Starting phenix.real_space_refine (version: 1.21rc1) on Sat Oct 7 20:06:27 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzg_24759/10_2023/7rzg_24759.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzg_24759/10_2023/7rzg_24759.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzg_24759/10_2023/7rzg_24759.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzg_24759/10_2023/7rzg_24759.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzg_24759/10_2023/7rzg_24759.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzg_24759/10_2023/7rzg_24759.pdb" } resolution = 4.1 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 43 5.16 5 C 9912 2.51 5 N 2588 2.21 5 O 2842 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 65": "NH1" <-> "NH2" Residue "A PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 163": "OD1" <-> "OD2" Residue "A PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 229": "NH1" <-> "NH2" Residue "A TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 262": "OE1" <-> "OE2" Residue "A PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 295": "OE1" <-> "OE2" Residue "A TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 349": "OE1" <-> "OE2" Residue "A ARG 402": "NH1" <-> "NH2" Residue "A GLU 413": "OE1" <-> "OE2" Residue "A PHE 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 431": "NH1" <-> "NH2" Residue "A TYR 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 469": "OD1" <-> "OD2" Residue "A GLU 474": "OE1" <-> "OE2" Residue "A ASP 490": "OD1" <-> "OD2" Residue "A TYR 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 503": "OE1" <-> "OE2" Residue "A TYR 584": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 586": "OD1" <-> "OD2" Residue "A TYR 634": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 685": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 711": "NH1" <-> "NH2" Residue "A GLU 726": "OE1" <-> "OE2" Residue "A GLU 860": "OE1" <-> "OE2" Residue "A ARG 862": "NH1" <-> "NH2" Residue "A GLU 875": "OE1" <-> "OE2" Residue "A ARG 892": "NH1" <-> "NH2" Residue "A GLU 910": "OE1" <-> "OE2" Residue "A GLU 962": "OE1" <-> "OE2" Residue "B ARG 65": "NH1" <-> "NH2" Residue "B TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 145": "OE1" <-> "OE2" Residue "B GLU 189": "OE1" <-> "OE2" Residue "B ARG 229": "NH1" <-> "NH2" Residue "B TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 341": "OE1" <-> "OE2" Residue "B ARG 402": "NH1" <-> "NH2" Residue "B ARG 431": "NH1" <-> "NH2" Residue "B ASP 469": "OD1" <-> "OD2" Residue "B PHE 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 634": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 666": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 711": "NH1" <-> "NH2" Residue "B TYR 766": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 792": "OE1" <-> "OE2" Residue "B TYR 795": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 834": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 853": "OE1" <-> "OE2" Residue "B GLU 860": "OE1" <-> "OE2" Residue "B ARG 862": "NH1" <-> "NH2" Residue "B GLU 864": "OE1" <-> "OE2" Residue "B ARG 892": "NH1" <-> "NH2" Residue "B GLU 903": "OE1" <-> "OE2" Residue "B ASP 947": "OD1" <-> "OD2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 15385 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 948, 7718 Classifications: {'peptide': 948} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 50, 'TRANS': 897} Chain breaks: 2 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 4} Unresolved non-hydrogen planarities: 16 Chain: "B" Number of atoms: 7667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 940, 7667 Classifications: {'peptide': 940} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 49, 'TRANS': 890} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 Time building chain proxies: 7.82, per 1000 atoms: 0.51 Number of scatterers: 15385 At special positions: 0 Unit cell: (109.504, 130.104, 159.377, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 43 16.00 O 2842 8.00 N 2588 7.00 C 9912 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.59 Conformation dependent library (CDL) restraints added in 2.2 seconds 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3600 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 14 sheets defined 48.1% alpha, 15.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.61 Creating SS restraints... Processing helix chain 'A' and resid 95 through 99 removed outlier: 3.599A pdb=" N SER A 98 " --> pdb=" O GLY A 95 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASP A 99 " --> pdb=" O SER A 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 95 through 99' Processing helix chain 'A' and resid 105 through 114 Processing helix chain 'A' and resid 125 through 134 Processing helix chain 'A' and resid 157 through 167 removed outlier: 3.585A pdb=" N ARG A 164 " --> pdb=" O GLY A 160 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLN A 167 " --> pdb=" O ASP A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 193 removed outlier: 4.429A pdb=" N ASN A 184 " --> pdb=" O ASP A 180 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ASN A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 208 Processing helix chain 'A' and resid 213 through 217 Processing helix chain 'A' and resid 222 through 227 Processing helix chain 'A' and resid 227 through 232 Processing helix chain 'A' and resid 236 through 248 removed outlier: 3.651A pdb=" N GLU A 240 " --> pdb=" O ASP A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 275 removed outlier: 3.998A pdb=" N LYS A 273 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 326 removed outlier: 3.514A pdb=" N TYR A 326 " --> pdb=" O GLN A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 339 removed outlier: 3.794A pdb=" N TYR A 333 " --> pdb=" O ASN A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 354 Processing helix chain 'A' and resid 380 through 386 Processing helix chain 'A' and resid 386 through 405 removed outlier: 3.818A pdb=" N ILE A 390 " --> pdb=" O HIS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 424 Processing helix chain 'A' and resid 432 through 441 Processing helix chain 'A' and resid 442 through 444 No H-bonds generated for 'chain 'A' and resid 442 through 444' Processing helix chain 'A' and resid 460 through 471 removed outlier: 3.777A pdb=" N ILE A 464 " --> pdb=" O ARG A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 516 Processing helix chain 'A' and resid 581 through 584 removed outlier: 4.006A pdb=" N TYR A 584 " --> pdb=" O PRO A 581 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 581 through 584' Processing helix chain 'A' and resid 586 through 604 Processing helix chain 'A' and resid 604 through 615 removed outlier: 5.029A pdb=" N ALA A 610 " --> pdb=" O GLU A 606 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ALA A 611 " --> pdb=" O TYR A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 651 removed outlier: 3.764A pdb=" N THR A 651 " --> pdb=" O GLU A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 671 removed outlier: 4.156A pdb=" N ASN A 671 " --> pdb=" O MET A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 675 Processing helix chain 'A' and resid 677 through 690 Processing helix chain 'A' and resid 696 through 703 Processing helix chain 'A' and resid 704 through 706 No H-bonds generated for 'chain 'A' and resid 704 through 706' Processing helix chain 'A' and resid 708 through 722 Proline residue: A 717 - end of helix removed outlier: 4.549A pdb=" N ARG A 722 " --> pdb=" O GLN A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 754 Processing helix chain 'A' and resid 801 through 815 removed outlier: 3.902A pdb=" N MET A 806 " --> pdb=" O THR A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 823 Processing helix chain 'A' and resid 855 through 877 removed outlier: 4.042A pdb=" N GLU A 875 " --> pdb=" O GLU A 871 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASP A 876 " --> pdb=" O LYS A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 894 removed outlier: 4.794A pdb=" N ALA A 888 " --> pdb=" O LYS A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 899 through 912 removed outlier: 3.701A pdb=" N GLU A 903 " --> pdb=" O LYS A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 929 removed outlier: 3.624A pdb=" N LYS A 929 " --> pdb=" O VAL A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 944 removed outlier: 4.117A pdb=" N GLU A 942 " --> pdb=" O LYS A 938 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N MET A 943 " --> pdb=" O PHE A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1001 removed outlier: 4.472A pdb=" N GLY A1001 " --> pdb=" O GLU A 997 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 99 Processing helix chain 'B' and resid 105 through 114 Processing helix chain 'B' and resid 125 through 134 Processing helix chain 'B' and resid 157 through 164 Processing helix chain 'B' and resid 166 through 171 removed outlier: 3.793A pdb=" N LEU B 170 " --> pdb=" O ALA B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 193 removed outlier: 4.073A pdb=" N ASN B 184 " --> pdb=" O ASP B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 208 removed outlier: 3.818A pdb=" N THR B 208 " --> pdb=" O LEU B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 217 Processing helix chain 'B' and resid 222 through 228 removed outlier: 3.668A pdb=" N LEU B 226 " --> pdb=" O ASN B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 234 removed outlier: 3.672A pdb=" N GLN B 232 " --> pdb=" O THR B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 249 removed outlier: 3.862A pdb=" N GLU B 240 " --> pdb=" O ASP B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 275 removed outlier: 3.590A pdb=" N LYS B 273 " --> pdb=" O ASN B 269 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU B 274 " --> pdb=" O LEU B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 339 Processing helix chain 'B' and resid 345 through 353 Processing helix chain 'B' and resid 381 through 385 Processing helix chain 'B' and resid 386 through 405 Processing helix chain 'B' and resid 408 through 424 Processing helix chain 'B' and resid 429 through 442 removed outlier: 3.921A pdb=" N TYR B 433 " --> pdb=" O ARG B 429 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N THR B 434 " --> pdb=" O PRO B 430 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N SER B 435 " --> pdb=" O ARG B 431 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N HIS B 442 " --> pdb=" O ALA B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 471 Processing helix chain 'B' and resid 506 through 515 removed outlier: 3.747A pdb=" N TRP B 513 " --> pdb=" O VAL B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 584 removed outlier: 4.190A pdb=" N TYR B 584 " --> pdb=" O PRO B 581 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 581 through 584' Processing helix chain 'B' and resid 586 through 613 removed outlier: 4.872A pdb=" N GLU B 606 " --> pdb=" O ASP B 602 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N TYR B 607 " --> pdb=" O SER B 603 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N ALA B 610 " --> pdb=" O GLU B 606 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ALA B 611 " --> pdb=" O TYR B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 651 removed outlier: 3.627A pdb=" N THR B 651 " --> pdb=" O GLU B 647 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 672 Processing helix chain 'B' and resid 673 through 676 removed outlier: 4.230A pdb=" N GLU B 676 " --> pdb=" O PHE B 673 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 673 through 676' Processing helix chain 'B' and resid 677 through 690 Processing helix chain 'B' and resid 696 through 703 Processing helix chain 'B' and resid 704 through 707 removed outlier: 3.822A pdb=" N VAL B 707 " --> pdb=" O LEU B 704 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 704 through 707' Processing helix chain 'B' and resid 708 through 722 Proline residue: B 717 - end of helix removed outlier: 4.438A pdb=" N ARG B 722 " --> pdb=" O GLN B 718 " (cutoff:3.500A) Processing helix chain 'B' and resid 734 through 754 Processing helix chain 'B' and resid 801 through 815 removed outlier: 4.155A pdb=" N MET B 806 " --> pdb=" O THR B 802 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 823 Processing helix chain 'B' and resid 855 through 876 removed outlier: 3.682A pdb=" N GLU B 875 " --> pdb=" O GLU B 871 " (cutoff:3.500A) Processing helix chain 'B' and resid 878 through 894 removed outlier: 3.622A pdb=" N PHE B 882 " --> pdb=" O THR B 878 " (cutoff:3.500A) Processing helix chain 'B' and resid 899 through 912 Processing helix chain 'B' and resid 919 through 929 removed outlier: 3.888A pdb=" N LYS B 929 " --> pdb=" O VAL B 925 " (cutoff:3.500A) Processing helix chain 'B' and resid 932 through 945 removed outlier: 3.811A pdb=" N ILE B 936 " --> pdb=" O THR B 932 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N GLU B 942 " --> pdb=" O LYS B 938 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N MET B 943 " --> pdb=" O PHE B 939 " (cutoff:3.500A) Processing helix chain 'B' and resid 994 through 1001 removed outlier: 4.503A pdb=" N GLY B1001 " --> pdb=" O GLU B 997 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 63 through 69 removed outlier: 6.038A pdb=" N LYS A 74 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N VAL A 258 " --> pdb=" O LYS A 74 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N LEU A 76 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N GLY A 260 " --> pdb=" O LEU A 76 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ILE A 78 " --> pdb=" O GLY A 260 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ALA A 88 " --> pdb=" O PHE A 151 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE A 141 " --> pdb=" O ASN A 148 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 63 through 69 removed outlier: 6.038A pdb=" N LYS A 74 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N VAL A 258 " --> pdb=" O LYS A 74 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N LEU A 76 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N GLY A 260 " --> pdb=" O LEU A 76 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ILE A 78 " --> pdb=" O GLY A 260 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP A 91 " --> pdb=" O ALA A 255 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE A 141 " --> pdb=" O ASN A 148 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 303 through 304 removed outlier: 3.561A pdb=" N MET A 371 " --> pdb=" O ILE A 319 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 491 through 492 removed outlier: 3.523A pdb=" N ARG A 491 " --> pdb=" O TYR A 500 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 549 through 553 removed outlier: 6.680A pdb=" N LEU A 559 " --> pdb=" O ILE A 551 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LYS A 558 " --> pdb=" O ALA A 727 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N LEU A 729 " --> pdb=" O LYS A 558 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N TRP A 560 " --> pdb=" O LEU A 729 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N GLY A 731 " --> pdb=" O TRP A 560 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LYS A 562 " --> pdb=" O GLY A 731 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY A 633 " --> pdb=" O ALA A 572 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 549 through 553 removed outlier: 6.680A pdb=" N LEU A 559 " --> pdb=" O ILE A 551 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LYS A 558 " --> pdb=" O ALA A 727 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N LEU A 729 " --> pdb=" O LYS A 558 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N TRP A 560 " --> pdb=" O LEU A 729 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N GLY A 731 " --> pdb=" O TRP A 560 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LYS A 562 " --> pdb=" O GLY A 731 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 776 through 777 removed outlier: 5.936A pdb=" N PHE A 777 " --> pdb=" O SER A 955 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N HIS A 957 " --> pdb=" O PHE A 777 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N GLN A 781 " --> pdb=" O LEU A 959 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 776 through 777 removed outlier: 5.936A pdb=" N PHE A 777 " --> pdb=" O SER A 955 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N HIS A 957 " --> pdb=" O PHE A 777 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N GLY A 790 " --> pdb=" O SER A 852 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N SER A 852 " --> pdb=" O GLY A 790 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N GLU A 792 " --> pdb=" O ILE A 850 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N ILE A 850 " --> pdb=" O GLU A 792 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N TYR A 794 " --> pdb=" O PHE A 848 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N PHE A 848 " --> pdb=" O TYR A 794 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N GLN A 796 " --> pdb=" O LEU A 846 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N LEU A 846 " --> pdb=" O GLN A 796 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ASP A 798 " --> pdb=" O GLN A 844 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY A 836 " --> pdb=" O ARG A 847 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ILE A 832 " --> pdb=" O GLN A 851 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 63 through 69 removed outlier: 3.653A pdb=" N GLU B 63 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N VAL B 258 " --> pdb=" O LEU B 76 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ILE B 78 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLY B 260 " --> pdb=" O ILE B 78 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER B 87 " --> pdb=" O LEU B 259 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE B 141 " --> pdb=" O ASN B 148 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 303 through 304 Processing sheet with id=AB2, first strand: chain 'B' and resid 491 through 492 Processing sheet with id=AB3, first strand: chain 'B' and resid 549 through 553 removed outlier: 5.878A pdb=" N LEU B 550 " --> pdb=" O PHE B 561 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N PHE B 561 " --> pdb=" O LEU B 550 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS B 552 " --> pdb=" O LEU B 559 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LYS B 558 " --> pdb=" O ALA B 727 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N LEU B 729 " --> pdb=" O LYS B 558 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N TRP B 560 " --> pdb=" O LEU B 729 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N GLY B 731 " --> pdb=" O TRP B 560 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N LYS B 562 " --> pdb=" O GLY B 731 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 776 through 777 removed outlier: 6.054A pdb=" N PHE B 777 " --> pdb=" O SER B 955 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N HIS B 957 " --> pdb=" O PHE B 777 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N GLN B 781 " --> pdb=" O LEU B 959 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 776 through 777 removed outlier: 6.054A pdb=" N PHE B 777 " --> pdb=" O SER B 955 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N HIS B 957 " --> pdb=" O PHE B 777 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU B 792 " --> pdb=" O VAL B 956 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY B 836 " --> pdb=" O ARG B 847 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ILE B 832 " --> pdb=" O GLN B 851 " (cutoff:3.500A) 714 hydrogen bonds defined for protein. 2031 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.70 Time building geometry restraints manager: 6.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4460 1.33 - 1.46: 3022 1.46 - 1.58: 8201 1.58 - 1.70: 0 1.70 - 1.82: 86 Bond restraints: 15769 Sorted by residual: bond pdb=" N ILE B 94 " pdb=" CA ILE B 94 " ideal model delta sigma weight residual 1.456 1.497 -0.042 1.11e-02 8.12e+03 1.41e+01 bond pdb=" N ILE A 843 " pdb=" CA ILE A 843 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.19e-02 7.06e+03 1.08e+01 bond pdb=" N GLY B 95 " pdb=" CA GLY B 95 " ideal model delta sigma weight residual 1.444 1.476 -0.032 1.02e-02 9.61e+03 1.00e+01 bond pdb=" CA PRO B 100 " pdb=" C PRO B 100 " ideal model delta sigma weight residual 1.517 1.546 -0.029 9.30e-03 1.16e+04 9.94e+00 bond pdb=" N ILE A 874 " pdb=" CA ILE A 874 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.19e-02 7.06e+03 9.14e+00 ... (remaining 15764 not shown) Histogram of bond angle deviations from ideal: 96.73 - 104.20: 281 104.20 - 111.68: 6639 111.68 - 119.15: 6262 119.15 - 126.62: 7943 126.62 - 134.10: 203 Bond angle restraints: 21328 Sorted by residual: angle pdb=" N PRO B 100 " pdb=" CA PRO B 100 " pdb=" C PRO B 100 " ideal model delta sigma weight residual 110.70 118.98 -8.28 1.22e+00 6.72e-01 4.60e+01 angle pdb=" CB ARG A 658 " pdb=" CG ARG A 658 " pdb=" CD ARG A 658 " ideal model delta sigma weight residual 111.30 100.23 11.07 2.30e+00 1.89e-01 2.32e+01 angle pdb=" N GLY B1001 " pdb=" CA GLY B1001 " pdb=" C GLY B1001 " ideal model delta sigma weight residual 113.18 123.56 -10.38 2.37e+00 1.78e-01 1.92e+01 angle pdb=" CA GLY A 830 " pdb=" C GLY A 830 " pdb=" N TYR A 831 " ideal model delta sigma weight residual 114.58 118.19 -3.61 8.60e-01 1.35e+00 1.76e+01 angle pdb=" CA GLY A 830 " pdb=" C GLY A 830 " pdb=" O GLY A 830 " ideal model delta sigma weight residual 121.49 117.55 3.94 9.60e-01 1.09e+00 1.68e+01 ... (remaining 21323 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.07: 8734 17.07 - 34.14: 644 34.14 - 51.21: 129 51.21 - 68.28: 13 68.28 - 85.35: 17 Dihedral angle restraints: 9537 sinusoidal: 3968 harmonic: 5569 Sorted by residual: dihedral pdb=" CA SER B 57 " pdb=" C SER B 57 " pdb=" N PRO B 58 " pdb=" CA PRO B 58 " ideal model delta harmonic sigma weight residual -180.00 -153.62 -26.38 0 5.00e+00 4.00e-02 2.78e+01 dihedral pdb=" CA TYR B 940 " pdb=" C TYR B 940 " pdb=" N LYS B 941 " pdb=" CA LYS B 941 " ideal model delta harmonic sigma weight residual -180.00 -154.62 -25.38 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA GLN B 800 " pdb=" C GLN B 800 " pdb=" N SER B 801 " pdb=" CA SER B 801 " ideal model delta harmonic sigma weight residual 180.00 155.31 24.69 0 5.00e+00 4.00e-02 2.44e+01 ... (remaining 9534 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1541 0.057 - 0.114: 562 0.114 - 0.172: 159 0.172 - 0.229: 24 0.229 - 0.286: 7 Chirality restraints: 2293 Sorted by residual: chirality pdb=" CB ILE B 505 " pdb=" CA ILE B 505 " pdb=" CG1 ILE B 505 " pdb=" CG2 ILE B 505 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" CA LYS B 884 " pdb=" N LYS B 884 " pdb=" C LYS B 884 " pdb=" CB LYS B 884 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" CB THR B 380 " pdb=" CA THR B 380 " pdb=" OG1 THR B 380 " pdb=" CG2 THR B 380 " both_signs ideal model delta sigma weight residual False 2.55 2.28 0.27 2.00e-01 2.50e+01 1.87e+00 ... (remaining 2290 not shown) Planarity restraints: 2760 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR B 224 " 0.024 2.00e-02 2.50e+03 4.83e-02 2.33e+01 pdb=" C TYR B 224 " -0.084 2.00e-02 2.50e+03 pdb=" O TYR B 224 " 0.031 2.00e-02 2.50e+03 pdb=" N THR B 225 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG A 472 " 0.078 5.00e-02 4.00e+02 1.20e-01 2.31e+01 pdb=" N PRO A 473 " -0.208 5.00e-02 4.00e+02 pdb=" CA PRO A 473 " 0.065 5.00e-02 4.00e+02 pdb=" CD PRO A 473 " 0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA HIS B 245 " -0.022 2.00e-02 2.50e+03 4.44e-02 1.97e+01 pdb=" C HIS B 245 " 0.077 2.00e-02 2.50e+03 pdb=" O HIS B 245 " -0.029 2.00e-02 2.50e+03 pdb=" N SER B 246 " -0.026 2.00e-02 2.50e+03 ... (remaining 2757 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 248 2.64 - 3.21: 14576 3.21 - 3.77: 23347 3.77 - 4.34: 31984 4.34 - 4.90: 51089 Nonbonded interactions: 121244 Sorted by model distance: nonbonded pdb=" O HIS A 297 " pdb=" NH1 ARG A 477 " model vdw 2.077 2.520 nonbonded pdb=" OG SER B 348 " pdb=" OE2 GLU B 606 " model vdw 2.156 2.440 nonbonded pdb=" OE1 GLN A 887 " pdb=" NZ LYS A 929 " model vdw 2.168 2.520 nonbonded pdb=" O ARG A 668 " pdb=" ND2 ASN A 672 " model vdw 2.184 2.520 nonbonded pdb=" O VAL B 785 " pdb=" NH1 ARG B 961 " model vdw 2.187 2.520 ... (remaining 121239 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 46 through 585 or (resid 586 and (name N or name CA or nam \ e C or name O or name CB )) or resid 587 through 656 or (resid 657 and (name N o \ r name CA or name C or name O or name CB )) or resid 658 through 704 or (resid 7 \ 05 and (name N or name CA or name C or name O or name CB )) or resid 706 through \ 763 or (resid 764 through 765 and (name N or name CA or name C or name O or nam \ e CB )) or resid 766 through 769 or (resid 770 and (name N or name CA or name C \ or name O or name CB )) or resid 771 through 962 or resid 989 through 1011)) selection = (chain 'B' and (resid 46 through 57 or resid 59 through 257 or (resid 258 and (n \ ame N or name CA or name C or name O or name CB )) or resid 259 through 349 or ( \ resid 350 and (name N or name CA or name C or name O or name CB )) or resid 351 \ through 439 or (resid 440 and (name N or name CA or name C or name O or name CB \ )) or resid 441 through 541 or (resid 542 through 544 and (name N or name CA or \ name C or name O or name CB )) or resid 545 through 573 or (resid 574 and (name \ N or name CA or name C or name O or name CB )) or resid 575 through 587 or (resi \ d 588 and (name N or name CA or name C or name O or name CB )) or resid 589 thro \ ugh 603 or (resid 604 and (name N or name CA or name C or name O or name CB )) o \ r resid 605 through 757 or (resid 758 and (name N or name CA or name C or name O \ or name CB )) or resid 759 through 1011)) } 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: 0.850 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: 4.640 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 40.010 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6726 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 : 0.007 0.069 15769 Z= 0.437 Angle : 1.165 11.074 21328 Z= 0.670 Chirality : 0.064 0.286 2293 Planarity : 0.009 0.120 2760 Dihedral : 12.777 85.351 5937 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 19.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 0.18 % Allowed : 2.11 % Favored : 97.71 % 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: -3.80 (0.16), residues: 1878 helix: -2.57 (0.14), residues: 785 sheet: -1.76 (0.26), residues: 344 loop : -2.62 (0.20), residues: 749 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 258 time to evaluate : 1.802 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 259 average time/residue: 0.2688 time to fit residues: 104.9853 Evaluate side-chains 167 residues out of total 1682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 1.757 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 158 optimal weight: 5.9990 chunk 142 optimal weight: 6.9990 chunk 79 optimal weight: 0.9980 chunk 48 optimal weight: 20.0000 chunk 96 optimal weight: 30.0000 chunk 76 optimal weight: 0.9990 chunk 147 optimal weight: 0.9990 chunk 57 optimal weight: 5.9990 chunk 89 optimal weight: 9.9990 chunk 109 optimal weight: 10.0000 chunk 170 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 ASN A 828 GLN B 146 HIS B 329 ASN B 332 HIS ** B 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 528 ASN B 762 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6733 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 15769 Z= 0.217 Angle : 0.675 7.281 21328 Z= 0.353 Chirality : 0.045 0.189 2293 Planarity : 0.005 0.078 2760 Dihedral : 5.568 23.463 2050 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 0.18 % Allowed : 3.74 % Favored : 96.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.18), residues: 1878 helix: -0.46 (0.17), residues: 822 sheet: -1.26 (0.26), residues: 344 loop : -2.14 (0.22), residues: 712 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 267 time to evaluate : 1.934 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 269 average time/residue: 0.2830 time to fit residues: 114.7890 Evaluate side-chains 174 residues out of total 1682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 1.655 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 94 optimal weight: 20.0000 chunk 52 optimal weight: 6.9990 chunk 142 optimal weight: 6.9990 chunk 116 optimal weight: 8.9990 chunk 47 optimal weight: 0.9990 chunk 171 optimal weight: 10.0000 chunk 184 optimal weight: 3.9990 chunk 152 optimal weight: 9.9990 chunk 169 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 137 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 HIS A 357 ASN ** A 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 HIS ** B 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 HIS ** B 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 412 GLN B 442 HIS B 762 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6878 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 15769 Z= 0.318 Angle : 0.735 9.669 21328 Z= 0.383 Chirality : 0.046 0.195 2293 Planarity : 0.005 0.066 2760 Dihedral : 5.603 23.137 2050 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 0.06 % Allowed : 5.91 % Favored : 94.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.18), residues: 1878 helix: -0.10 (0.17), residues: 827 sheet: -1.11 (0.26), residues: 365 loop : -1.92 (0.23), residues: 686 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 224 time to evaluate : 1.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 224 average time/residue: 0.2844 time to fit residues: 96.6253 Evaluate side-chains 166 residues out of total 1682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 1.690 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 168 optimal weight: 5.9990 chunk 128 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 81 optimal weight: 5.9990 chunk 114 optimal weight: 20.0000 chunk 171 optimal weight: 5.9990 chunk 181 optimal weight: 8.9990 chunk 89 optimal weight: 2.9990 chunk 162 optimal weight: 1.9990 chunk 48 optimal weight: 7.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 HIS ** B 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 442 HIS B 762 GLN B 786 HIS ** B 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6848 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 15769 Z= 0.231 Angle : 0.654 7.513 21328 Z= 0.338 Chirality : 0.044 0.167 2293 Planarity : 0.005 0.059 2760 Dihedral : 5.339 23.605 2050 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 0.06 % Allowed : 3.13 % Favored : 96.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.19), residues: 1878 helix: 0.30 (0.17), residues: 817 sheet: -0.75 (0.27), residues: 351 loop : -1.85 (0.22), residues: 710 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 241 time to evaluate : 1.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 241 average time/residue: 0.3204 time to fit residues: 112.9930 Evaluate side-chains 164 residues out of total 1682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 1.861 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 151 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 2 optimal weight: 9.9990 chunk 135 optimal weight: 9.9990 chunk 74 optimal weight: 6.9990 chunk 155 optimal weight: 8.9990 chunk 125 optimal weight: 20.0000 chunk 0 optimal weight: 9.9990 chunk 92 optimal weight: 0.3980 chunk 163 optimal weight: 1.9990 chunk 45 optimal weight: 9.9990 overall best weight: 3.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 805 ASN A 851 GLN A 988 GLN ** B 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 671 ASN B 762 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6903 moved from start: 0.3371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 15769 Z= 0.269 Angle : 0.678 8.824 21328 Z= 0.351 Chirality : 0.045 0.176 2293 Planarity : 0.005 0.054 2760 Dihedral : 5.350 26.179 2050 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 0.12 % Allowed : 3.68 % Favored : 96.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.19), residues: 1878 helix: 0.32 (0.17), residues: 813 sheet: -0.79 (0.27), residues: 352 loop : -1.78 (0.22), residues: 713 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 234 time to evaluate : 1.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 235 average time/residue: 0.2741 time to fit residues: 96.5110 Evaluate side-chains 154 residues out of total 1682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 1.704 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 61 optimal weight: 0.1980 chunk 163 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 106 optimal weight: 20.0000 chunk 44 optimal weight: 10.0000 chunk 181 optimal weight: 10.0000 chunk 150 optimal weight: 10.0000 chunk 84 optimal weight: 0.6980 chunk 15 optimal weight: 6.9990 chunk 60 optimal weight: 0.9990 chunk 95 optimal weight: 7.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 805 ASN A 851 GLN ** B 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 407 GLN B 762 GLN B 796 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6833 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15769 Z= 0.179 Angle : 0.619 9.627 21328 Z= 0.316 Chirality : 0.043 0.210 2293 Planarity : 0.004 0.048 2760 Dihedral : 5.095 24.766 2050 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.19), residues: 1878 helix: 0.61 (0.18), residues: 817 sheet: -0.65 (0.27), residues: 351 loop : -1.66 (0.22), residues: 710 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 236 time to evaluate : 1.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 236 average time/residue: 0.2662 time to fit residues: 94.9224 Evaluate side-chains 167 residues out of total 1682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 1.784 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 175 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 103 optimal weight: 9.9990 chunk 132 optimal weight: 9.9990 chunk 102 optimal weight: 0.9990 chunk 153 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 181 optimal weight: 0.0670 chunk 113 optimal weight: 1.9990 chunk 110 optimal weight: 7.9990 chunk 83 optimal weight: 0.4980 overall best weight: 1.1124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 851 GLN ** B 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6791 moved from start: 0.3749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15769 Z= 0.159 Angle : 0.592 8.175 21328 Z= 0.302 Chirality : 0.042 0.164 2293 Planarity : 0.004 0.047 2760 Dihedral : 4.819 24.264 2050 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.19), residues: 1878 helix: 0.81 (0.18), residues: 818 sheet: -0.53 (0.27), residues: 351 loop : -1.51 (0.23), residues: 709 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 260 time to evaluate : 1.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 260 average time/residue: 0.2733 time to fit residues: 107.3751 Evaluate side-chains 172 residues out of total 1682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 1.746 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 112 optimal weight: 0.4980 chunk 72 optimal weight: 0.0570 chunk 108 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 35 optimal weight: 7.9990 chunk 115 optimal weight: 10.0000 chunk 123 optimal weight: 9.9990 chunk 89 optimal weight: 8.9990 chunk 16 optimal weight: 6.9990 chunk 142 optimal weight: 5.9990 chunk 164 optimal weight: 1.9990 overall best weight: 3.1104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 HIS ** A 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 184 ASN ** B 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 730 HIS B 762 GLN ** B 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6882 moved from start: 0.4017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15769 Z= 0.237 Angle : 0.678 10.232 21328 Z= 0.345 Chirality : 0.045 0.191 2293 Planarity : 0.005 0.046 2760 Dihedral : 5.038 25.700 2050 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.19), residues: 1878 helix: 0.71 (0.18), residues: 819 sheet: -0.53 (0.28), residues: 346 loop : -1.61 (0.23), residues: 713 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 238 time to evaluate : 1.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 238 average time/residue: 0.2766 time to fit residues: 99.9541 Evaluate side-chains 160 residues out of total 1682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 1.801 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 173 optimal weight: 2.9990 chunk 158 optimal weight: 6.9990 chunk 168 optimal weight: 6.9990 chunk 101 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 132 optimal weight: 20.0000 chunk 51 optimal weight: 0.9990 chunk 152 optimal weight: 9.9990 chunk 159 optimal weight: 0.2980 chunk 110 optimal weight: 9.9990 chunk 178 optimal weight: 0.9980 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** B 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6850 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 : 0.003 0.040 15769 Z= 0.183 Angle : 0.636 9.658 21328 Z= 0.324 Chirality : 0.044 0.164 2293 Planarity : 0.004 0.046 2760 Dihedral : 4.924 24.621 2050 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.19), residues: 1878 helix: 0.77 (0.18), residues: 820 sheet: -0.53 (0.27), residues: 353 loop : -1.53 (0.23), residues: 705 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 228 time to evaluate : 1.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 228 average time/residue: 0.2795 time to fit residues: 96.6538 Evaluate side-chains 168 residues out of total 1682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 1.938 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 108 optimal weight: 10.0000 chunk 84 optimal weight: 8.9990 chunk 124 optimal weight: 7.9990 chunk 187 optimal weight: 1.9990 chunk 172 optimal weight: 10.0000 chunk 149 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 chunk 115 optimal weight: 6.9990 chunk 91 optimal weight: 20.0000 chunk 118 optimal weight: 20.0000 chunk 158 optimal weight: 0.9980 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 155 HIS A 407 GLN ** A 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 805 ASN ** A 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** B 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.4451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 15769 Z= 0.311 Angle : 0.764 9.710 21328 Z= 0.393 Chirality : 0.048 0.227 2293 Planarity : 0.005 0.047 2760 Dihedral : 5.456 26.335 2050 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.19), residues: 1878 helix: 0.43 (0.18), residues: 814 sheet: -0.65 (0.27), residues: 347 loop : -1.75 (0.22), residues: 717 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 216 time to evaluate : 1.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 216 average time/residue: 0.2953 time to fit residues: 96.5009 Evaluate side-chains 159 residues out of total 1682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 1.745 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 45 optimal weight: 7.9990 chunk 137 optimal weight: 10.0000 chunk 22 optimal weight: 7.9990 chunk 41 optimal weight: 8.9990 chunk 149 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 chunk 153 optimal weight: 4.9990 chunk 18 optimal weight: 0.0770 chunk 27 optimal weight: 10.0000 chunk 131 optimal weight: 7.9990 chunk 8 optimal weight: 5.9990 overall best weight: 4.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 680 GLN A 732 ASN A 851 GLN ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.143897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.120686 restraints weight = 43681.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.122300 restraints weight = 27741.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.122928 restraints weight = 18146.789| |-----------------------------------------------------------------------------| r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 moved from start: 0.4648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 15769 Z= 0.290 Angle : 0.735 9.725 21328 Z= 0.379 Chirality : 0.047 0.269 2293 Planarity : 0.005 0.048 2760 Dihedral : 5.487 25.772 2050 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.19), residues: 1878 helix: 0.29 (0.17), residues: 816 sheet: -0.56 (0.28), residues: 333 loop : -1.85 (0.22), residues: 729 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2854.75 seconds wall clock time: 53 minutes 13.42 seconds (3193.42 seconds total)