 159 HIS Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 412 GLU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 548 SER Chi-restraints excluded: chain B residue 580 SER Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 33 ARG Chi-restraints excluded: chain D residue 29 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 0.4980 chunk 40 optimal weight: 4.9990 chunk 121 optimal weight: 0.0370 chunk 19 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 131 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 135 optimal weight: 0.7980 chunk 16 optimal weight: 7.9990 chunk 24 optimal weight: 2.9990 chunk 115 optimal weight: 0.7980 overall best weight: 0.8260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.083637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.064420 restraints weight = 35365.795| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.85 r_work: 0.3064 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14044 Z= 0.209 Angle : 0.568 12.292 19002 Z= 0.283 Chirality : 0.041 0.186 2058 Planarity : 0.004 0.108 2441 Dihedral : 6.223 92.643 1858 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.00 % Favored : 94.70 % Rotamer: Outliers : 1.47 % Allowed : 20.81 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.22), residues: 1661 helix: 1.55 (0.18), residues: 924 sheet: 0.76 (0.45), residues: 143 loop : -0.25 (0.27), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 561 HIS 0.008 0.001 HIS B 322 PHE 0.012 0.001 PHE A 565 TYR 0.022 0.001 TYR A 674 ARG 0.012 0.000 ARG B 531 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4200.65 seconds wall clock time: 76 minutes 40.31 seconds (4600.31 seconds total)