Starting phenix.real_space_refine (version: 1.21rc1) on Mon Apr 24 06:52:20 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h8c_34542/04_2023/8h8c_34542.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h8c_34542/04_2023/8h8c_34542.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h8c_34542/04_2023/8h8c_34542.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h8c_34542/04_2023/8h8c_34542.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h8c_34542/04_2023/8h8c_34542.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h8c_34542/04_2023/8h8c_34542.pdb" } resolution = 3.36 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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 24 5.16 5 C 10662 2.51 5 N 2938 2.21 5 O 3316 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 161": "OE1" <-> "OE2" Residue "B GLU 162": "OE1" <-> "OE2" Residue "B GLU 170": "OE1" <-> "OE2" Residue "B ARG 188": "NH1" <-> "NH2" Residue "B PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 209": "OD1" <-> "OD2" Residue "B ARG 255": "NH1" <-> "NH2" Residue "B ARG 280": "NH1" <-> "NH2" Residue "B ARG 293": "NH1" <-> "NH2" Residue "B GLU 299": "OE1" <-> "OE2" Residue "B GLU 327": "OE1" <-> "OE2" Residue "B GLU 355": "OE1" <-> "OE2" Residue "B ARG 367": "NH1" <-> "NH2" Residue "B GLU 376": "OE1" <-> "OE2" Residue "B ARG 399": "NH1" <-> "NH2" Residue "B GLU 403": "OE1" <-> "OE2" Residue "B GLU 423": "OE1" <-> "OE2" Residue "B ARG 447": "NH1" <-> "NH2" Residue "B GLU 525": "OE1" <-> "OE2" Residue "B ARG 535": "NH1" <-> "NH2" Residue "B GLU 536": "OE1" <-> "OE2" Residue "B ARG 552": "NH1" <-> "NH2" Residue "B ARG 564": "NH1" <-> "NH2" Residue "B ARG 594": "NH1" <-> "NH2" Residue "B GLU 611": "OE1" <-> "OE2" Residue "B GLU 736": "OE1" <-> "OE2" Residue "B ARG 746": "NH1" <-> "NH2" Residue "B ARG 770": "NH1" <-> "NH2" Residue "B GLU 776": "OE1" <-> "OE2" Residue "B GLU 779": "OE1" <-> "OE2" Residue "B ARG 783": "NH1" <-> "NH2" Residue "B ARG 787": "NH1" <-> "NH2" Residue "B GLU 837": "OE1" <-> "OE2" Residue "B ARG 840": "NH1" <-> "NH2" Residue "B GLU 841": "OE1" <-> "OE2" Residue "B ARG 859": "NH1" <-> "NH2" Residue "B GLU 905": "OE1" <-> "OE2" Residue "B ARG 931": "NH1" <-> "NH2" Residue "B ARG 943": "NH1" <-> "NH2" Residue "B ARG 952": "NH1" <-> "NH2" Residue "B GLU 962": "OE1" <-> "OE2" Residue "B GLU 973": "OE1" <-> "OE2" Residue "B ARG 980": "NH1" <-> "NH2" Residue "B ARG 1009": "NH1" <-> "NH2" Residue "B ARG 1042": "NH1" <-> "NH2" Residue "B GLU 1067": "OE1" <-> "OE2" Residue "B ARG 1070": "NH1" <-> "NH2" Residue "B ARG 1074": "NH1" <-> "NH2" Residue "B GLU 1083": "OE1" <-> "OE2" Residue "B ARG 1100": "NH1" <-> "NH2" Residue "C GLU 1146": "OE1" <-> "OE2" Residue "C GLU 1156": "OE1" <-> "OE2" Residue "C GLU 1163": "OE1" <-> "OE2" Residue "A GLU 149": "OE1" <-> "OE2" Residue "A GLU 162": "OE1" <-> "OE2" Residue "A GLU 170": "OE1" <-> "OE2" Residue "A ARG 188": "NH1" <-> "NH2" Residue "A GLU 206": "OE1" <-> "OE2" Residue "A ASP 209": "OD1" <-> "OD2" Residue "A GLU 210": "OE1" <-> "OE2" Residue "A ARG 255": "NH1" <-> "NH2" Residue "A ARG 280": "NH1" <-> "NH2" Residue "A ARG 293": "NH1" <-> "NH2" Residue "A GLU 320": "OE1" <-> "OE2" Residue "A GLU 352": "OE1" <-> "OE2" Residue "A GLU 355": "OE1" <-> "OE2" Residue "A ARG 367": "NH1" <-> "NH2" Residue "A GLU 380": "OE1" <-> "OE2" Residue "A ARG 399": "NH1" <-> "NH2" Residue "A GLU 403": "OE1" <-> "OE2" Residue "A GLU 423": "OE1" <-> "OE2" Residue "A ARG 447": "NH1" <-> "NH2" Residue "A GLU 449": "OE1" <-> "OE2" Residue "A ARG 535": "NH1" <-> "NH2" Residue "A GLU 536": "OE1" <-> "OE2" Residue "A GLU 538": "OE1" <-> "OE2" Residue "A ARG 552": "NH1" <-> "NH2" Residue "A ARG 564": "NH1" <-> "NH2" Residue "A ARG 594": "NH1" <-> "NH2" Residue "A GLU 603": "OE1" <-> "OE2" Residue "A GLU 627": "OE1" <-> "OE2" Residue "A GLU 673": "OE1" <-> "OE2" Residue "A TYR 715": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 746": "NH1" <-> "NH2" Residue "A ARG 770": "NH1" <-> "NH2" Residue "A GLU 776": "OE1" <-> "OE2" Residue "A GLU 779": "OE1" <-> "OE2" Residue "A GLU 780": "OE1" <-> "OE2" Residue "A ARG 783": "NH1" <-> "NH2" Residue "A ARG 787": "NH1" <-> "NH2" Residue "A GLU 835": "OE1" <-> "OE2" Residue "A GLU 837": "OE1" <-> "OE2" Residue "A ARG 840": "NH1" <-> "NH2" Residue "A GLU 841": "OE1" <-> "OE2" Residue "A ARG 859": "NH1" <-> "NH2" Residue "A GLU 860": "OE1" <-> "OE2" Residue "A GLU 897": "OE1" <-> "OE2" Residue "A ARG 931": "NH1" <-> "NH2" Residue "A ARG 943": "NH1" <-> "NH2" Residue "A ARG 952": "NH1" <-> "NH2" Residue "A ARG 980": "NH1" <-> "NH2" Residue "A GLU 991": "OE1" <-> "OE2" Residue "A ARG 1009": "NH1" <-> "NH2" Residue "A ARG 1042": "NH1" <-> "NH2" Residue "A GLU 1068": "OE1" <-> "OE2" Residue "A ARG 1070": "NH1" <-> "NH2" Residue "A ARG 1074": "NH1" <-> "NH2" Residue "A ARG 1100": "NH1" <-> "NH2" Residue "D GLU 1135": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 16940 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 7860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 964, 7860 Classifications: {'peptide': 964} Link IDs: {'PTRANS': 22, 'TRANS': 941} Chain breaks: 1 Chain: "C" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 610 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain breaks: 1 Chain: "A" Number of atoms: 7860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 964, 7860 Classifications: {'peptide': 964} Link IDs: {'PTRANS': 22, 'TRANS': 941} Chain breaks: 1 Chain: "D" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 610 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain breaks: 1 Time building chain proxies: 8.74, per 1000 atoms: 0.52 Number of scatterers: 16940 At special positions: 0 Unit cell: (93.09, 118.32, 140.07, 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 24 16.00 O 3316 8.00 N 2938 7.00 C 10662 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.12 Conformation dependent library (CDL) restraints added in 2.4 seconds 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3812 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 36 sheets defined 2.0% alpha, 26.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'C' and resid 1139 through 1148 removed outlier: 3.751A pdb=" N ALA C1145 " --> pdb=" O GLN C1141 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLU C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN C1148 " --> pdb=" O LEU C1144 " (cutoff:3.500A) Processing helix chain 'C' and resid 1154 through 1162 removed outlier: 4.596A pdb=" N GLN C1160 " --> pdb=" O GLU C1156 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE C1161 " --> pdb=" O VAL C1157 " (cutoff:3.500A) Processing helix chain 'C' and resid 1163 through 1166 removed outlier: 4.103A pdb=" N LYS C1166 " --> pdb=" O GLU C1163 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1163 through 1166' Processing helix chain 'D' and resid 1139 through 1148 removed outlier: 3.514A pdb=" N ALA D1145 " --> pdb=" O GLN D1141 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU D1146 " --> pdb=" O GLN D1142 " (cutoff:3.500A) Processing helix chain 'D' and resid 1154 through 1162 removed outlier: 4.333A pdb=" N GLN D1160 " --> pdb=" O GLU D1156 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE D1161 " --> pdb=" O VAL D1157 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU D1162 " --> pdb=" O CYS D1158 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 165 through 170 removed outlier: 7.164A pdb=" N TRP B 177 " --> pdb=" O ASP B 168 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 268 through 270 removed outlier: 3.755A pdb=" N LEU B 275 " --> pdb=" O VAL B 270 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 288 through 291 removed outlier: 6.590A pdb=" N GLN B 288 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N VAL B 300 " --> pdb=" O GLN B 288 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ARG B 290 " --> pdb=" O ILE B 298 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N ILE B 298 " --> pdb=" O CYS B 310 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU B 320 " --> pdb=" O GLN B 311 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU B 321 " --> pdb=" O THR B 331 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR B 331 " --> pdb=" O LEU B 321 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 334 through 335 removed outlier: 6.657A pdb=" N ILE B 334 " --> pdb=" O VAL B 342 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 354 through 356 removed outlier: 7.022A pdb=" N GLU B 355 " --> pdb=" O ALA B 363 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N ALA B 363 " --> pdb=" O PHE B 375 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE B 390 " --> pdb=" O TYR B 374 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU B 376 " --> pdb=" O ARG B 388 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N ARG B 388 " --> pdb=" O GLU B 376 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 399 through 402 removed outlier: 3.601A pdb=" N GLU B 429 " --> pdb=" O ILE B 420 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 439 through 442 removed outlier: 3.556A pdb=" N GLN B 439 " --> pdb=" O VAL B 452 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N GLU B 449 " --> pdb=" O TYR B 461 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N ASN B 464 " --> pdb=" O LEU B 469 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LEU B 469 " --> pdb=" O ASN B 464 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 514 through 515 removed outlier: 5.687A pdb=" N VAL B 533 " --> pdb=" O TRP B 545 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N LYS B 541 " --> pdb=" O SER B 537 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ARG B 544 " --> pdb=" O HIS B 556 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N HIS B 556 " --> pdb=" O ARG B 544 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N TRP B 546 " --> pdb=" O VAL B 554 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N VAL B 554 " --> pdb=" O TYR B 565 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ARG B 564 " --> pdb=" O ILE B 576 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ILE B 576 " --> pdb=" O ARG B 564 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N SER B 566 " --> pdb=" O ASN B 574 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 584 through 587 removed outlier: 4.066A pdb=" N ILE B 597 " --> pdb=" O GLU B 610 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N TYR B 599 " --> pdb=" O TYR B 608 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N TYR B 608 " --> pdb=" O TYR B 599 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLN B 622 " --> pdb=" O ALA B 613 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N ALA B 621 " --> pdb=" O TYR B 632 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.905A pdb=" N GLU B 654 " --> pdb=" O THR B 662 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 673 through 676 removed outlier: 6.627A pdb=" N GLU B 673 " --> pdb=" O THR B 685 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N THR B 685 " --> pdb=" O GLU B 673 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N TRP B 675 " --> pdb=" O SER B 683 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 696 through 697 removed outlier: 7.295A pdb=" N LYS B 696 " --> pdb=" O ILE B 704 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 715 through 717 removed outlier: 7.422A pdb=" N SER B 716 " --> pdb=" O GLN B 724 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN B 724 " --> pdb=" O SER B 716 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N GLN B 724 " --> pdb=" O PHE B 739 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE B 726 " --> pdb=" O ASN B 737 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N HIS B 738 " --> pdb=" O SER B 751 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER B 751 " --> pdb=" O HIS B 738 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 778 through 781 removed outlier: 3.806A pdb=" N GLU B 780 " --> pdb=" O SER B 789 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N SER B 789 " --> pdb=" O GLU B 780 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N VAL B 788 " --> pdb=" O PHE B 800 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N PHE B 800 " --> pdb=" O VAL B 788 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLN B 790 " --> pdb=" O PHE B 798 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ASP B 803 " --> pdb=" O LEU B 808 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LEU B 808 " --> pdb=" O ASP B 803 " (cutoff:3.500A) removed outlier: 11.290A pdb=" N ARG B 807 " --> pdb=" O TYR B 825 " (cutoff:3.500A) removed outlier: 9.228A pdb=" N TYR B 825 " --> pdb=" O ARG B 807 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N SER B 809 " --> pdb=" O PHE B 823 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N GLU B 822 " --> pdb=" O THR B 834 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N THR B 834 " --> pdb=" O GLU B 822 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N GLN B 824 " --> pdb=" O SER B 832 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N SER B 832 " --> pdb=" O LYS B 843 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU B 853 " --> pdb=" O LEU B 844 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N VAL B 852 " --> pdb=" O TYR B 863 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N SER B 872 " --> pdb=" O TYR B 884 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL B 895 " --> pdb=" O SER B 902 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 926 through 927 removed outlier: 3.532A pdb=" N LYS B 942 " --> pdb=" O LYS B 933 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N VAL B 941 " --> pdb=" O ARG B 952 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG B 943 " --> pdb=" O GLN B 950 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN B 950 " --> pdb=" O ARG B 943 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU B 962 " --> pdb=" O VAL B 953 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 971 through 974 removed outlier: 6.045A pdb=" N THR B 981 " --> pdb=" O PHE B 992 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE B 992 " --> pdb=" O THR B 981 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS B 983 " --> pdb=" O THR B 990 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N THR B 990 " --> pdb=" O LYS B 983 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N GLU B 995 " --> pdb=" O LEU B 999 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU B 999 " --> pdb=" O GLU B 995 " (cutoff:3.500A) removed outlier: 11.029A pdb=" N ARG B 998 " --> pdb=" O TYR B1013 " (cutoff:3.500A) removed outlier: 9.707A pdb=" N TYR B1013 " --> pdb=" O ARG B 998 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N LEU B1000 " --> pdb=" O TYR B1011 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU B1021 " --> pdb=" O TYR B1032 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG B1042 " --> pdb=" O GLU B1033 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ASP B1045 " --> pdb=" O ILE B1050 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ILE B1050 " --> pdb=" O ASP B1045 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 1087 through 1088 Processing sheet with id=AB9, first strand: chain 'B' and resid 1125 through 1126 removed outlier: 3.598A pdb=" N ILE B1126 " --> pdb=" O ASN C1188 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASN C1188 " --> pdb=" O ILE B1126 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'A' and resid 166 through 170 removed outlier: 7.077A pdb=" N TRP A 177 " --> pdb=" O ASP A 168 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 268 through 270 removed outlier: 3.853A pdb=" N LEU A 275 " --> pdb=" O VAL A 270 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 288 through 291 removed outlier: 7.783A pdb=" N ILE A 298 " --> pdb=" O GLU A 309 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N GLU A 309 " --> pdb=" O ILE A 298 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL A 300 " --> pdb=" O VAL A 307 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 354 through 356 removed outlier: 7.188A pdb=" N GLU A 355 " --> pdb=" O ALA A 363 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 376 through 377 removed outlier: 3.806A pdb=" N GLU A 376 " --> pdb=" O ILE A 387 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 399 through 403 removed outlier: 3.539A pdb=" N THR A 418 " --> pdb=" O SER A 431 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N LEU A 428 " --> pdb=" O TRP A 440 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS A 450 " --> pdb=" O HIS A 441 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N GLU A 449 " --> pdb=" O TYR A 461 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ASN A 464 " --> pdb=" O LEU A 469 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LEU A 469 " --> pdb=" O ASN A 464 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 492 through 494 Processing sheet with id=AC8, first strand: chain 'A' and resid 514 through 515 removed outlier: 5.486A pdb=" N VAL A 533 " --> pdb=" O TRP A 545 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N LYS A 541 " --> pdb=" O SER A 537 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N VAL A 554 " --> pdb=" O TYR A 565 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N HIS A 556 " --> pdb=" O LEU A 563 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY A 575 " --> pdb=" O SER A 566 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N ASN A 574 " --> pdb=" O ILE A 586 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE A 586 " --> pdb=" O ASN A 574 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N TYR A 599 " --> pdb=" O TYR A 608 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N TYR A 608 " --> pdb=" O TYR A 599 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU A 611 " --> pdb=" O GLN A 624 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN A 622 " --> pdb=" O ALA A 613 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N ALA A 621 " --> pdb=" O TYR A 632 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA A 642 " --> pdb=" O GLN A 633 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.663A pdb=" N GLU A 654 " --> pdb=" O THR A 662 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 673 through 676 removed outlier: 4.657A pdb=" N GLY A 684 " --> pdb=" O TRP A 675 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 696 through 697 removed outlier: 3.904A pdb=" N ARG A 705 " --> pdb=" O LYS A 696 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 725 through 726 removed outlier: 3.612A pdb=" N ASN A 737 " --> pdb=" O ILE A 726 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 749 through 751 Processing sheet with id=AD5, first strand: chain 'A' and resid 780 through 781 removed outlier: 3.797A pdb=" N GLU A 780 " --> pdb=" O VAL A 788 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 791 through 792 removed outlier: 3.543A pdb=" N THR A 796 " --> pdb=" O LEU A 792 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N SER A 809 " --> pdb=" O PHE A 823 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE A 823 " --> pdb=" O SER A 809 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N SER A 832 " --> pdb=" O LYS A 843 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU A 844 " --> pdb=" O GLU A 853 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLU A 853 " --> pdb=" O LEU A 844 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N VAL A 852 " --> pdb=" O TYR A 863 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N SER A 872 " --> pdb=" O TYR A 884 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 926 through 927 removed outlier: 6.640A pdb=" N ARG A 931 " --> pdb=" O ARG A 943 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ARG A 943 " --> pdb=" O ARG A 931 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LYS A 933 " --> pdb=" O VAL A 941 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N VAL A 941 " --> pdb=" O ARG A 952 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLU A 962 " --> pdb=" O VAL A 953 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 971 through 973 removed outlier: 3.539A pdb=" N LYS A 982 " --> pdb=" O GLU A 973 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N LEU A1000 " --> pdb=" O TYR A1011 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU A1021 " --> pdb=" O TYR A1032 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG A1042 " --> pdb=" O GLU A1033 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N VAL A1066 " --> pdb=" O SER A1053 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 1125 through 1126 removed outlier: 3.674A pdb=" N ILE A1126 " --> pdb=" O ASN D1188 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASN D1188 " --> pdb=" O ILE A1126 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 332 hydrogen bonds defined for protein. 897 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: 7.40 Time building geometry restraints manager: 6.70 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: 5682 1.34 - 1.46: 3863 1.46 - 1.58: 7765 1.58 - 1.69: 0 1.69 - 1.81: 32 Bond restraints: 17342 Sorted by residual: bond pdb=" CA THR B 208 " pdb=" CB THR B 208 " ideal model delta sigma weight residual 1.530 1.542 -0.011 9.80e-03 1.04e+04 1.36e+00 bond pdb=" CA PHE B 202 " pdb=" C PHE B 202 " ideal model delta sigma weight residual 1.531 1.516 0.015 1.46e-02 4.69e+03 1.12e+00 bond pdb=" C SER A 216 " pdb=" O SER A 216 " ideal model delta sigma weight residual 1.236 1.225 0.012 1.15e-02 7.56e+03 1.02e+00 bond pdb=" C ASP A 153 " pdb=" N PRO A 154 " ideal model delta sigma weight residual 1.340 1.368 -0.028 2.76e-02 1.31e+03 1.01e+00 bond pdb=" C ALA A 577 " pdb=" N TYR A 578 " ideal model delta sigma weight residual 1.333 1.360 -0.027 2.74e-02 1.33e+03 9.96e-01 ... (remaining 17337 not shown) Histogram of bond angle deviations from ideal: 100.84 - 107.47: 443 107.47 - 114.10: 9263 114.10 - 120.72: 6835 120.72 - 127.35: 6747 127.35 - 133.98: 174 Bond angle restraints: 23462 Sorted by residual: angle pdb=" N VAL A 241 " pdb=" CA VAL A 241 " pdb=" C VAL A 241 " ideal model delta sigma weight residual 110.53 115.21 -4.68 9.40e-01 1.13e+00 2.48e+01 angle pdb=" C GLU A 210 " pdb=" CA GLU A 210 " pdb=" CB GLU A 210 " ideal model delta sigma weight residual 115.89 109.32 6.57 1.32e+00 5.74e-01 2.48e+01 angle pdb=" C VAL A 241 " pdb=" CA VAL A 241 " pdb=" CB VAL A 241 " ideal model delta sigma weight residual 112.02 107.97 4.05 1.31e+00 5.83e-01 9.54e+00 angle pdb=" N ILE B 480 " pdb=" CA ILE B 480 " pdb=" C ILE B 480 " ideal model delta sigma weight residual 111.81 109.19 2.62 8.60e-01 1.35e+00 9.29e+00 angle pdb=" N HIS A 212 " pdb=" CA HIS A 212 " pdb=" C HIS A 212 " ideal model delta sigma weight residual 111.54 107.58 3.96 1.36e+00 5.41e-01 8.48e+00 ... (remaining 23457 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 9280 17.70 - 35.39: 693 35.39 - 53.09: 131 53.09 - 70.79: 34 70.79 - 88.48: 14 Dihedral angle restraints: 10152 sinusoidal: 4122 harmonic: 6030 Sorted by residual: dihedral pdb=" CB GLU A 538 " pdb=" CG GLU A 538 " pdb=" CD GLU A 538 " pdb=" OE1 GLU A 538 " ideal model delta sinusoidal sigma weight residual 0.00 88.48 -88.48 1 3.00e+01 1.11e-03 1.04e+01 dihedral pdb=" CB GLU A 355 " pdb=" CG GLU A 355 " pdb=" CD GLU A 355 " pdb=" OE1 GLU A 355 " ideal model delta sinusoidal sigma weight residual 0.00 87.74 -87.74 1 3.00e+01 1.11e-03 1.02e+01 dihedral pdb=" CB GLU B 149 " pdb=" CG GLU B 149 " pdb=" CD GLU B 149 " pdb=" OE1 GLU B 149 " ideal model delta sinusoidal sigma weight residual 0.00 -86.99 86.99 1 3.00e+01 1.11e-03 1.01e+01 ... (remaining 10149 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1474 0.027 - 0.054: 612 0.054 - 0.082: 131 0.082 - 0.109: 138 0.109 - 0.136: 47 Chirality restraints: 2402 Sorted by residual: chirality pdb=" CA ILE B 256 " pdb=" N ILE B 256 " pdb=" C ILE B 256 " pdb=" CB ILE B 256 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.64e-01 chirality pdb=" CB THR B 836 " pdb=" CA THR B 836 " pdb=" OG1 THR B 836 " pdb=" CG2 THR B 836 " both_signs ideal model delta sigma weight residual False 2.55 2.42 0.13 2.00e-01 2.50e+01 4.49e-01 chirality pdb=" CA VAL A 342 " pdb=" N VAL A 342 " pdb=" C VAL A 342 " pdb=" CB VAL A 342 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.20e-01 ... (remaining 2399 not shown) Planarity restraints: 3092 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 153 " -0.026 5.00e-02 4.00e+02 4.02e-02 2.59e+00 pdb=" N PRO B 154 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO B 154 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 154 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 453 " -0.025 5.00e-02 4.00e+02 3.80e-02 2.30e+00 pdb=" N PRO A 454 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 454 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 454 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 625 " 0.023 5.00e-02 4.00e+02 3.51e-02 1.97e+00 pdb=" N PRO B 626 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO B 626 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 626 " 0.020 5.00e-02 4.00e+02 ... (remaining 3089 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2146 2.76 - 3.29: 14611 3.29 - 3.83: 26232 3.83 - 4.36: 30263 4.36 - 4.90: 55006 Nonbonded interactions: 128258 Sorted by model distance: nonbonded pdb=" OD2 ASP A 656 " pdb=" OG1 THR A 662 " model vdw 2.223 2.440 nonbonded pdb=" OG1 THR A 742 " pdb=" O GLY A 745 " model vdw 2.267 2.440 nonbonded pdb=" OG1 THR B 742 " pdb=" O GLY B 745 " model vdw 2.287 2.440 nonbonded pdb=" OE2 GLU B1002 " pdb=" OH TYR B1011 " model vdw 2.291 2.440 nonbonded pdb=" OG SER A1055 " pdb=" OG SER A1063 " model vdw 2.293 2.440 ... (remaining 128253 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' selection = chain 'B' } ncs_group { reference = chain 'C' 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=0.00 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: 0.670 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: 0.020 Extract box with map and model: 4.120 Check model and map are aligned: 0.260 Set scattering table: 0.140 Process input model: 44.970 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.090 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 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 : 0.002 0.028 17342 Z= 0.106 Angle : 0.470 9.051 23462 Z= 0.288 Chirality : 0.039 0.136 2402 Planarity : 0.003 0.040 3092 Dihedral : 13.151 88.482 6340 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.12 % Favored : 90.88 % Rotamer Outliers : 1.83 % 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: -4.07 (0.15), residues: 2062 helix: -5.11 (0.20), residues: 44 sheet: -1.28 (0.33), residues: 248 loop : -3.19 (0.12), residues: 1770 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 370 time to evaluate : 2.161 Fit side-chains outliers start: 33 outliers final: 21 residues processed: 399 average time/residue: 0.3185 time to fit residues: 183.5391 Evaluate side-chains 241 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 220 time to evaluate : 1.901 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.1512 time to fit residues: 8.6143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 173 optimal weight: 0.4980 chunk 156 optimal weight: 5.9990 chunk 86 optimal weight: 7.9990 chunk 53 optimal weight: 0.0060 chunk 105 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 161 optimal weight: 9.9990 chunk 62 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 120 optimal weight: 20.0000 chunk 187 optimal weight: 0.9990 overall best weight: 1.5002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 189 ASN B 198 HIS B 278 GLN B 294 ASN B 373 HIS B 510 GLN B 551 GLN B 585 GLN B 639 GLN B 692 HIS B 724 GLN B 733 ASN B 738 HIS ** B 754 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN B 772 GLN ** B 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 971 HIS B1071 ASN B1089 ASN B1121 ASN C1213 ASN ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 240 GLN A 251 ASN A 303 ASN A 373 HIS A 474 HIS A 481 GLN A 510 GLN A 550 GLN A 574 ASN A 585 GLN A 658 GLN A 692 HIS A 725 HIS A 740 ASN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 772 GLN A 786 GLN A 855 GLN A 940 GLN A1026 ASN D1148 GLN D1160 GLN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 17342 Z= 0.187 Angle : 0.540 15.082 23462 Z= 0.281 Chirality : 0.042 0.151 2402 Planarity : 0.004 0.045 3092 Dihedral : 3.231 14.754 2346 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.74 % Favored : 88.26 % Rotamer Outliers : 2.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.68 (0.15), residues: 2062 helix: -3.96 (0.54), residues: 42 sheet: -0.57 (0.30), residues: 306 loop : -3.08 (0.12), residues: 1714 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 223 time to evaluate : 2.006 Fit side-chains outliers start: 53 outliers final: 30 residues processed: 260 average time/residue: 0.3079 time to fit residues: 119.9255 Evaluate side-chains 225 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 195 time to evaluate : 2.021 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.1616 time to fit residues: 11.8955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 103 optimal weight: 10.0000 chunk 58 optimal weight: 10.0000 chunk 155 optimal weight: 4.9990 chunk 127 optimal weight: 9.9990 chunk 51 optimal weight: 10.0000 chunk 187 optimal weight: 0.9980 chunk 202 optimal weight: 9.9990 chunk 166 optimal weight: 7.9990 chunk 185 optimal weight: 9.9990 chunk 63 optimal weight: 3.9990 chunk 150 optimal weight: 6.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 360 HIS B 869 ASN B 885 GLN ** B 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1117 GLN ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 421 HIS A 506 ASN A 640 GLN A 657 GLN A 738 HIS ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1026 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.4136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.066 17342 Z= 0.464 Angle : 0.754 13.686 23462 Z= 0.402 Chirality : 0.048 0.171 2402 Planarity : 0.005 0.050 3092 Dihedral : 5.015 22.154 2346 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.69 % Favored : 85.31 % Rotamer Outliers : 3.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.90 (0.15), residues: 2062 helix: -3.90 (0.57), residues: 44 sheet: -0.80 (0.28), residues: 364 loop : -3.31 (0.12), residues: 1654 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 211 time to evaluate : 2.042 Fit side-chains revert: symmetry clash outliers start: 59 outliers final: 31 residues processed: 259 average time/residue: 0.3133 time to fit residues: 120.9545 Evaluate side-chains 209 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 178 time to evaluate : 2.158 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.1753 time to fit residues: 13.1382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 185 optimal weight: 3.9990 chunk 140 optimal weight: 4.9990 chunk 97 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 89 optimal weight: 0.3980 chunk 125 optimal weight: 9.9990 chunk 188 optimal weight: 0.9980 chunk 199 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 178 optimal weight: 9.9990 chunk 53 optimal weight: 4.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 885 GLN ** B 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1026 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.4180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 17342 Z= 0.243 Angle : 0.608 14.056 23462 Z= 0.322 Chirality : 0.044 0.166 2402 Planarity : 0.004 0.052 3092 Dihedral : 4.527 19.284 2346 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.85 % Favored : 87.15 % Rotamer Outliers : 2.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.81 (0.15), residues: 2062 helix: -3.71 (0.58), residues: 44 sheet: -1.20 (0.29), residues: 338 loop : -3.09 (0.12), residues: 1680 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 192 time to evaluate : 2.130 Fit side-chains revert: symmetry clash outliers start: 40 outliers final: 25 residues processed: 221 average time/residue: 0.3363 time to fit residues: 109.9405 Evaluate side-chains 202 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 177 time to evaluate : 2.048 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.1605 time to fit residues: 10.3859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 165 optimal weight: 0.9990 chunk 113 optimal weight: 9.9990 chunk 2 optimal weight: 9.9990 chunk 148 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 chunk 169 optimal weight: 2.9990 chunk 137 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 101 optimal weight: 6.9990 chunk 178 optimal weight: 9.9990 chunk 50 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 460 GLN B 574 ASN B 885 GLN ** B 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 248 HIS ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.4621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.043 17342 Z= 0.339 Angle : 0.670 14.171 23462 Z= 0.357 Chirality : 0.046 0.175 2402 Planarity : 0.004 0.054 3092 Dihedral : 4.876 22.087 2346 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.05 % Favored : 83.95 % Rotamer Outliers : 2.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.91 (0.15), residues: 2062 helix: -3.65 (0.58), residues: 44 sheet: -1.40 (0.29), residues: 330 loop : -3.13 (0.12), residues: 1688 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 194 time to evaluate : 2.129 Fit side-chains revert: symmetry clash outliers start: 43 outliers final: 20 residues processed: 230 average time/residue: 0.3200 time to fit residues: 109.6362 Evaluate side-chains 202 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 182 time to evaluate : 2.033 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1574 time to fit residues: 8.7225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 66 optimal weight: 10.0000 chunk 179 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 116 optimal weight: 20.0000 chunk 49 optimal weight: 5.9990 chunk 199 optimal weight: 0.0060 chunk 165 optimal weight: 0.1980 chunk 92 optimal weight: 3.9990 chunk 16 optimal weight: 20.0000 chunk 65 optimal weight: 0.6980 chunk 104 optimal weight: 10.0000 overall best weight: 1.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 574 ASN B 658 GLN B 885 GLN ** B 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1089 ASN B1114 ASN A 201 GLN A 288 GLN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.4525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 17342 Z= 0.190 Angle : 0.576 14.396 23462 Z= 0.306 Chirality : 0.043 0.165 2402 Planarity : 0.004 0.053 3092 Dihedral : 4.462 21.758 2346 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.71 % Favored : 87.29 % Rotamer Outliers : 1.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.64 (0.16), residues: 2062 helix: -3.24 (0.63), residues: 44 sheet: -0.95 (0.29), residues: 356 loop : -3.03 (0.12), residues: 1662 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 192 time to evaluate : 2.131 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 20 residues processed: 215 average time/residue: 0.3282 time to fit residues: 105.8844 Evaluate side-chains 207 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 187 time to evaluate : 2.135 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1641 time to fit residues: 9.0100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 192 optimal weight: 9.9990 chunk 22 optimal weight: 9.9990 chunk 113 optimal weight: 0.9990 chunk 145 optimal weight: 9.9990 chunk 112 optimal weight: 6.9990 chunk 167 optimal weight: 7.9990 chunk 111 optimal weight: 0.9990 chunk 198 optimal weight: 0.7980 chunk 124 optimal weight: 20.0000 chunk 121 optimal weight: 10.0000 chunk 91 optimal weight: 4.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 639 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 GLN ** B 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 288 GLN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.4769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 17342 Z= 0.281 Angle : 0.638 14.382 23462 Z= 0.338 Chirality : 0.045 0.168 2402 Planarity : 0.004 0.053 3092 Dihedral : 4.740 23.856 2346 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.76 % Favored : 84.24 % Rotamer Outliers : 1.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.72 (0.16), residues: 2062 helix: -3.29 (0.60), residues: 46 sheet: -1.25 (0.28), residues: 372 loop : -3.03 (0.12), residues: 1644 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 192 time to evaluate : 2.407 Fit side-chains revert: symmetry clash outliers start: 30 outliers final: 15 residues processed: 213 average time/residue: 0.3403 time to fit residues: 107.6517 Evaluate side-chains 199 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 184 time to evaluate : 2.142 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1597 time to fit residues: 7.4938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 122 optimal weight: 0.8980 chunk 79 optimal weight: 9.9990 chunk 118 optimal weight: 7.9990 chunk 59 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 126 optimal weight: 10.0000 chunk 135 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 chunk 156 optimal weight: 4.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 639 GLN ** B 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 288 GLN A 401 HIS A 444 HIS ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.4833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 17342 Z= 0.266 Angle : 0.630 14.320 23462 Z= 0.334 Chirality : 0.045 0.168 2402 Planarity : 0.004 0.053 3092 Dihedral : 4.733 24.352 2346 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.40 % Favored : 85.60 % Rotamer Outliers : 0.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.70 (0.16), residues: 2062 helix: -3.13 (0.63), residues: 46 sheet: -1.12 (0.29), residues: 364 loop : -3.05 (0.12), residues: 1652 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 188 time to evaluate : 2.095 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 12 residues processed: 195 average time/residue: 0.3348 time to fit residues: 96.0571 Evaluate side-chains 191 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 179 time to evaluate : 2.038 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1851 time to fit residues: 6.7355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 180 optimal weight: 10.0000 chunk 190 optimal weight: 4.9990 chunk 173 optimal weight: 10.0000 chunk 185 optimal weight: 3.9990 chunk 111 optimal weight: 0.4980 chunk 80 optimal weight: 7.9990 chunk 145 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 chunk 167 optimal weight: 0.7980 chunk 174 optimal weight: 0.9990 chunk 184 optimal weight: 3.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 885 GLN ** B 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 288 GLN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.4714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 17342 Z= 0.169 Angle : 0.580 14.512 23462 Z= 0.307 Chirality : 0.043 0.160 2402 Planarity : 0.004 0.053 3092 Dihedral : 4.351 22.781 2346 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.19 % Favored : 86.81 % Rotamer Outliers : 0.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.51 (0.16), residues: 2062 helix: -2.88 (0.65), residues: 46 sheet: -0.86 (0.30), residues: 340 loop : -2.92 (0.13), residues: 1676 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 199 time to evaluate : 2.101 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 204 average time/residue: 0.3352 time to fit residues: 101.2406 Evaluate side-chains 186 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 183 time to evaluate : 1.878 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1474 time to fit residues: 3.5169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 121 optimal weight: 9.9990 chunk 195 optimal weight: 5.9990 chunk 119 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 136 optimal weight: 0.5980 chunk 205 optimal weight: 5.9990 chunk 188 optimal weight: 4.9990 chunk 163 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 126 optimal weight: 0.8980 chunk 100 optimal weight: 0.8980 overall best weight: 2.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 ASN A 288 GLN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.4879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 17342 Z= 0.246 Angle : 0.626 14.469 23462 Z= 0.333 Chirality : 0.045 0.163 2402 Planarity : 0.004 0.053 3092 Dihedral : 4.614 23.974 2346 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.55 % Favored : 85.45 % Rotamer Outliers : 0.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.56 (0.16), residues: 2062 helix: -2.92 (0.63), residues: 46 sheet: -0.99 (0.29), residues: 360 loop : -2.95 (0.13), residues: 1656 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 180 time to evaluate : 2.117 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 8 residues processed: 186 average time/residue: 0.3541 time to fit residues: 97.9571 Evaluate side-chains 180 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 172 time to evaluate : 2.052 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1654 time to fit residues: 5.3586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 129 optimal weight: 4.9990 chunk 174 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 150 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 45 optimal weight: 10.0000 chunk 163 optimal weight: 0.7980 chunk 68 optimal weight: 5.9990 chunk 168 optimal weight: 0.9980 chunk 20 optimal weight: 10.0000 chunk 30 optimal weight: 6.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 885 GLN ** B 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.177416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.150242 restraints weight = 22124.010| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 2.46 r_work: 0.3539 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3412 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.4793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 17342 Z= 0.174 Angle : 0.590 15.247 23462 Z= 0.309 Chirality : 0.043 0.172 2402 Planarity : 0.004 0.053 3092 Dihedral : 4.370 22.921 2346 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.39 % Favored : 86.61 % Rotamer Outliers : 0.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.43 (0.16), residues: 2062 helix: -2.66 (0.68), residues: 46 sheet: -0.68 (0.31), residues: 330 loop : -2.89 (0.13), residues: 1686 =============================================================================== Job complete usr+sys time: 3520.08 seconds wall clock time: 64 minutes 37.06 seconds (3877.06 seconds total)