Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 22 15:21:03 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oiu_12933/04_2023/7oiu_12933.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oiu_12933/04_2023/7oiu_12933.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oiu_12933/04_2023/7oiu_12933.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oiu_12933/04_2023/7oiu_12933.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oiu_12933/04_2023/7oiu_12933.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oiu_12933/04_2023/7oiu_12933.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 1.653 sd= 4.053 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 43 5.16 5 C 8174 2.51 5 N 2197 2.21 5 O 2330 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 19": "NH1" <-> "NH2" Residue "C ASP 67": "OD1" <-> "OD2" Residue "C ARG 72": "NH1" <-> "NH2" Residue "C PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 83": "NH1" <-> "NH2" Residue "C ARG 85": "NH1" <-> "NH2" Residue "C ARG 101": "NH1" <-> "NH2" Residue "A ARG 7": "NH1" <-> "NH2" Residue "A GLU 37": "OE1" <-> "OE2" Residue "A TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 62": "NH1" <-> "NH2" Residue "A GLU 63": "OE1" <-> "OE2" Residue "A ARG 69": "NH1" <-> "NH2" Residue "A ARG 86": "NH1" <-> "NH2" Residue "A GLU 109": "OE1" <-> "OE2" Residue "A ASP 120": "OD1" <-> "OD2" Residue "A ARG 128": "NH1" <-> "NH2" Residue "A ARG 152": "NH1" <-> "NH2" Residue "A GLU 177": "OE1" <-> "OE2" Residue "A ARG 211": "NH1" <-> "NH2" Residue "A ARG 222": "NH1" <-> "NH2" Residue "A GLU 269": "OE1" <-> "OE2" Residue "A GLU 286": "OE1" <-> "OE2" Residue "A TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 290": "NH1" <-> "NH2" Residue "A GLU 311": "OE1" <-> "OE2" Residue "A PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 341": "NH1" <-> "NH2" Residue "A ARG 380": "NH1" <-> "NH2" Residue "A ARG 382": "NH1" <-> "NH2" Residue "A PHE 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 485": "OE1" <-> "OE2" Residue "A GLU 621": "OE1" <-> "OE2" Residue "A TYR 635": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 648": "NH1" <-> "NH2" Residue "A PHE 656": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 719": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 764": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 780": "OE1" <-> "OE2" Residue "B ASP 28": "OD1" <-> "OD2" Residue "B GLU 63": "OE1" <-> "OE2" Residue "B ARG 69": "NH1" <-> "NH2" Residue "B GLU 89": "OE1" <-> "OE2" Residue "B ARG 101": "NH1" <-> "NH2" Residue "B ASP 104": "OD1" <-> "OD2" Residue "B ARG 108": "NH1" <-> "NH2" Residue "B ARG 128": "NH1" <-> "NH2" Residue "B GLU 154": "OE1" <-> "OE2" Residue "B ARG 173": "NH1" <-> "NH2" Residue "B GLU 183": "OE1" <-> "OE2" Residue "B ARG 222": "NH1" <-> "NH2" Residue "B ARG 235": "NH1" <-> "NH2" Residue "B ARG 249": "NH1" <-> "NH2" Residue "B GLU 256": "OE1" <-> "OE2" Residue "B ARG 281": "NH1" <-> "NH2" Residue "B ARG 290": "NH1" <-> "NH2" Residue "B ASP 297": "OD1" <-> "OD2" Residue "B GLU 311": "OE1" <-> "OE2" Residue "B TYR 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 362": "OD1" <-> "OD2" Residue "B ARG 382": "NH1" <-> "NH2" Residue "B ARG 482": "NH1" <-> "NH2" Residue "B ARG 489": "NH1" <-> "NH2" Residue "B TYR 635": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 664": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 677": "NH1" <-> "NH2" Residue "B GLU 780": "OE1" <-> "OE2" Residue "B ASP 789": "OD1" <-> "OD2" Residue "D TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 25": "OE1" <-> "OE2" Residue "D ARG 26": "NH1" <-> "NH2" Residue "D PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 20": "OE1" <-> "OE2" Residue "E ARG 26": "NH1" <-> "NH2" Residue "E PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 36": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 12744 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 776 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 9, 'TRANS': 94} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 2, 'TRP:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 45 Chain: "A" Number of atoms: 5701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 752, 5701 Classifications: {'peptide': 752} Incomplete info: {'truncation_to_alanine': 96} Link IDs: {'PTRANS': 35, 'TRANS': 716} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 359 Unresolved non-hydrogen angles: 445 Unresolved non-hydrogen dihedrals: 293 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 14, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 4, 'GLU:plan': 16, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 228 Chain: "B" Number of atoms: 5318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 685, 5318 Classifications: {'peptide': 685} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 31, 'TRANS': 653} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 209 Unresolved non-hydrogen angles: 253 Unresolved non-hydrogen dihedrals: 172 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 6, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 8, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 127 Chain: "D" Number of atoms: 346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 346 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'TRANS': 49} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "E" Number of atoms: 355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 355 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'TRANS': 50} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "F" Number of atoms: 248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 248 Classifications: {'peptide': 41} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'TRANS': 40} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Time building chain proxies: 6.64, per 1000 atoms: 0.52 Number of scatterers: 12744 At special positions: 0 Unit cell: (137.643, 92.829, 161.117, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 43 16.00 O 2330 8.00 N 2197 7.00 C 8174 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: 5.00 Conformation dependent library (CDL) restraints added in 2.0 seconds 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3152 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 13 sheets defined 50.0% alpha, 14.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'C' and resid 27 through 45 removed outlier: 3.518A pdb=" N THR C 44 " --> pdb=" O VAL C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 67 removed outlier: 3.561A pdb=" N LEU C 56 " --> pdb=" O LEU C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 81 removed outlier: 3.995A pdb=" N ILE C 73 " --> pdb=" O LYS C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 91 Processing helix chain 'A' and resid 3 through 13 Processing helix chain 'A' and resid 15 through 20 removed outlier: 3.997A pdb=" N GLN A 18 " --> pdb=" O PRO A 15 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE A 20 " --> pdb=" O GLY A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 72 removed outlier: 3.631A pdb=" N PHE A 58 " --> pdb=" O GLU A 54 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLY A 70 " --> pdb=" O ASN A 66 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ILE A 71 " --> pdb=" O THR A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 110 Processing helix chain 'A' and resid 134 through 141 removed outlier: 3.550A pdb=" N PHE A 138 " --> pdb=" O VAL A 134 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG A 141 " --> pdb=" O PHE A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 171 Processing helix chain 'A' and resid 191 through 202 removed outlier: 3.607A pdb=" N PHE A 195 " --> pdb=" O ALA A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 264 Processing helix chain 'A' and resid 280 through 297 Processing helix chain 'A' and resid 303 through 319 removed outlier: 4.105A pdb=" N GLU A 307 " --> pdb=" O THR A 303 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N GLU A 311 " --> pdb=" O GLU A 307 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N ALA A 312 " --> pdb=" O GLU A 308 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LEU A 313 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ASN A 314 " --> pdb=" O ASP A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 354 removed outlier: 3.795A pdb=" N VAL A 354 " --> pdb=" O ALA A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 Processing helix chain 'A' and resid 387 through 395 Processing helix chain 'A' and resid 455 through 469 Processing helix chain 'A' and resid 470 through 472 No H-bonds generated for 'chain 'A' and resid 470 through 472' Processing helix chain 'A' and resid 484 through 491 removed outlier: 3.526A pdb=" N MET A 491 " --> pdb=" O SER A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 528 removed outlier: 4.060A pdb=" N LYS A 522 " --> pdb=" O LEU A 518 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN A 523 " --> pdb=" O ILE A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 553 removed outlier: 3.964A pdb=" N MET A 550 " --> pdb=" O ALA A 546 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASP A 553 " --> pdb=" O ALA A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 590 removed outlier: 3.816A pdb=" N ARG A 586 " --> pdb=" O THR A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 645 Proline residue: A 631 - end of helix removed outlier: 4.181A pdb=" N SER A 642 " --> pdb=" O TYR A 638 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N MET A 643 " --> pdb=" O ARG A 639 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ASP A 645 " --> pdb=" O GLU A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 661 Processing helix chain 'A' and resid 664 through 679 removed outlier: 4.617A pdb=" N ASN A 671 " --> pdb=" O ASP A 667 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N LYS A 674 " --> pdb=" O LYS A 670 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLN A 679 " --> pdb=" O THR A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 694 removed outlier: 3.925A pdb=" N LEU A 694 " --> pdb=" O PRO A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 706 removed outlier: 3.670A pdb=" N LYS A 700 " --> pdb=" O SER A 696 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N THR A 701 " --> pdb=" O ASN A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 725 Processing helix chain 'A' and resid 729 through 739 Processing helix chain 'A' and resid 777 through 785 removed outlier: 4.403A pdb=" N LEU A 782 " --> pdb=" O ASP A 778 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER A 785 " --> pdb=" O LEU A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 802 Processing helix chain 'A' and resid 805 through 807 No H-bonds generated for 'chain 'A' and resid 805 through 807' Processing helix chain 'A' and resid 808 through 820 removed outlier: 4.012A pdb=" N PHE A 812 " --> pdb=" O TRP A 808 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ARG A 815 " --> pdb=" O ILE A 811 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LYS A 817 " --> pdb=" O LEU A 813 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N ALA A 818 " --> pdb=" O ASP A 814 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLU A 819 " --> pdb=" O ARG A 815 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 71 removed outlier: 3.843A pdb=" N VAL B 57 " --> pdb=" O SER B 53 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE B 58 " --> pdb=" O GLU B 54 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 110 Processing helix chain 'B' and resid 148 through 171 Processing helix chain 'B' and resid 191 through 202 removed outlier: 3.760A pdb=" N PHE B 195 " --> pdb=" O ALA B 191 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL B 200 " --> pdb=" O LEU B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 218 removed outlier: 4.303A pdb=" N TYR B 217 " --> pdb=" O ARG B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 265 removed outlier: 3.772A pdb=" N GLU B 265 " --> pdb=" O VAL B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 297 Processing helix chain 'B' and resid 302 through 319 removed outlier: 4.049A pdb=" N ILE B 317 " --> pdb=" O LEU B 313 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER B 318 " --> pdb=" O ASN B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 354 removed outlier: 3.614A pdb=" N VAL B 354 " --> pdb=" O ALA B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 371 Processing helix chain 'B' and resid 388 through 395 Processing helix chain 'B' and resid 456 through 469 Processing helix chain 'B' and resid 470 through 472 No H-bonds generated for 'chain 'B' and resid 470 through 472' Processing helix chain 'B' and resid 483 through 491 removed outlier: 4.200A pdb=" N SER B 487 " --> pdb=" O GLY B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 530 Processing helix chain 'B' and resid 628 through 645 removed outlier: 4.127A pdb=" N VAL B 632 " --> pdb=" O ALA B 628 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR B 638 " --> pdb=" O MET B 634 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG B 639 " --> pdb=" O TYR B 635 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ILE B 644 " --> pdb=" O THR B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 661 removed outlier: 3.652A pdb=" N GLN B 661 " --> pdb=" O TRP B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 679 removed outlier: 4.971A pdb=" N LYS B 674 " --> pdb=" O LYS B 670 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N THR B 675 " --> pdb=" O ASN B 671 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 694 Processing helix chain 'B' and resid 699 through 705 Processing helix chain 'B' and resid 718 through 727 removed outlier: 3.514A pdb=" N PHE B 726 " --> pdb=" O TYR B 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 740 Processing helix chain 'B' and resid 776 through 785 Processing helix chain 'B' and resid 787 through 802 removed outlier: 4.020A pdb=" N GLY B 802 " --> pdb=" O ILE B 798 " (cutoff:3.500A) Processing helix chain 'B' and resid 807 through 821 removed outlier: 3.877A pdb=" N ASP B 814 " --> pdb=" O PRO B 810 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL B 816 " --> pdb=" O PHE B 812 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LYS B 817 " --> pdb=" O LEU B 813 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLU B 819 " --> pdb=" O ARG B 815 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 26 Processing helix chain 'D' and resid 27 through 62 removed outlier: 3.838A pdb=" N SER D 62 " --> pdb=" O ILE D 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 61 Processing helix chain 'F' and resid 23 through 62 removed outlier: 4.178A pdb=" N ARG F 36 " --> pdb=" O PHE F 32 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N SER F 62 " --> pdb=" O ILE F 58 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 93 through 94 removed outlier: 3.683A pdb=" N ILE A 248 " --> pdb=" O CYS A 328 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N CYS A 328 " --> pdb=" O ILE A 248 " (cutoff:3.500A) removed outlier: 9.350A pdb=" N GLU A 250 " --> pdb=" O HIS A 326 " (cutoff:3.500A) removed outlier: 11.679A pdb=" N HIS A 326 " --> pdb=" O GLU A 250 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 177 through 178 removed outlier: 3.842A pdb=" N TYR A 38 " --> pdb=" O TYR A 127 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU A 121 " --> pdb=" O ILE A 44 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A 272 " --> pdb=" O ILE A 82 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER A 275 " --> pdb=" O HIS A 327 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N HIS A 327 " --> pdb=" O SER A 275 " (cutoff:3.500A) removed outlier: 11.679A pdb=" N HIS A 326 " --> pdb=" O GLU A 250 " (cutoff:3.500A) removed outlier: 9.350A pdb=" N GLU A 250 " --> pdb=" O HIS A 326 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N CYS A 328 " --> pdb=" O ILE A 248 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE A 248 " --> pdb=" O CYS A 328 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 25 through 27 Processing sheet with id=AA4, first strand: chain 'A' and resid 181 through 184 removed outlier: 3.656A pdb=" N HIS A 187 " --> pdb=" O LYS A 184 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 425 through 427 removed outlier: 3.511A pdb=" N THR A 415 " --> pdb=" O PHE A 427 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 493 through 494 removed outlier: 6.556A pdb=" N ILE A 475 " --> pdb=" O TYR A 615 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N THR A 474 " --> pdb=" O MET A 650 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N VAL A 652 " --> pdb=" O THR A 474 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N VAL A 476 " --> pdb=" O VAL A 652 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N VAL A 684 " --> pdb=" O PHE A 649 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N TYR A 651 " --> pdb=" O VAL A 684 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N ALA A 686 " --> pdb=" O TYR A 651 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N THR A 447 " --> pdb=" O PHE A 685 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N THR A 687 " --> pdb=" O THR A 447 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LEU A 449 " --> pdb=" O THR A 687 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N MET A 448 " --> pdb=" O ILE A 710 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N LEU A 712 " --> pdb=" O MET A 448 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ILE A 450 " --> pdb=" O LEU A 712 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR A 709 " --> pdb=" O LYS A 749 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 22 through 26 removed outlier: 3.674A pdb=" N HIS B 24 " --> pdb=" O SER B 32 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 176 through 178 removed outlier: 3.876A pdb=" N LEU B 121 " --> pdb=" O ILE B 44 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N LEU B 76 " --> pdb=" O VAL B 278 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL B 278 " --> pdb=" O LEU B 76 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N PHE B 270 " --> pdb=" O ARG B 84 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER B 275 " --> pdb=" O HIS B 327 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N HIS B 327 " --> pdb=" O SER B 275 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N CYS B 328 " --> pdb=" O ILE B 248 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY B 244 " --> pdb=" O VAL B 332 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 224 through 225 removed outlier: 3.694A pdb=" N GLY B 244 " --> pdb=" O VAL B 332 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N CYS B 328 " --> pdb=" O ILE B 248 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 181 through 182 Processing sheet with id=AB2, first strand: chain 'B' and resid 415 through 418 removed outlier: 3.520A pdb=" N THR B 415 " --> pdb=" O PHE B 427 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 447 through 450 removed outlier: 6.098A pdb=" N MET B 448 " --> pdb=" O ILE B 710 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N LEU B 712 " --> pdb=" O MET B 448 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ILE B 450 " --> pdb=" O LEU B 712 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 614 through 618 removed outlier: 5.799A pdb=" N ILE B 475 " --> pdb=" O TYR B 615 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N PHE B 617 " --> pdb=" O ILE B 475 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ALA B 477 " --> pdb=" O PHE B 617 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N VAL B 476 " --> pdb=" O VAL B 652 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N PHE B 649 " --> pdb=" O ILE B 682 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL B 684 " --> pdb=" O PHE B 649 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N TYR B 651 " --> pdb=" O VAL B 684 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 666 hydrogen bonds defined for protein. 1932 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: 4.46 Time building geometry restraints manager: 5.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4177 1.34 - 1.46: 2629 1.46 - 1.58: 6161 1.58 - 1.69: 0 1.69 - 1.81: 75 Bond restraints: 13042 Sorted by residual: bond pdb=" CA ILE B 20 " pdb=" CB ILE B 20 " ideal model delta sigma weight residual 1.536 1.515 0.021 1.19e-02 7.06e+03 3.18e+00 bond pdb=" CA SER A 77 " pdb=" CB SER A 77 " ideal model delta sigma weight residual 1.533 1.509 0.023 1.65e-02 3.67e+03 2.01e+00 bond pdb=" N ILE A 82 " pdb=" CA ILE A 82 " ideal model delta sigma weight residual 1.474 1.454 0.020 1.57e-02 4.06e+03 1.61e+00 bond pdb=" N VAL B 684 " pdb=" CA VAL B 684 " ideal model delta sigma weight residual 1.474 1.455 0.020 1.57e-02 4.06e+03 1.55e+00 bond pdb=" N GLU B 502 " pdb=" CA GLU B 502 " ideal model delta sigma weight residual 1.462 1.451 0.011 9.30e-03 1.16e+04 1.44e+00 ... (remaining 13037 not shown) Histogram of bond angle deviations from ideal: 98.89 - 105.95: 286 105.95 - 113.01: 6939 113.01 - 120.07: 4539 120.07 - 127.13: 5792 127.13 - 134.19: 166 Bond angle restraints: 17722 Sorted by residual: angle pdb=" CA GLU B 780 " pdb=" CB GLU B 780 " pdb=" CG GLU B 780 " ideal model delta sigma weight residual 114.10 122.02 -7.92 2.00e+00 2.50e-01 1.57e+01 angle pdb=" C LEU C 13 " pdb=" N PHE C 14 " pdb=" CA PHE C 14 " ideal model delta sigma weight residual 121.54 128.06 -6.52 1.91e+00 2.74e-01 1.17e+01 angle pdb=" C THR B 27 " pdb=" CA THR B 27 " pdb=" CB THR B 27 " ideal model delta sigma weight residual 111.23 106.01 5.22 1.63e+00 3.76e-01 1.03e+01 angle pdb=" C LEU A 609 " pdb=" N SER A 610 " pdb=" CA SER A 610 " ideal model delta sigma weight residual 121.54 127.37 -5.83 1.91e+00 2.74e-01 9.33e+00 angle pdb=" C TYR B 495 " pdb=" N LEU B 496 " pdb=" CA LEU B 496 " ideal model delta sigma weight residual 123.46 119.54 3.92 1.35e+00 5.49e-01 8.41e+00 ... (remaining 17717 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.78: 6984 16.78 - 33.57: 573 33.57 - 50.35: 96 50.35 - 67.14: 12 67.14 - 83.92: 8 Dihedral angle restraints: 7673 sinusoidal: 2798 harmonic: 4875 Sorted by residual: dihedral pdb=" CA PHE B 95 " pdb=" C PHE B 95 " pdb=" N ASP B 96 " pdb=" CA ASP B 96 " ideal model delta harmonic sigma weight residual -180.00 -153.05 -26.95 0 5.00e+00 4.00e-02 2.90e+01 dihedral pdb=" CA GLU A 627 " pdb=" C GLU A 627 " pdb=" N ALA A 628 " pdb=" CA ALA A 628 " ideal model delta harmonic sigma weight residual 180.00 157.31 22.69 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA HIS A 24 " pdb=" C HIS A 24 " pdb=" N HIS A 25 " pdb=" CA HIS A 25 " ideal model delta harmonic sigma weight residual 180.00 159.03 20.97 0 5.00e+00 4.00e-02 1.76e+01 ... (remaining 7670 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1758 0.065 - 0.130: 202 0.130 - 0.196: 7 0.196 - 0.261: 0 0.261 - 0.326: 1 Chirality restraints: 1968 Sorted by residual: chirality pdb=" CB ILE A 416 " pdb=" CA ILE A 416 " pdb=" CG1 ILE A 416 " pdb=" CG2 ILE A 416 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.66e+00 chirality pdb=" CA GLU B 780 " pdb=" N GLU B 780 " pdb=" C GLU B 780 " pdb=" CB GLU B 780 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.51e-01 chirality pdb=" CA PRO B 21 " pdb=" N PRO B 21 " pdb=" C PRO B 21 " pdb=" CB PRO B 21 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.69e-01 ... (remaining 1965 not shown) Planarity restraints: 2296 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 804 " -0.052 5.00e-02 4.00e+02 7.80e-02 9.74e+00 pdb=" N PRO A 805 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO A 805 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 805 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 40 " -0.016 2.00e-02 2.50e+03 1.16e-02 3.37e+00 pdb=" CG TRP E 40 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 TRP E 40 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP E 40 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP E 40 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP E 40 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP E 40 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 40 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 40 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP E 40 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 809 " -0.029 5.00e-02 4.00e+02 4.41e-02 3.11e+00 pdb=" N PRO A 810 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 810 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 810 " -0.025 5.00e-02 4.00e+02 ... (remaining 2293 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 114 2.63 - 3.20: 12191 3.20 - 3.76: 19376 3.76 - 4.33: 25941 4.33 - 4.90: 42709 Nonbonded interactions: 100331 Sorted by model distance: nonbonded pdb=" OH TYR A 38 " pdb=" OE1 GLN A 153 " model vdw 2.059 2.440 nonbonded pdb=" OG1 THR B 787 " pdb=" OD1 ASP B 789 " model vdw 2.179 2.440 nonbonded pdb=" OG1 THR C 80 " pdb=" OE2 GLU A 366 " model vdw 2.199 2.440 nonbonded pdb=" O ASP A 342 " pdb=" ND1 HIS A 346 " model vdw 2.212 2.520 nonbonded pdb=" OH TYR B 495 " pdb=" OD1 ASP B 618 " model vdw 2.216 2.440 ... (remaining 100326 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 15 through 130 or (resid 147 through 150 and (name N or na \ me CA or name C or name O or name CB )) or resid 151 through 176 or (resid 177 a \ nd (name N or name CA or name C or name O or name CB )) or resid 178 through 237 \ or resid 241 through 431 or (resid 432 through 433 and (name N or name CA or na \ me C or name O or name CB )) or resid 441 through 498 or (resid 499 and (name N \ or name CA or name C or name O or name CB )) or resid 500 through 503 or resid 5 \ 15 through 531 or resid 607 through 622 or (resid 623 through 629 and (name N or \ name CA or name C or name O or name CB )) or resid 630 through 633 or (resid 63 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 635 through \ 638 or (resid 639 and (name N or name CA or name C or name O or name CB )) or re \ sid 640 or (resid 641 through 645 and (name N or name CA or name C or name O or \ name CB )) or (resid 646 through 648 and (name N or name CA or name C or name O \ or name CB )) or resid 649 through 662 or (resid 663 and (name N or name CA or n \ ame C or name O or name CB )) or resid 664 through 726 or (resid 727 and (name N \ or name CA or name C or name O or name CB )) or resid 728 or (resid 729 through \ 730 and (name N or name CA or name C or name O or name CB )) or resid 731 throu \ gh 740 or (resid 741 and (name N or name CA or name C or name O or name CB )) or \ resid 742 through 764 or (resid 765 through 776 and (name N or name CA or name \ C or name O or name CB )) or resid 777 through 821)) selection = (chain 'B' and (resid 15 through 53 or (resid 54 through 55 and (name N or name \ CA or name C or name O or name CB )) or resid 56 through 254 or (resid 255 throu \ gh 256 and (name N or name CA or name C or name O or name CB )) or resid 257 thr \ ough 296 or (resid 297 through 304 and (name N or name CA or name C or name O or \ name CB )) or resid 305 through 441 or (resid 442 and (name N or name CA or nam \ e C or name O or name CB )) or resid 443 through 493 or (resid 494 and (name N o \ r name CA or name C or name O or name CB )) or resid 495 through 606 or (resid 6 \ 07 through 608 and (name N or name CA or name C or name O or name CB )) or resid \ 609 through 657 or (resid 658 and (name N or name CA or name C or name O or nam \ e CB )) or resid 659 through 660 or (resid 661 through 663 and (name N or name C \ A or name C or name O or name CB )) or resid 664 through 690 or (resid 691 throu \ gh 697 and (name N or name CA or name C or name O or name CB )) or resid 698 thr \ ough 699 or (resid 700 and (name N or name CA or name C or name O or name CB )) \ or resid 701 through 703 or (resid 704 through 705 and (name N or name CA or nam \ e C or name O or name CB )) or resid 706 through 720 or (resid 721 and (name N o \ r name CA or name C or name O or name CB )) or resid 722 through 731 or (resid 7 \ 32 and (name N or name CA or name C or name O or name CB )) or resid 733 through \ 762 or (resid 763 and (name N or name CA or name C or name O or name CB )) or r \ esid 764 through 799 or (resid 800 and (name N or name CA or name C or name O or \ name CB )) or resid 801 through 818 or (resid 819 through 821 and (name N or na \ me CA or name C or name O or name CB )))) } ncs_group { reference = (chain 'D' and (resid 13 through 24 or (resid 25 and (name N or name CA or name \ C or name O or name CB )) or resid 26 through 36 or (resid 37 and (name N or nam \ e CA or name C or name O or name CB )) or resid 38 through 41 or (resid 42 throu \ gh 43 and (name N or name CA or name C or name O or name CB )) or resid 44 throu \ gh 45 or (resid 46 and (name N or name CA or name C or name O or name CB )) or r \ esid 47 through 62)) selection = (chain 'E' and ((resid 13 through 15 and (name N or name CA or name C or name O \ or name CB )) or resid 16 through 21 or (resid 22 and (name N or name CA or name \ C or name O or name CB )) or resid 23 through 54 or (resid 55 through 56 and (n \ ame N or name CA or name C or name O or name CB )) or resid 57 through 62)) } 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: 0.010 Normalize map: mean=0, sd=1: 0.080 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: 1.730 Check model and map are aligned: 0.190 Set scattering table: 0.100 Process input model: 35.020 Find NCS groups from input model: 1.040 Set up NCS constraints: 0.060 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 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 : 0.004 0.040 13042 Z= 0.286 Angle : 0.680 7.924 17722 Z= 0.397 Chirality : 0.042 0.326 1968 Planarity : 0.004 0.078 2296 Dihedral : 12.595 83.919 4521 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer Outliers : 0.00 % 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: -0.19 (0.20), residues: 1647 helix: 1.02 (0.19), residues: 735 sheet: -0.24 (0.33), residues: 268 loop : -1.39 (0.23), residues: 644 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 1.545 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.2306 time to fit residues: 50.2150 Evaluate side-chains 116 residues out of total 1447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 1.538 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 141 optimal weight: 50.0000 chunk 126 optimal weight: 20.0000 chunk 70 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 85 optimal weight: 10.0000 chunk 67 optimal weight: 0.9980 chunk 130 optimal weight: 40.0000 chunk 50 optimal weight: 20.0000 chunk 79 optimal weight: 10.0000 chunk 97 optimal weight: 6.9990 chunk 151 optimal weight: 40.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 86 ASN ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 790 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.0913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 13042 Z= 0.239 Angle : 0.598 8.507 17722 Z= 0.318 Chirality : 0.041 0.248 1968 Planarity : 0.005 0.077 2296 Dihedral : 4.877 21.473 1806 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer Outliers : 1.39 % 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: -0.00 (0.20), residues: 1647 helix: 1.24 (0.19), residues: 743 sheet: -0.23 (0.33), residues: 264 loop : -1.37 (0.23), residues: 640 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 132 time to evaluate : 1.716 Fit side-chains outliers start: 17 outliers final: 13 residues processed: 140 average time/residue: 0.2202 time to fit residues: 47.8715 Evaluate side-chains 130 residues out of total 1447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 117 time to evaluate : 1.553 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1223 time to fit residues: 5.0450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 84 optimal weight: 8.9990 chunk 47 optimal weight: 0.5980 chunk 126 optimal weight: 8.9990 chunk 103 optimal weight: 6.9990 chunk 41 optimal weight: 10.0000 chunk 151 optimal weight: 0.0470 chunk 164 optimal weight: 8.9990 chunk 135 optimal weight: 40.0000 chunk 150 optimal weight: 5.9990 chunk 51 optimal weight: 0.0000 chunk 121 optimal weight: 9.9990 overall best weight: 2.7286 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 HIS B 97 ASN ** B 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 13042 Z= 0.160 Angle : 0.546 9.210 17722 Z= 0.285 Chirality : 0.039 0.173 1968 Planarity : 0.004 0.078 2296 Dihedral : 4.566 18.860 1806 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer Outliers : 0.33 % 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: 0.22 (0.21), residues: 1647 helix: 1.50 (0.19), residues: 755 sheet: -0.25 (0.33), residues: 263 loop : -1.37 (0.23), residues: 629 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 128 time to evaluate : 1.549 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 131 average time/residue: 0.2169 time to fit residues: 44.3245 Evaluate side-chains 122 residues out of total 1447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 120 time to evaluate : 1.425 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1185 time to fit residues: 2.3192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 150 optimal weight: 30.0000 chunk 114 optimal weight: 10.0000 chunk 78 optimal weight: 20.0000 chunk 16 optimal weight: 10.0000 chunk 72 optimal weight: 20.0000 chunk 102 optimal weight: 1.9990 chunk 152 optimal weight: 7.9990 chunk 161 optimal weight: 20.0000 chunk 79 optimal weight: 3.9990 chunk 144 optimal weight: 30.0000 chunk 43 optimal weight: 5.9990 overall best weight: 5.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 ASN B 24 HIS B 97 ASN ** B 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 13042 Z= 0.236 Angle : 0.559 8.901 17722 Z= 0.293 Chirality : 0.040 0.155 1968 Planarity : 0.005 0.075 2296 Dihedral : 4.585 18.054 1806 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer Outliers : 1.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.21), residues: 1647 helix: 1.52 (0.19), residues: 755 sheet: -0.38 (0.33), residues: 263 loop : -1.40 (0.23), residues: 629 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 119 time to evaluate : 1.415 Fit side-chains outliers start: 19 outliers final: 14 residues processed: 131 average time/residue: 0.2108 time to fit residues: 43.9918 Evaluate side-chains 125 residues out of total 1447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 111 time to evaluate : 1.539 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1411 time to fit residues: 6.2424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 134 optimal weight: 20.0000 chunk 91 optimal weight: 5.9990 chunk 2 optimal weight: 10.0000 chunk 120 optimal weight: 4.9990 chunk 66 optimal weight: 9.9990 chunk 137 optimal weight: 20.0000 chunk 111 optimal weight: 8.9990 chunk 0 optimal weight: 50.0000 chunk 82 optimal weight: 8.9990 chunk 144 optimal weight: 30.0000 chunk 40 optimal weight: 8.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 ASN ** B 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 13042 Z= 0.281 Angle : 0.585 9.375 17722 Z= 0.308 Chirality : 0.041 0.180 1968 Planarity : 0.005 0.075 2296 Dihedral : 4.715 19.761 1806 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer Outliers : 1.23 % 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: 0.01 (0.21), residues: 1647 helix: 1.39 (0.19), residues: 754 sheet: -0.51 (0.33), residues: 263 loop : -1.48 (0.23), residues: 630 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 117 time to evaluate : 1.376 Fit side-chains outliers start: 15 outliers final: 10 residues processed: 128 average time/residue: 0.1990 time to fit residues: 41.2165 Evaluate side-chains 123 residues out of total 1447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 113 time to evaluate : 1.496 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1176 time to fit residues: 4.2166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 54 optimal weight: 8.9990 chunk 145 optimal weight: 20.0000 chunk 31 optimal weight: 20.0000 chunk 94 optimal weight: 6.9990 chunk 39 optimal weight: 20.0000 chunk 161 optimal weight: 30.0000 chunk 134 optimal weight: 30.0000 chunk 74 optimal weight: 8.9990 chunk 13 optimal weight: 5.9990 chunk 53 optimal weight: 40.0000 chunk 84 optimal weight: 0.8980 overall best weight: 6.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 ASN ** B 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 13042 Z= 0.246 Angle : 0.570 9.639 17722 Z= 0.299 Chirality : 0.040 0.173 1968 Planarity : 0.005 0.076 2296 Dihedral : 4.648 19.706 1806 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer Outliers : 1.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.21), residues: 1647 helix: 1.42 (0.19), residues: 756 sheet: -0.44 (0.33), residues: 253 loop : -1.53 (0.23), residues: 638 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 120 time to evaluate : 1.545 Fit side-chains outliers start: 13 outliers final: 8 residues processed: 127 average time/residue: 0.2164 time to fit residues: 43.3011 Evaluate side-chains 120 residues out of total 1447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 112 time to evaluate : 1.802 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1245 time to fit residues: 3.9165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 155 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 chunk 92 optimal weight: 8.9990 chunk 117 optimal weight: 7.9990 chunk 91 optimal weight: 5.9990 chunk 136 optimal weight: 20.0000 chunk 90 optimal weight: 20.0000 chunk 160 optimal weight: 10.0000 chunk 100 optimal weight: 20.0000 chunk 98 optimal weight: 9.9990 chunk 74 optimal weight: 6.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 469 GLN A 613 GLN B 97 ASN ** B 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 688 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.036 13042 Z= 0.296 Angle : 0.601 9.451 17722 Z= 0.317 Chirality : 0.041 0.178 1968 Planarity : 0.005 0.075 2296 Dihedral : 4.778 20.935 1806 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer Outliers : 1.14 % 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: -0.15 (0.21), residues: 1647 helix: 1.33 (0.19), residues: 750 sheet: -0.54 (0.34), residues: 253 loop : -1.66 (0.22), residues: 644 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 119 time to evaluate : 1.542 Fit side-chains outliers start: 14 outliers final: 8 residues processed: 131 average time/residue: 0.2135 time to fit residues: 44.2454 Evaluate side-chains 124 residues out of total 1447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 116 time to evaluate : 1.467 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1199 time to fit residues: 3.8233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 99 optimal weight: 9.9990 chunk 64 optimal weight: 30.0000 chunk 96 optimal weight: 20.0000 chunk 48 optimal weight: 5.9990 chunk 31 optimal weight: 20.0000 chunk 102 optimal weight: 8.9990 chunk 109 optimal weight: 7.9990 chunk 79 optimal weight: 20.0000 chunk 15 optimal weight: 6.9990 chunk 126 optimal weight: 10.0000 chunk 146 optimal weight: 20.0000 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 13042 Z= 0.292 Angle : 0.614 10.985 17722 Z= 0.320 Chirality : 0.041 0.177 1968 Planarity : 0.005 0.076 2296 Dihedral : 4.815 21.670 1806 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer Outliers : 1.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.21), residues: 1647 helix: 1.31 (0.19), residues: 751 sheet: -0.67 (0.33), residues: 255 loop : -1.69 (0.23), residues: 641 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 118 time to evaluate : 1.671 Fit side-chains outliers start: 13 outliers final: 8 residues processed: 130 average time/residue: 0.2307 time to fit residues: 47.6165 Evaluate side-chains 126 residues out of total 1447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 118 time to evaluate : 1.412 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1189 time to fit residues: 3.6995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 154 optimal weight: 30.0000 chunk 140 optimal weight: 4.9990 chunk 149 optimal weight: 5.9990 chunk 90 optimal weight: 20.0000 chunk 65 optimal weight: 0.9980 chunk 117 optimal weight: 10.0000 chunk 46 optimal weight: 7.9990 chunk 135 optimal weight: 0.0670 chunk 141 optimal weight: 40.0000 chunk 98 optimal weight: 20.0000 chunk 158 optimal weight: 10.0000 overall best weight: 4.0124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 ASN B 705 GLN B 790 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 13042 Z= 0.186 Angle : 0.571 10.116 17722 Z= 0.294 Chirality : 0.040 0.185 1968 Planarity : 0.005 0.078 2296 Dihedral : 4.559 19.316 1806 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer Outliers : 0.57 % 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: -0.01 (0.21), residues: 1647 helix: 1.50 (0.19), residues: 753 sheet: -0.60 (0.33), residues: 255 loop : -1.62 (0.23), residues: 639 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 119 time to evaluate : 1.498 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 123 average time/residue: 0.2345 time to fit residues: 45.6206 Evaluate side-chains 119 residues out of total 1447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 115 time to evaluate : 1.568 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1262 time to fit residues: 3.0848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 96 optimal weight: 20.0000 chunk 75 optimal weight: 10.0000 chunk 110 optimal weight: 9.9990 chunk 166 optimal weight: 20.0000 chunk 153 optimal weight: 20.0000 chunk 132 optimal weight: 20.0000 chunk 13 optimal weight: 20.0000 chunk 102 optimal weight: 7.9990 chunk 81 optimal weight: 0.9980 chunk 105 optimal weight: 20.0000 chunk 141 optimal weight: 1.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 13042 Z= 0.242 Angle : 0.591 10.413 17722 Z= 0.305 Chirality : 0.041 0.194 1968 Planarity : 0.005 0.077 2296 Dihedral : 4.594 19.685 1806 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer Outliers : 0.41 % 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: -0.06 (0.21), residues: 1647 helix: 1.47 (0.19), residues: 753 sheet: -0.60 (0.33), residues: 255 loop : -1.66 (0.23), residues: 639 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 117 time to evaluate : 1.637 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 121 average time/residue: 0.2185 time to fit residues: 41.9734 Evaluate side-chains 118 residues out of total 1447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 115 time to evaluate : 1.525 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1359 time to fit residues: 2.6593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 40 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 19 optimal weight: 8.9990 chunk 36 optimal weight: 6.9990 chunk 132 optimal weight: 20.0000 chunk 55 optimal weight: 6.9990 chunk 136 optimal weight: 9.9990 chunk 16 optimal weight: 9.9990 chunk 24 optimal weight: 6.9990 chunk 116 optimal weight: 6.9990 chunk 7 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.096155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.086144 restraints weight = 42329.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.088024 restraints weight = 21352.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.089246 restraints weight = 13155.137| |-----------------------------------------------------------------------------| r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 13042 Z= 0.209 Angle : 0.575 10.262 17722 Z= 0.296 Chirality : 0.040 0.184 1968 Planarity : 0.005 0.077 2296 Dihedral : 4.524 19.212 1806 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer Outliers : 0.49 % 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: 0.01 (0.21), residues: 1647 helix: 1.53 (0.19), residues: 754 sheet: -0.55 (0.34), residues: 253 loop : -1.65 (0.23), residues: 640 =============================================================================== Job complete usr+sys time: 1878.88 seconds wall clock time: 35 minutes 37.67 seconds (2137.67 seconds total)