Starting phenix.real_space_refine on Sat Dec 9 12:23:14 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bsp_30163/12_2023/7bsp_30163_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bsp_30163/12_2023/7bsp_30163.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bsp_30163/12_2023/7bsp_30163.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bsp_30163/12_2023/7bsp_30163.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bsp_30163/12_2023/7bsp_30163_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bsp_30163/12_2023/7bsp_30163_trim_updated.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 58 5.16 5 C 7112 2.51 5 N 1807 2.21 5 O 2030 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 135": "NH1" <-> "NH2" Residue "A GLU 212": "OE1" <-> "OE2" Residue "A ARG 237": "NH1" <-> "NH2" Residue "A ARG 332": "NH1" <-> "NH2" Residue "A GLU 383": "OE1" <-> "OE2" Residue "A GLU 387": "OE1" <-> "OE2" Residue "A GLU 423": "OE1" <-> "OE2" Residue "A GLU 488": "OE1" <-> "OE2" Residue "A ARG 521": "NH1" <-> "NH2" Residue "A GLU 528": "OE1" <-> "OE2" Residue "A GLU 530": "OE1" <-> "OE2" Residue "A GLU 555": "OE1" <-> "OE2" Residue "A GLU 579": "OE1" <-> "OE2" Residue "A GLU 586": "OE1" <-> "OE2" Residue "A GLU 602": "OE1" <-> "OE2" Residue "A GLU 609": "OE1" <-> "OE2" Residue "A GLU 649": "OE1" <-> "OE2" Residue "A GLU 658": "OE1" <-> "OE2" Residue "A GLU 699": "OE1" <-> "OE2" Residue "A ARG 839": "NH1" <-> "NH2" Residue "A GLU 966": "OE1" <-> "OE2" Residue "A GLU 985": "OE1" <-> "OE2" Residue "A PHE 1017": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1052": "NH1" <-> "NH2" Residue "A GLU 1081": "OE1" <-> "OE2" Residue "C ARG 27": "NH1" <-> "NH2" Residue "C ARG 76": "NH1" <-> "NH2" Residue "C GLU 86": "OE1" <-> "OE2" Residue "C ARG 132": "NH1" <-> "NH2" Residue "C ARG 270": "NH1" <-> "NH2" Residue "C ARG 309": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 11010 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 8311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1028, 8311 Classifications: {'peptide': 1028} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 1002} Chain breaks: 3 Chain: "C" Number of atoms: 2613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2613 Classifications: {'peptide': 324} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 25, 'TRANS': 298} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ACP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 6.17, per 1000 atoms: 0.56 Number of scatterers: 11010 At special positions: 0 Unit cell: (107.07, 87.15, 161.02, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 58 16.00 P 3 15.00 O 2030 8.00 N 1807 7.00 C 7112 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS C 91 " - pdb=" SG CYS C 104 " distance=2.03 Simple disulfide: pdb=" SG CYS C 94 " - pdb=" SG CYS C 102 " distance=2.03 Simple disulfide: pdb=" SG CYS C 157 " - pdb=" SG CYS C 171 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied BETA1-3 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG B 1 " - " ASN C 180 " " NAG C 403 " - " ASN C 294 " " NAG C 404 " - " ASN C 107 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.62 Conformation dependent library (CDL) restraints added in 2.1 seconds 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2562 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 56 helices and 10 sheets defined 37.4% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.60 Creating SS restraints... Processing helix chain 'A' and resid 55 through 64 removed outlier: 4.360A pdb=" N PHE A 61 " --> pdb=" O PRO A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 81 removed outlier: 3.646A pdb=" N PHE A 72 " --> pdb=" O ALA A 68 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LEU A 73 " --> pdb=" O ASN A 69 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE A 76 " --> pdb=" O PHE A 72 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLN A 79 " --> pdb=" O ILE A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 122 removed outlier: 5.786A pdb=" N LEU A 93 " --> pdb=" O THR A 90 " (cutoff:3.500A) Proline residue: A 94 - end of helix removed outlier: 4.831A pdb=" N PHE A 97 " --> pdb=" O PRO A 94 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VAL A 98 " --> pdb=" O LEU A 95 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE A 99 " --> pdb=" O PHE A 96 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N VAL A 101 " --> pdb=" O VAL A 98 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ALA A 103 " --> pdb=" O THR A 100 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ILE A 104 " --> pdb=" O VAL A 101 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N GLU A 109 " --> pdb=" O GLN A 106 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LEU A 112 " --> pdb=" O GLU A 109 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG A 115 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ASN A 118 " --> pdb=" O ARG A 115 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ASN A 121 " --> pdb=" O ASN A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 194 No H-bonds generated for 'chain 'A' and resid 191 through 194' Processing helix chain 'A' and resid 271 through 273 No H-bonds generated for 'chain 'A' and resid 271 through 273' Processing helix chain 'A' and resid 287 through 297 removed outlier: 3.911A pdb=" N LEU A 292 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE A 293 " --> pdb=" O ASN A 289 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL A 294 " --> pdb=" O ALA A 290 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE A 297 " --> pdb=" O ILE A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 313 removed outlier: 3.791A pdb=" N CYS A 306 " --> pdb=" O LYS A 302 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU A 309 " --> pdb=" O VAL A 305 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N LYS A 310 " --> pdb=" O CYS A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 333 removed outlier: 3.515A pdb=" N GLU A 333 " --> pdb=" O GLN A 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 329 through 333' Processing helix chain 'A' and resid 336 through 344 removed outlier: 4.078A pdb=" N PHE A 344 " --> pdb=" O MET A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 349 No H-bonds generated for 'chain 'A' and resid 346 through 349' Processing helix chain 'A' and resid 352 through 354 No H-bonds generated for 'chain 'A' and resid 352 through 354' Processing helix chain 'A' and resid 359 through 369 removed outlier: 4.873A pdb=" N GLU A 364 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LYS A 367 " --> pdb=" O VAL A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 376 removed outlier: 3.756A pdb=" N TRP A 376 " --> pdb=" O PHE A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 399 Processing helix chain 'A' and resid 410 through 413 No H-bonds generated for 'chain 'A' and resid 410 through 413' Processing helix chain 'A' and resid 459 through 467 Processing helix chain 'A' and resid 496 through 507 removed outlier: 4.563A pdb=" N LEU A 501 " --> pdb=" O ASP A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 568 No H-bonds generated for 'chain 'A' and resid 566 through 568' Processing helix chain 'A' and resid 575 through 590 removed outlier: 5.249A pdb=" N GLU A 579 " --> pdb=" O HIS A 576 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A 580 " --> pdb=" O GLU A 577 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N VAL A 583 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASN A 588 " --> pdb=" O VAL A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 618 removed outlier: 3.553A pdb=" N GLU A 609 " --> pdb=" O PRO A 605 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ARG A 610 " --> pdb=" O ASP A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 634 removed outlier: 3.583A pdb=" N VAL A 632 " --> pdb=" O LYS A 628 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE A 633 " --> pdb=" O MET A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 659 through 666 removed outlier: 3.767A pdb=" N HIS A 664 " --> pdb=" O ILE A 660 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA A 665 " --> pdb=" O GLU A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 688 removed outlier: 3.669A pdb=" N TYR A 686 " --> pdb=" O LYS A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 723 removed outlier: 4.669A pdb=" N TYR A 722 " --> pdb=" O LEU A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 761 removed outlier: 3.806A pdb=" N SER A 757 " --> pdb=" O GLY A 753 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE A 759 " --> pdb=" O THR A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 781 removed outlier: 3.797A pdb=" N GLN A 777 " --> pdb=" O SER A 773 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE A 778 " --> pdb=" O ILE A 774 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N CYS A 779 " --> pdb=" O PHE A 775 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET A 780 " --> pdb=" O LEU A 776 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LYS A 781 " --> pdb=" O GLN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 803 removed outlier: 4.616A pdb=" N VAL A 799 " --> pdb=" O LYS A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 824 removed outlier: 4.147A pdb=" N SER A 822 " --> pdb=" O ASN A 819 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ILE A 824 " --> pdb=" O VAL A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 859 removed outlier: 3.637A pdb=" N LYS A 856 " --> pdb=" O LYS A 853 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LEU A 858 " --> pdb=" O LEU A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 868 No H-bonds generated for 'chain 'A' and resid 865 through 868' Processing helix chain 'A' and resid 871 through 874 No H-bonds generated for 'chain 'A' and resid 871 through 874' Processing helix chain 'A' and resid 876 through 884 removed outlier: 4.907A pdb=" N ASN A 881 " --> pdb=" O PHE A 877 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N CYS A 883 " --> pdb=" O TYR A 879 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N PHE A 884 " --> pdb=" O LYS A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 892 removed outlier: 4.102A pdb=" N GLN A 892 " --> pdb=" O GLN A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 906 through 913 removed outlier: 4.035A pdb=" N MET A 910 " --> pdb=" O ALA A 906 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N TYR A 911 " --> pdb=" O TYR A 907 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ASN A 912 " --> pdb=" O LEU A 908 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE A 913 " --> pdb=" O THR A 909 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 906 through 913' Processing helix chain 'A' and resid 918 through 925 removed outlier: 3.657A pdb=" N TYR A 923 " --> pdb=" O PRO A 919 " (cutoff:3.500A) Processing helix chain 'A' and resid 932 through 936 removed outlier: 3.832A pdb=" N THR A 936 " --> pdb=" O ILE A 932 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 932 through 936' Processing helix chain 'A' and resid 949 through 951 No H-bonds generated for 'chain 'A' and resid 949 through 951' Processing helix chain 'A' and resid 953 through 978 removed outlier: 3.604A pdb=" N LEU A 957 " --> pdb=" O LEU A 953 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR A 958 " --> pdb=" O GLY A 954 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N PHE A 965 " --> pdb=" O PHE A 961 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N PHE A 970 " --> pdb=" O GLU A 966 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE A 971 " --> pdb=" O GLY A 967 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE A 976 " --> pdb=" O PHE A 972 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LEU A 977 " --> pdb=" O GLY A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 993 through 1004 removed outlier: 4.581A pdb=" N THR A 997 " --> pdb=" O THR A 994 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ILE A 998 " --> pdb=" O PHE A 995 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N VAL A1002 " --> pdb=" O VAL A 999 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N VAL A1004 " --> pdb=" O THR A1001 " (cutoff:3.500A) Processing helix chain 'A' and resid 1006 through 1012 removed outlier: 4.458A pdb=" N LEU A1011 " --> pdb=" O VAL A1007 " (cutoff:3.500A) Processing helix chain 'A' and resid 1020 through 1041 removed outlier: 3.968A pdb=" N TRP A1027 " --> pdb=" O HIS A1023 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA A1031 " --> pdb=" O TRP A1027 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N PHE A1032 " --> pdb=" O GLY A1028 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N PHE A1035 " --> pdb=" O ALA A1031 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N PHE A1038 " --> pdb=" O VAL A1034 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1060 Processing helix chain 'A' and resid 1064 through 1078 removed outlier: 3.980A pdb=" N LEU A1068 " --> pdb=" O VAL A1064 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ALA A1069 " --> pdb=" O SER A1065 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU A1072 " --> pdb=" O LEU A1068 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N PHE A1075 " --> pdb=" O ILE A1071 " (cutoff:3.500A) Processing helix chain 'A' and resid 1082 through 1089 removed outlier: 3.798A pdb=" N VAL A1086 " --> pdb=" O ILE A1082 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 73 Proline residue: C 52 - end of helix removed outlier: 3.669A pdb=" N PHE C 55 " --> pdb=" O LEU C 51 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ILE C 57 " --> pdb=" O ILE C 53 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU C 59 " --> pdb=" O PHE C 55 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE C 60 " --> pdb=" O ILE C 56 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE C 62 " --> pdb=" O GLY C 58 " (cutoff:3.500A) Proline residue: C 63 - end of helix removed outlier: 3.811A pdb=" N GLY C 67 " --> pdb=" O PRO C 63 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N THR C 71 " --> pdb=" O GLY C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 94 No H-bonds generated for 'chain 'C' and resid 92 through 94' Processing helix chain 'C' and resid 132 through 135 No H-bonds generated for 'chain 'C' and resid 132 through 135' Processing helix chain 'C' and resid 140 through 143 No H-bonds generated for 'chain 'C' and resid 140 through 143' Processing helix chain 'C' and resid 147 through 151 removed outlier: 3.818A pdb=" N LEU C 151 " --> pdb=" O SER C 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 147 through 151' Processing helix chain 'C' and resid 173 through 176 No H-bonds generated for 'chain 'C' and resid 173 through 176' Processing helix chain 'C' and resid 208 through 211 No H-bonds generated for 'chain 'C' and resid 208 through 211' Processing helix chain 'C' and resid 240 through 242 No H-bonds generated for 'chain 'C' and resid 240 through 242' Processing helix chain 'C' and resid 247 through 249 No H-bonds generated for 'chain 'C' and resid 247 through 249' Processing helix chain 'C' and resid 255 through 261 Processing helix chain 'C' and resid 324 through 332 Processing helix chain 'C' and resid 336 through 348 removed outlier: 4.383A pdb=" N VAL C 341 " --> pdb=" O PHE C 337 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 124 through 128 removed outlier: 3.583A pdb=" N LYS A 136 " --> pdb=" O VAL A 125 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 146 through 150 removed outlier: 3.681A pdb=" N VAL A 149 " --> pdb=" O ILE A 257 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 170 through 173 removed outlier: 3.717A pdb=" N CYS A 171 " --> pdb=" O HIS A 187 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N HIS A 187 " --> pdb=" O CYS A 171 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 224 through 227 removed outlier: 3.891A pdb=" N ILE A 227 " --> pdb=" O VAL A 235 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL A 235 " --> pdb=" O ILE A 227 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 811 through 813 removed outlier: 6.198A pdb=" N TYR A 405 " --> pdb=" O LEU A 812 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LYS A 669 " --> pdb=" O VAL A 406 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N THR A 408 " --> pdb=" O LYS A 669 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N TRP A 671 " --> pdb=" O THR A 408 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL A 785 " --> pdb=" O VAL A 672 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'A' and resid 558 through 564 removed outlier: 3.669A pdb=" N HIS A 536 " --> pdb=" O ILE A 550 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LYS A 552 " --> pdb=" O LEU A 534 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N LEU A 534 " --> pdb=" O LYS A 552 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 594 through 600 removed outlier: 6.044A pdb=" N PHE A 600 " --> pdb=" O LEU A 642 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N LEU A 642 " --> pdb=" O PHE A 600 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 77 through 79 Processing sheet with id= I, first strand: chain 'C' and resid 106 through 110 removed outlier: 5.886A pdb=" N ARG C 290 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ILE C 188 " --> pdb=" O ARG C 290 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 118 through 123 removed outlier: 5.826A pdb=" N TYR C 122 " --> pdb=" O LEU C 272 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N LEU C 272 " --> pdb=" O TYR C 122 " (cutoff:3.500A) 232 hydrogen bonds defined for protein. 570 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: 2.94 Time building geometry restraints manager: 5.00 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: 3462 1.34 - 1.46: 1988 1.46 - 1.57: 5723 1.57 - 1.69: 6 1.69 - 1.81: 89 Bond restraints: 11268 Sorted by residual: bond pdb=" O2B ACP A1101 " pdb=" PB ACP A1101 " ideal model delta sigma weight residual 1.507 1.609 -0.102 2.00e-02 2.50e+03 2.62e+01 bond pdb=" O3A ACP A1101 " pdb=" PB ACP A1101 " ideal model delta sigma weight residual 1.698 1.606 0.092 2.00e-02 2.50e+03 2.10e+01 bond pdb=" C4 ACP A1101 " pdb=" C5 ACP A1101 " ideal model delta sigma weight residual 1.386 1.463 -0.077 2.00e-02 2.50e+03 1.50e+01 bond pdb=" O3G ACP A1101 " pdb=" PG ACP A1101 " ideal model delta sigma weight residual 1.532 1.606 -0.074 2.00e-02 2.50e+03 1.37e+01 bond pdb=" O2G ACP A1101 " pdb=" PG ACP A1101 " ideal model delta sigma weight residual 1.537 1.608 -0.071 2.00e-02 2.50e+03 1.27e+01 ... (remaining 11263 not shown) Histogram of bond angle deviations from ideal: 99.90 - 107.13: 299 107.13 - 114.35: 6699 114.35 - 121.58: 5750 121.58 - 128.81: 2462 128.81 - 136.03: 68 Bond angle restraints: 15278 Sorted by residual: angle pdb=" N LYS A 880 " pdb=" CA LYS A 880 " pdb=" C LYS A 880 " ideal model delta sigma weight residual 111.82 107.26 4.56 1.16e+00 7.43e-01 1.54e+01 angle pdb=" O1B ACP A1101 " pdb=" PB ACP A1101 " pdb=" O2B ACP A1101 " ideal model delta sigma weight residual 119.60 108.01 11.59 3.00e+00 1.11e-01 1.49e+01 angle pdb=" C3B ACP A1101 " pdb=" PB ACP A1101 " pdb=" O3A ACP A1101 " ideal model delta sigma weight residual 98.05 109.14 -11.09 3.00e+00 1.11e-01 1.37e+01 angle pdb=" C ILE A1044 " pdb=" N TRP A1045 " pdb=" CA TRP A1045 " ideal model delta sigma weight residual 120.44 124.65 -4.21 1.30e+00 5.92e-01 1.05e+01 angle pdb=" C2 ACP A1101 " pdb=" N3 ACP A1101 " pdb=" C4 ACP A1101 " ideal model delta sigma weight residual 111.73 121.24 -9.51 3.00e+00 1.11e-01 1.00e+01 ... (remaining 15273 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.42: 6355 23.42 - 46.85: 347 46.85 - 70.27: 32 70.27 - 93.69: 22 93.69 - 117.11: 13 Dihedral angle restraints: 6769 sinusoidal: 2800 harmonic: 3969 Sorted by residual: dihedral pdb=" CA TRP A1045 " pdb=" C TRP A1045 " pdb=" N PRO A1046 " pdb=" CA PRO A1046 " ideal model delta harmonic sigma weight residual 180.00 -155.77 -24.23 0 5.00e+00 4.00e-02 2.35e+01 dihedral pdb=" CA PHE A 347 " pdb=" C PHE A 347 " pdb=" N MET A 348 " pdb=" CA MET A 348 " ideal model delta harmonic sigma weight residual 180.00 158.71 21.29 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" C2 NAG B 2 " pdb=" C3 NAG B 2 " pdb=" C4 NAG B 2 " pdb=" O4 NAG B 2 " ideal model delta sinusoidal sigma weight residual 175.11 58.00 117.11 1 3.00e+01 1.11e-03 1.55e+01 ... (remaining 6766 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 1632 0.086 - 0.173: 86 0.173 - 0.259: 4 0.259 - 0.346: 0 0.346 - 0.432: 1 Chirality restraints: 1723 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O3 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.29 -0.11 2.00e-02 2.50e+03 2.77e+01 chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN C 180 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.97 -0.43 2.00e-01 2.50e+01 4.67e+00 chirality pdb=" C2 NAG C 403 " pdb=" C1 NAG C 403 " pdb=" C3 NAG C 403 " pdb=" N2 NAG C 403 " both_signs ideal model delta sigma weight residual False -2.49 -2.25 -0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 1720 not shown) Planarity restraints: 1922 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 2 " -0.320 2.00e-02 2.50e+03 2.71e-01 9.21e+02 pdb=" C7 NAG B 2 " 0.081 2.00e-02 2.50e+03 pdb=" C8 NAG B 2 " -0.183 2.00e-02 2.50e+03 pdb=" N2 NAG B 2 " 0.472 2.00e-02 2.50e+03 pdb=" O7 NAG B 2 " -0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 404 " -0.309 2.00e-02 2.50e+03 2.65e-01 8.81e+02 pdb=" C7 NAG C 404 " 0.068 2.00e-02 2.50e+03 pdb=" C8 NAG C 404 " -0.001 2.00e-02 2.50e+03 pdb=" N2 NAG C 404 " 0.455 2.00e-02 2.50e+03 pdb=" O7 NAG C 404 " -0.213 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 403 " -0.304 2.00e-02 2.50e+03 2.61e-01 8.49e+02 pdb=" C7 NAG C 403 " 0.078 2.00e-02 2.50e+03 pdb=" C8 NAG C 403 " -0.177 2.00e-02 2.50e+03 pdb=" N2 NAG C 403 " 0.455 2.00e-02 2.50e+03 pdb=" O7 NAG C 403 " -0.051 2.00e-02 2.50e+03 ... (remaining 1919 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 170 2.52 - 3.12: 10702 3.12 - 3.71: 15612 3.71 - 4.31: 23990 4.31 - 4.90: 38352 Nonbonded interactions: 88826 Sorted by model distance: nonbonded pdb=" OG SER A1063 " pdb=" OG1 THR A1066 " model vdw 1.928 2.440 nonbonded pdb=" OH TYR A 879 " pdb=" OE1 GLU A 966 " model vdw 1.943 2.440 nonbonded pdb=" O ASP A 409 " pdb=" OG1 THR A 413 " model vdw 1.949 2.440 nonbonded pdb=" OD1 ASP A 904 " pdb=" N ALA A 905 " model vdw 1.968 2.520 nonbonded pdb=" OG1 THR A 553 " pdb=" O ASP A 557 " model vdw 1.989 2.440 ... (remaining 88821 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.230 Check model and map are aligned: 0.160 Set scattering table: 0.110 Process input model: 31.940 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.102 11268 Z= 0.323 Angle : 0.660 11.592 15278 Z= 0.370 Chirality : 0.042 0.432 1723 Planarity : 0.012 0.271 1919 Dihedral : 15.681 117.114 4198 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 53.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.61 % Favored : 85.39 % Rotamer: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % 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: -7.27 (0.14), residues: 1342 helix: -5.21 (0.07), residues: 500 sheet: -4.22 (0.32), residues: 166 loop : -4.75 (0.17), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1020 HIS 0.005 0.001 HIS A 864 PHE 0.016 0.001 PHE A 978 TYR 0.011 0.001 TYR A1054 ARG 0.003 0.000 ARG C 309 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 225 time to evaluate : 1.402 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 225 average time/residue: 0.2292 time to fit residues: 74.1345 Evaluate side-chains 161 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 1.272 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 113 optimal weight: 7.9990 chunk 101 optimal weight: 0.4980 chunk 56 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 68 optimal weight: 8.9990 chunk 54 optimal weight: 0.8980 chunk 105 optimal weight: 0.9980 chunk 40 optimal weight: 9.9990 chunk 63 optimal weight: 3.9990 chunk 78 optimal weight: 0.6980 chunk 121 optimal weight: 0.0770 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 641 ASN A 716 HIS A 794 GLN A 862 HIS ** A 929 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1089 ASN C 130 ASN C 131 HIS ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11268 Z= 0.214 Angle : 0.723 10.239 15278 Z= 0.364 Chirality : 0.047 0.256 1723 Planarity : 0.004 0.034 1919 Dihedral : 10.919 106.108 1580 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 1.66 % Allowed : 12.46 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.12 (0.19), residues: 1342 helix: -3.57 (0.16), residues: 526 sheet: -3.38 (0.34), residues: 178 loop : -3.18 (0.23), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 376 HIS 0.013 0.001 HIS C 302 PHE 0.023 0.002 PHE A 462 TYR 0.021 0.002 TYR A 431 ARG 0.006 0.001 ARG A 133 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 236 time to evaluate : 1.358 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 12 residues processed: 245 average time/residue: 0.2188 time to fit residues: 78.7837 Evaluate side-chains 186 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 174 time to evaluate : 1.394 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1128 time to fit residues: 4.4280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 67 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 chunk 101 optimal weight: 0.3980 chunk 82 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 121 optimal weight: 6.9990 chunk 131 optimal weight: 6.9990 chunk 108 optimal weight: 4.9990 chunk 120 optimal weight: 0.0570 chunk 41 optimal weight: 9.9990 chunk 97 optimal weight: 5.9990 overall best weight: 2.0302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 130 ASN A 213 GLN A 273 ASN A 314 GLN A 584 HIS ** A 929 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 GLN C 130 ASN ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 ASN C 302 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 11268 Z= 0.291 Angle : 0.686 10.190 15278 Z= 0.342 Chirality : 0.047 0.285 1723 Planarity : 0.004 0.037 1919 Dihedral : 9.115 102.359 1580 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 2.16 % Allowed : 16.28 % Favored : 81.56 % 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: -4.29 (0.21), residues: 1342 helix: -2.70 (0.19), residues: 525 sheet: -3.00 (0.35), residues: 179 loop : -2.87 (0.23), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 323 HIS 0.011 0.001 HIS C 302 PHE 0.015 0.002 PHE A 970 TYR 0.020 0.001 TYR A 318 ARG 0.004 0.000 ARG A 516 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 196 time to evaluate : 1.346 Fit side-chains revert: symmetry clash outliers start: 26 outliers final: 17 residues processed: 211 average time/residue: 0.1995 time to fit residues: 63.4823 Evaluate side-chains 190 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 173 time to evaluate : 1.338 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1025 time to fit residues: 5.0561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 58 optimal weight: 7.9990 chunk 81 optimal weight: 3.9990 chunk 122 optimal weight: 0.9980 chunk 129 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 929 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 130 ASN ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 11268 Z= 0.306 Angle : 0.672 9.108 15278 Z= 0.335 Chirality : 0.046 0.257 1723 Planarity : 0.004 0.041 1919 Dihedral : 8.404 102.503 1580 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.54 % Favored : 90.46 % Rotamer: Outliers : 3.07 % Allowed : 17.36 % Favored : 79.57 % 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: -3.72 (0.21), residues: 1342 helix: -2.17 (0.21), residues: 512 sheet: -2.69 (0.36), residues: 181 loop : -2.60 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 313 HIS 0.014 0.001 HIS C 302 PHE 0.014 0.002 PHE A 877 TYR 0.019 0.001 TYR A 771 ARG 0.005 0.000 ARG A 723 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 189 time to evaluate : 1.325 Fit side-chains revert: symmetry clash outliers start: 37 outliers final: 22 residues processed: 210 average time/residue: 0.1964 time to fit residues: 62.2542 Evaluate side-chains 192 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 170 time to evaluate : 1.315 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.1039 time to fit residues: 5.8815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 73 optimal weight: 0.9980 chunk 1 optimal weight: 0.0870 chunk 96 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 110 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 66 optimal weight: 6.9990 chunk 116 optimal weight: 0.0020 chunk 32 optimal weight: 0.9980 chunk 43 optimal weight: 10.0000 overall best weight: 0.5166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 319 ASN A 664 HIS A 804 ASN C 211 ASN C 302 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 11268 Z= 0.181 Angle : 0.639 9.164 15278 Z= 0.315 Chirality : 0.044 0.250 1723 Planarity : 0.004 0.040 1919 Dihedral : 8.115 102.214 1580 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 1.50 % Allowed : 19.35 % Favored : 79.15 % 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: -3.20 (0.22), residues: 1342 helix: -1.63 (0.22), residues: 517 sheet: -2.37 (0.37), residues: 181 loop : -2.43 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 292 HIS 0.007 0.001 HIS C 302 PHE 0.017 0.001 PHE C 214 TYR 0.021 0.001 TYR A 381 ARG 0.003 0.000 ARG A 940 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 201 time to evaluate : 1.349 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 9 residues processed: 212 average time/residue: 0.1957 time to fit residues: 63.1447 Evaluate side-chains 183 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 174 time to evaluate : 1.185 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1135 time to fit residues: 3.4780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 116 optimal weight: 6.9990 chunk 25 optimal weight: 0.0980 chunk 76 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 129 optimal weight: 0.8980 chunk 107 optimal weight: 6.9990 chunk 60 optimal weight: 0.9980 chunk 10 optimal weight: 20.0000 chunk 42 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 124 optimal weight: 0.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 ASN A 664 HIS ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11268 Z= 0.201 Angle : 0.613 9.178 15278 Z= 0.305 Chirality : 0.044 0.250 1723 Planarity : 0.004 0.040 1919 Dihedral : 7.819 99.535 1580 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 1.33 % Allowed : 21.68 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.95 (0.22), residues: 1342 helix: -1.38 (0.22), residues: 516 sheet: -2.27 (0.37), residues: 182 loop : -2.30 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 292 HIS 0.003 0.001 HIS A 716 PHE 0.014 0.001 PHE A 462 TYR 0.020 0.001 TYR A 431 ARG 0.004 0.000 ARG A 940 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 184 time to evaluate : 1.353 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 12 residues processed: 191 average time/residue: 0.1933 time to fit residues: 56.7532 Evaluate side-chains 175 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 163 time to evaluate : 1.209 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1292 time to fit residues: 4.4242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 14 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 109 optimal weight: 7.9990 chunk 72 optimal weight: 3.9990 chunk 129 optimal weight: 0.0870 chunk 80 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 59 optimal weight: 8.9990 chunk 79 optimal weight: 0.9990 chunk 51 optimal weight: 0.2980 overall best weight: 1.4764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 664 HIS C 74 ASN C 130 ASN ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11268 Z= 0.225 Angle : 0.630 9.159 15278 Z= 0.313 Chirality : 0.045 0.244 1723 Planarity : 0.004 0.040 1919 Dihedral : 7.721 99.020 1580 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 1.50 % Allowed : 23.09 % Favored : 75.42 % 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: -2.80 (0.23), residues: 1342 helix: -1.23 (0.23), residues: 522 sheet: -2.18 (0.38), residues: 182 loop : -2.25 (0.24), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 207 HIS 0.007 0.001 HIS C 302 PHE 0.017 0.001 PHE A 462 TYR 0.033 0.002 TYR C 134 ARG 0.005 0.000 ARG A 940 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 173 time to evaluate : 1.362 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 9 residues processed: 183 average time/residue: 0.2000 time to fit residues: 56.2517 Evaluate side-chains 174 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 165 time to evaluate : 1.247 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1134 time to fit residues: 3.7920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 25 optimal weight: 0.9980 chunk 82 optimal weight: 0.7980 chunk 87 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 12 optimal weight: 7.9990 chunk 101 optimal weight: 3.9990 chunk 117 optimal weight: 0.8980 chunk 123 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 664 HIS C 74 ASN ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.3631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11268 Z= 0.245 Angle : 0.640 9.154 15278 Z= 0.318 Chirality : 0.045 0.244 1723 Planarity : 0.004 0.040 1919 Dihedral : 7.643 97.866 1580 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 0.75 % Allowed : 23.92 % Favored : 75.33 % 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: -2.69 (0.23), residues: 1342 helix: -1.15 (0.23), residues: 515 sheet: -2.13 (0.37), residues: 188 loop : -2.17 (0.25), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP C 207 HIS 0.003 0.001 HIS A 716 PHE 0.021 0.001 PHE A 600 TYR 0.037 0.001 TYR A 608 ARG 0.008 0.000 ARG A 206 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 178 time to evaluate : 1.340 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 182 average time/residue: 0.2115 time to fit residues: 57.9710 Evaluate side-chains 172 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 166 time to evaluate : 1.245 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1099 time to fit residues: 2.9383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 0.9980 chunk 123 optimal weight: 0.0980 chunk 72 optimal weight: 0.0470 chunk 52 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 108 optimal weight: 10.0000 chunk 113 optimal weight: 0.4980 chunk 119 optimal weight: 5.9990 chunk 79 optimal weight: 4.9990 chunk 127 optimal weight: 5.9990 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 664 HIS C 35 GLN C 74 ASN ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.3886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 11268 Z= 0.178 Angle : 0.631 9.612 15278 Z= 0.310 Chirality : 0.044 0.248 1723 Planarity : 0.004 0.040 1919 Dihedral : 7.493 98.206 1580 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 0.33 % Allowed : 24.92 % Favored : 74.75 % 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: -2.59 (0.23), residues: 1342 helix: -1.03 (0.23), residues: 520 sheet: -2.07 (0.37), residues: 189 loop : -2.15 (0.24), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP C 207 HIS 0.003 0.001 HIS C 302 PHE 0.019 0.001 PHE C 214 TYR 0.032 0.001 TYR C 134 ARG 0.010 0.000 ARG A 206 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 192 time to evaluate : 1.252 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 193 average time/residue: 0.1923 time to fit residues: 56.5318 Evaluate side-chains 176 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 174 time to evaluate : 1.289 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1305 time to fit residues: 2.2335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 0.0020 chunk 60 optimal weight: 8.9990 chunk 88 optimal weight: 3.9990 chunk 133 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 11 optimal weight: 8.9990 chunk 82 optimal weight: 1.9990 chunk 65 optimal weight: 7.9990 chunk 84 optimal weight: 0.8980 chunk 113 optimal weight: 0.2980 overall best weight: 0.8390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 664 HIS ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.4010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 11268 Z= 0.225 Angle : 0.647 9.434 15278 Z= 0.321 Chirality : 0.044 0.249 1723 Planarity : 0.004 0.043 1919 Dihedral : 7.406 97.444 1580 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 0.42 % Allowed : 25.33 % Favored : 74.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.23), residues: 1342 helix: -0.99 (0.23), residues: 523 sheet: -2.04 (0.37), residues: 193 loop : -2.15 (0.24), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP C 207 HIS 0.002 0.001 HIS A 716 PHE 0.025 0.001 PHE A1075 TYR 0.021 0.001 TYR A 722 ARG 0.012 0.000 ARG A 206 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 175 time to evaluate : 1.229 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 178 average time/residue: 0.1952 time to fit residues: 53.6136 Evaluate side-chains 170 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 166 time to evaluate : 1.148 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1081 time to fit residues: 2.4156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 32 optimal weight: 0.3980 chunk 98 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 106 optimal weight: 6.9990 chunk 44 optimal weight: 7.9990 chunk 109 optimal weight: 9.9990 chunk 13 optimal weight: 5.9990 chunk 19 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 6 optimal weight: 0.0770 overall best weight: 0.6942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.117740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.090174 restraints weight = 18778.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.091978 restraints weight = 13335.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.092834 restraints weight = 8231.577| |-----------------------------------------------------------------------------| r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.4186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 11268 Z= 0.211 Angle : 0.649 9.815 15278 Z= 0.319 Chirality : 0.043 0.247 1723 Planarity : 0.004 0.040 1919 Dihedral : 7.332 97.393 1580 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 0.00 % Allowed : 26.16 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.23), residues: 1342 helix: -0.92 (0.23), residues: 530 sheet: -1.95 (0.37), residues: 193 loop : -2.12 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP C 207 HIS 0.004 0.001 HIS C 302 PHE 0.023 0.001 PHE A 600 TYR 0.037 0.001 TYR C 134 ARG 0.010 0.000 ARG A 206 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2253.98 seconds wall clock time: 46 minutes 42.35 seconds (2802.35 seconds total)