Starting phenix.real_space_refine (version: 1.21rc1) on Wed Jul 5 22:58:35 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jd2_36173/07_2023/8jd2_36173.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jd2_36173/07_2023/8jd2_36173.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jd2_36173/07_2023/8jd2_36173.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jd2_36173/07_2023/8jd2_36173.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jd2_36173/07_2023/8jd2_36173.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jd2_36173/07_2023/8jd2_36173.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.048 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 70 5.16 5 C 6749 2.51 5 N 1885 2.21 5 O 2026 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "2 ASP 95": "OD1" <-> "OD2" Residue "2 ASP 179": "OD1" <-> "OD2" Residue "2 TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 218": "OE1" <-> "OE2" Residue "2 GLU 277": "OE1" <-> "OE2" Residue "2 PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 373": "OE1" <-> "OE2" Residue "2 ASP 429": "OD1" <-> "OD2" Residue "2 PHE 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ASP 481": "OD1" <-> "OD2" Residue "3 TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 219": "OE1" <-> "OE2" Residue "3 ASP 221": "OD1" <-> "OD2" Residue "3 GLU 228": "OE1" <-> "OE2" Residue "3 GLU 231": "OE1" <-> "OE2" Residue "3 PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ASP 334": "OD1" <-> "OD2" Residue "3 ASP 380": "OD1" <-> "OD2" Residue "3 GLU 385": "OE1" <-> "OE2" Residue "3 PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 488": "OE1" <-> "OE2" Residue "3 GLU 1001": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 10730 Number of models: 1 Model: "" Number of chains: 4 Chain: "2" Number of atoms: 5258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 5258 Classifications: {'peptide': 750} Incomplete info: {'truncation_to_alanine': 154} Link IDs: {'PTRANS': 34, 'TRANS': 715} Chain breaks: 3 Unresolved non-hydrogen bonds: 617 Unresolved non-hydrogen angles: 795 Unresolved non-hydrogen dihedrals: 518 Unresolved non-hydrogen chiralities: 60 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 4, 'TYR:plan': 11, 'ASN:plan1': 7, 'TRP:plan': 2, 'HIS:plan': 4, 'PHE:plan': 12, 'GLU:plan': 13, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 362 Chain: "3" Number of atoms: 5424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 749, 5424 Classifications: {'peptide': 749} Incomplete info: {'truncation_to_alanine': 131} Link IDs: {'PTRANS': 29, 'TRANS': 719} Chain breaks: 3 Unresolved non-hydrogen bonds: 547 Unresolved non-hydrogen angles: 695 Unresolved non-hydrogen dihedrals: 476 Unresolved non-hydrogen chiralities: 46 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 6, 'TYR:plan': 8, 'ASN:plan1': 7, 'TRP:plan': 3, 'HIS:plan': 3, 'PHE:plan': 13, 'GLU:plan': 10, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 294 Chain: "2" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'NAG': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "3" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'NAG': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.68, per 1000 atoms: 0.53 Number of scatterers: 10730 At special positions: 0 Unit cell: (106.029, 93.177, 177.786, 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 70 16.00 O 2026 8.00 N 1885 7.00 C 6749 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS 2 50 " - pdb=" SG CYS 2 92 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 234 " - pdb=" SG CYS 2 518 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 355 " - pdb=" SG CYS 2 362 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 400 " - pdb=" SG CYS 2 407 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 500 " - pdb=" SG CYS 2 519 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 504 " - pdb=" SG CYS 2 522 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 525 " - pdb=" SG CYS 2 537 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 540 " - pdb=" SG CYS 2 553 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 632 " - pdb=" SG CYS 2 721 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 57 " - pdb=" SG CYS 3 99 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 240 " - pdb=" SG CYS 3 527 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 361 " - pdb=" SG CYS 3 373 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 412 " - pdb=" SG CYS 3 419 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 509 " - pdb=" SG CYS 3 528 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 513 " - pdb=" SG CYS 3 531 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 534 " - pdb=" SG CYS 3 546 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 549 " - pdb=" SG CYS 3 562 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 641 " - pdb=" SG CYS 3 730 " 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=0, symmetry=0 Links applied NAG-ASN " NAG 21102 " - " ASN 2 203 " " NAG 31002 " - " ASN 3 209 " Time building additional restraints: 4.20 Conformation dependent library (CDL) restraints added in 1.7 seconds 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2816 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 11 sheets defined 46.9% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain '2' and resid 58 through 74 Processing helix chain '2' and resid 94 through 108 removed outlier: 4.348A pdb=" N ASP 2 104 " --> pdb=" O GLU 2 100 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N PHE 2 105 " --> pdb=" O GLN 2 101 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL 2 106 " --> pdb=" O ALA 2 102 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA 2 108 " --> pdb=" O ASP 2 104 " (cutoff:3.500A) Processing helix chain '2' and resid 144 through 156 Processing helix chain '2' and resid 169 through 174 removed outlier: 3.512A pdb=" N LEU 2 172 " --> pdb=" O SER 2 169 " (cutoff:3.500A) Processing helix chain '2' and resid 187 through 202 removed outlier: 3.880A pdb=" N GLN 2 191 " --> pdb=" O PRO 2 187 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LYS 2 193 " --> pdb=" O PHE 2 189 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE 2 202 " --> pdb=" O ILE 2 198 " (cutoff:3.500A) Processing helix chain '2' and resid 215 through 231 removed outlier: 4.037A pdb=" N THR 2 219 " --> pdb=" O ASP 2 215 " (cutoff:3.500A) Processing helix chain '2' and resid 246 through 259 Processing helix chain '2' and resid 271 through 285 Processing helix chain '2' and resid 324 through 333 Processing helix chain '2' and resid 344 through 353 Processing helix chain '2' and resid 375 through 377 No H-bonds generated for 'chain '2' and resid 375 through 377' Processing helix chain '2' and resid 378 through 400 Processing helix chain '2' and resid 414 through 422 removed outlier: 3.654A pdb=" N LEU 2 418 " --> pdb=" O ASN 2 414 " (cutoff:3.500A) Processing helix chain '2' and resid 482 through 485 Processing helix chain '2' and resid 489 through 493 Processing helix chain '2' and resid 568 through 593 Processing helix chain '2' and resid 604 through 624 removed outlier: 3.745A pdb=" N GLY 2 611 " --> pdb=" O TYR 2 607 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N CYS 2 618 " --> pdb=" O PHE 2 614 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N THR 2 620 " --> pdb=" O CYS 2 616 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N PHE 2 621 " --> pdb=" O TYR 2 617 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE 2 622 " --> pdb=" O CYS 2 618 " (cutoff:3.500A) Processing helix chain '2' and resid 631 through 657 removed outlier: 3.953A pdb=" N ARG 2 635 " --> pdb=" O VAL 2 631 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ARG 2 636 " --> pdb=" O CYS 2 632 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU 2 637 " --> pdb=" O THR 2 633 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLY 2 640 " --> pdb=" O ARG 2 636 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR 2 641 " --> pdb=" O LEU 2 637 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE 2 643 " --> pdb=" O LEU 2 639 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N CYS 2 646 " --> pdb=" O ALA 2 642 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU 2 650 " --> pdb=" O CYS 2 646 " (cutoff:3.500A) Processing helix chain '2' and resid 678 through 702 removed outlier: 3.753A pdb=" N GLN 2 690 " --> pdb=" O LEU 2 686 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ILE 2 693 " --> pdb=" O GLY 2 689 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL 2 694 " --> pdb=" O GLN 2 690 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N VAL 2 700 " --> pdb=" O ALA 2 696 " (cutoff:3.500A) Processing helix chain '2' and resid 721 through 750 removed outlier: 3.591A pdb=" N ASP 2 725 " --> pdb=" O CYS 2 721 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N MET 2 728 " --> pdb=" O ARG 2 724 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N LEU 2 729 " --> pdb=" O ASP 2 725 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU 2 737 " --> pdb=" O ALA 2 733 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU 2 738 " --> pdb=" O TYR 2 734 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR 2 745 " --> pdb=" O LEU 2 741 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA 2 746 " --> pdb=" O CYS 2 742 " (cutoff:3.500A) Processing helix chain '2' and resid 755 through 775 Processing helix chain '2' and resid 775 through 784 removed outlier: 3.855A pdb=" N ILE 2 779 " --> pdb=" O ALA 2 775 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR 2 781 " --> pdb=" O LEU 2 777 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL 2 782 " --> pdb=" O PRO 2 778 " (cutoff:3.500A) Processing helix chain '2' and resid 790 through 810 removed outlier: 3.968A pdb=" N MET 2 794 " --> pdb=" O GLN 2 790 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE 2 810 " --> pdb=" O LEU 2 806 " (cutoff:3.500A) Processing helix chain '3' and resid 61 through 66 removed outlier: 3.602A pdb=" N ILE 3 66 " --> pdb=" O GLU 3 62 " (cutoff:3.500A) Processing helix chain '3' and resid 66 through 81 Processing helix chain '3' and resid 101 through 115 removed outlier: 3.712A pdb=" N GLU 3 107 " --> pdb=" O THR 3 103 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLU 3 111 " --> pdb=" O GLU 3 107 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N PHE 3 112 " --> pdb=" O GLN 3 108 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL 3 113 " --> pdb=" O SER 3 109 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ALA 3 115 " --> pdb=" O GLU 3 111 " (cutoff:3.500A) Processing helix chain '3' and resid 150 through 162 removed outlier: 3.559A pdb=" N LEU 3 160 " --> pdb=" O GLN 3 156 " (cutoff:3.500A) Processing helix chain '3' and resid 175 through 180 Processing helix chain '3' and resid 193 through 208 removed outlier: 4.012A pdb=" N GLN 3 197 " --> pdb=" O PRO 3 193 " (cutoff:3.500A) Processing helix chain '3' and resid 222 through 237 removed outlier: 3.685A pdb=" N LEU 3 236 " --> pdb=" O GLN 3 232 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG 3 237 " --> pdb=" O GLU 3 233 " (cutoff:3.500A) Processing helix chain '3' and resid 252 through 264 Processing helix chain '3' and resid 277 through 290 Processing helix chain '3' and resid 313 through 318 removed outlier: 3.735A pdb=" N ALA 3 317 " --> pdb=" O SER 3 313 " (cutoff:3.500A) Processing helix chain '3' and resid 330 through 338 removed outlier: 3.598A pdb=" N ARG 3 335 " --> pdb=" O ARG 3 331 " (cutoff:3.500A) Processing helix chain '3' and resid 350 through 359 Processing helix chain '3' and resid 387 through 389 No H-bonds generated for 'chain '3' and resid 387 through 389' Processing helix chain '3' and resid 390 through 412 removed outlier: 3.521A pdb=" N THR 3 410 " --> pdb=" O LYS 3 406 " (cutoff:3.500A) Processing helix chain '3' and resid 419 through 423 Processing helix chain '3' and resid 426 through 434 Processing helix chain '3' and resid 449 through 451 No H-bonds generated for 'chain '3' and resid 449 through 451' Processing helix chain '3' and resid 494 through 497 Processing helix chain '3' and resid 574 through 597 removed outlier: 4.297A pdb=" N GLY 3 579 " --> pdb=" O ALA 3 575 " (cutoff:3.500A) Proline residue: 3 580 - end of helix removed outlier: 3.525A pdb=" N LEU 3 586 " --> pdb=" O THR 3 582 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N CYS 3 592 " --> pdb=" O PHE 3 588 " (cutoff:3.500A) Processing helix chain '3' and resid 614 through 622 Processing helix chain '3' and resid 622 through 633 removed outlier: 3.582A pdb=" N PHE 3 630 " --> pdb=" O TYR 3 626 " (cutoff:3.500A) Processing helix chain '3' and resid 639 through 664 removed outlier: 3.833A pdb=" N LEU 3 643 " --> pdb=" O VAL 3 639 " (cutoff:3.500A) Processing helix chain '3' and resid 690 through 702 removed outlier: 3.547A pdb=" N VAL 3 701 " --> pdb=" O LEU 3 697 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N MET 3 702 " --> pdb=" O VAL 3 698 " (cutoff:3.500A) Processing helix chain '3' and resid 734 through 757 removed outlier: 3.887A pdb=" N LEU 3 738 " --> pdb=" O ASP 3 734 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU 3 750 " --> pdb=" O ILE 3 746 " (cutoff:3.500A) Processing helix chain '3' and resid 766 through 783 removed outlier: 3.712A pdb=" N PHE 3 770 " --> pdb=" O ASN 3 766 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY 3 772 " --> pdb=" O ALA 3 768 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE 3 780 " --> pdb=" O TYR 3 776 " (cutoff:3.500A) Processing helix chain '3' and resid 795 through 827 removed outlier: 3.535A pdb=" N CYS 3 817 " --> pdb=" O VAL 3 813 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA 3 820 " --> pdb=" O GLY 3 816 " (cutoff:3.500A) Proline residue: 3 821 - end of helix Processing sheet with id=AA1, first strand: chain '2' and resid 26 through 28 removed outlier: 3.712A pdb=" N ALA 2 86 " --> pdb=" O LEU 2 28 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU 2 32 " --> pdb=" O GLY 2 85 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N HIS 2 87 " --> pdb=" O LEU 2 32 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU 2 34 " --> pdb=" O HIS 2 87 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N LEU 2 89 " --> pdb=" O LEU 2 34 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N GLY 2 36 " --> pdb=" O LEU 2 89 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL 2 33 " --> pdb=" O GLY 2 138 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N ILE 2 140 " --> pdb=" O VAL 2 33 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N GLY 2 35 " --> pdb=" O ILE 2 140 " (cutoff:3.500A) removed outlier: 8.445A pdb=" N ILE 2 163 " --> pdb=" O THR 2 137 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N VAL 2 139 " --> pdb=" O ILE 2 163 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N GLN 2 162 " --> pdb=" O ALA 2 182 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '2' and resid 41 through 43 removed outlier: 4.705A pdb=" N GLN 2 42 " --> pdb=" O GLY 2 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '2' and resid 234 through 241 removed outlier: 6.255A pdb=" N VAL 2 207 " --> pdb=" O VAL 2 235 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N THR 2 237 " --> pdb=" O VAL 2 207 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N TYR 2 206 " --> pdb=" O VAL 2 265 " (cutoff:3.500A) removed outlier: 8.407A pdb=" N VAL 2 267 " --> pdb=" O TYR 2 206 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N SER 2 208 " --> pdb=" O VAL 2 267 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N PHE 2 269 " --> pdb=" O SER 2 208 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N VAL 2 210 " --> pdb=" O PHE 2 269 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N TRP 2 291 " --> pdb=" O ILE 2 315 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N ILE 2 317 " --> pdb=" O TRP 2 291 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ALA 2 293 " --> pdb=" O ILE 2 317 " (cutoff:3.500A) removed outlier: 9.161A pdb=" N LEU 2 319 " --> pdb=" O ALA 2 293 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N TYR 2 453 " --> pdb=" O TYR 2 473 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N TYR 2 473 " --> pdb=" O TYR 2 453 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE 2 455 " --> pdb=" O VAL 2 471 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR 2 473 " --> pdb=" O THR 2 479 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR 2 479 " --> pdb=" O TYR 2 473 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '2' and resid 427 through 429 removed outlier: 3.680A pdb=" N PHE 2 428 " --> pdb=" O VAL 2 441 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '3' and resid 33 through 35 removed outlier: 6.292A pdb=" N LEU 3 39 " --> pdb=" O GLY 3 92 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N HIS 3 94 " --> pdb=" O LEU 3 39 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU 3 41 " --> pdb=" O HIS 3 94 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N LEU 3 96 " --> pdb=" O LEU 3 41 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N GLY 3 43 " --> pdb=" O LEU 3 96 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL 3 40 " --> pdb=" O ILE 3 142 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLY 3 144 " --> pdb=" O VAL 3 40 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '3' and resid 169 through 170 Processing sheet with id=AA7, first strand: chain '3' and resid 240 through 247 removed outlier: 7.872A pdb=" N VAL 3 213 " --> pdb=" O ALA 3 242 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ALA 3 244 " --> pdb=" O VAL 3 213 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N THR 3 215 " --> pdb=" O ALA 3 244 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N LYS 3 246 " --> pdb=" O THR 3 215 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ALA 3 217 " --> pdb=" O LYS 3 246 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N TYR 3 212 " --> pdb=" O VAL 3 271 " (cutoff:3.500A) removed outlier: 8.487A pdb=" N VAL 3 273 " --> pdb=" O TYR 3 212 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N SER 3 214 " --> pdb=" O VAL 3 273 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N PHE 3 275 " --> pdb=" O SER 3 214 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL 3 216 " --> pdb=" O PHE 3 275 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N TRP 3 297 " --> pdb=" O ILE 3 321 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N LEU 3 323 " --> pdb=" O TRP 3 297 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ALA 3 299 " --> pdb=" O LEU 3 323 " (cutoff:3.500A) removed outlier: 9.068A pdb=" N LEU 3 325 " --> pdb=" O ALA 3 299 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ASN 3 470 " --> pdb=" O LYS 3 482 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N LYS 3 482 " --> pdb=" O ASN 3 470 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N GLN 3 472 " --> pdb=" O TYR 3 480 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N TYR 3 480 " --> pdb=" O GLN 3 472 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N VAL 3 474 " --> pdb=" O TYR 3 478 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N TYR 3 478 " --> pdb=" O VAL 3 474 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '3' and resid 440 through 441 removed outlier: 3.503A pdb=" N PHE 3 440 " --> pdb=" O VAL 3 454 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain '3' and resid 518 through 521 removed outlier: 3.798A pdb=" N LYS 3 519 " --> pdb=" O ILE 3 532 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain '3' and resid 539 through 540 removed outlier: 3.600A pdb=" N TYR 3 539 " --> pdb=" O MET 3 547 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain '3' and resid 553 through 555 492 hydrogen bonds defined for protein. 1431 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: 3.37 Time building geometry restraints manager: 4.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3626 1.34 - 1.46: 2514 1.46 - 1.58: 4713 1.58 - 1.70: 1 1.70 - 1.82: 88 Bond restraints: 10942 Sorted by residual: bond pdb=" CG PRO 3 512 " pdb=" CD PRO 3 512 " ideal model delta sigma weight residual 1.503 1.589 -0.086 3.40e-02 8.65e+02 6.46e+00 bond pdb=" CB PRO 3 512 " pdb=" CG PRO 3 512 " ideal model delta sigma weight residual 1.492 1.571 -0.079 5.00e-02 4.00e+02 2.53e+00 bond pdb=" C GLU 31001 " pdb=" O GLU 31001 " ideal model delta sigma weight residual 1.231 1.259 -0.028 2.00e-02 2.50e+03 1.93e+00 bond pdb=" C GLU 21101 " pdb=" O GLU 21101 " ideal model delta sigma weight residual 1.231 1.259 -0.028 2.00e-02 2.50e+03 1.92e+00 bond pdb=" C GLU 31001 " pdb=" OXT GLU 31001 " ideal model delta sigma weight residual 1.231 1.258 -0.027 2.00e-02 2.50e+03 1.86e+00 ... (remaining 10937 not shown) Histogram of bond angle deviations from ideal: 100.51 - 107.20: 333 107.20 - 113.90: 6107 113.90 - 120.60: 4409 120.60 - 127.29: 3980 127.29 - 133.99: 108 Bond angle restraints: 14937 Sorted by residual: angle pdb=" CA PRO 3 512 " pdb=" N PRO 3 512 " pdb=" CD PRO 3 512 " ideal model delta sigma weight residual 112.00 104.95 7.05 1.40e+00 5.10e-01 2.53e+01 angle pdb=" N VAL 2 597 " pdb=" CA VAL 2 597 " pdb=" C VAL 2 597 " ideal model delta sigma weight residual 113.53 110.56 2.97 9.80e-01 1.04e+00 9.19e+00 angle pdb=" C PRO 2 546 " pdb=" N ASN 2 547 " pdb=" CA ASN 2 547 " ideal model delta sigma weight residual 121.54 126.10 -4.56 1.91e+00 2.74e-01 5.70e+00 angle pdb=" CA VAL 3 639 " pdb=" C VAL 3 639 " pdb=" N ILE 3 640 " ideal model delta sigma weight residual 116.60 119.81 -3.21 1.45e+00 4.76e-01 4.89e+00 angle pdb=" CA VAL 2 597 " pdb=" C VAL 2 597 " pdb=" N VAL 2 598 " ideal model delta sigma weight residual 119.31 116.80 2.51 1.15e+00 7.56e-01 4.78e+00 ... (remaining 14932 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 5975 17.80 - 35.61: 428 35.61 - 53.41: 93 53.41 - 71.21: 19 71.21 - 89.02: 14 Dihedral angle restraints: 6529 sinusoidal: 2181 harmonic: 4348 Sorted by residual: dihedral pdb=" CB CYS 2 500 " pdb=" SG CYS 2 500 " pdb=" SG CYS 2 519 " pdb=" CB CYS 2 519 " ideal model delta sinusoidal sigma weight residual 93.00 10.10 82.90 1 1.00e+01 1.00e-02 8.41e+01 dihedral pdb=" CB CYS 3 240 " pdb=" SG CYS 3 240 " pdb=" SG CYS 3 527 " pdb=" CB CYS 3 527 " ideal model delta sinusoidal sigma weight residual 93.00 14.08 78.92 1 1.00e+01 1.00e-02 7.76e+01 dihedral pdb=" CB CYS 3 534 " pdb=" SG CYS 3 534 " pdb=" SG CYS 3 546 " pdb=" CB CYS 3 546 " ideal model delta sinusoidal sigma weight residual -86.00 -164.34 78.34 1 1.00e+01 1.00e-02 7.66e+01 ... (remaining 6526 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1559 0.062 - 0.124: 178 0.124 - 0.186: 3 0.186 - 0.247: 1 0.247 - 0.309: 1 Chirality restraints: 1742 Sorted by residual: chirality pdb=" C1 NAG 31002 " pdb=" ND2 ASN 3 209 " pdb=" C2 NAG 31002 " pdb=" O5 NAG 31002 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.39e+00 chirality pdb=" C1 NAG 21102 " pdb=" ND2 ASN 2 203 " pdb=" C2 NAG 21102 " pdb=" O5 NAG 21102 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 9.57e-01 chirality pdb=" C4 NAG 21102 " pdb=" C3 NAG 21102 " pdb=" C5 NAG 21102 " pdb=" O4 NAG 21102 " both_signs ideal model delta sigma weight residual False -2.53 -2.39 -0.14 2.00e-01 2.50e+01 4.93e-01 ... (remaining 1739 not shown) Planarity restraints: 1960 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP 3 511 " 0.071 5.00e-02 4.00e+02 1.04e-01 1.72e+01 pdb=" N PRO 3 512 " -0.179 5.00e-02 4.00e+02 pdb=" CA PRO 3 512 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO 3 512 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG 2 411 " 0.050 5.00e-02 4.00e+02 7.66e-02 9.39e+00 pdb=" N PRO 2 412 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO 2 412 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO 2 412 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY 2 570 " 0.027 5.00e-02 4.00e+02 4.07e-02 2.65e+00 pdb=" N PRO 2 571 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO 2 571 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO 2 571 " 0.023 5.00e-02 4.00e+02 ... (remaining 1957 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1224 2.75 - 3.29: 10401 3.29 - 3.83: 17679 3.83 - 4.36: 20514 4.36 - 4.90: 35220 Nonbonded interactions: 85038 Sorted by model distance: nonbonded pdb=" O4 NAG 21102 " pdb=" O7 NAG 21102 " model vdw 2.213 2.440 nonbonded pdb=" O4 NAG 31002 " pdb=" O7 NAG 31002 " model vdw 2.225 2.440 nonbonded pdb=" O TYR 3 212 " pdb=" OG SER 3 507 " model vdw 2.268 2.440 nonbonded pdb=" O ALA 2 170 " pdb=" OG SER 2 173 " model vdw 2.286 2.440 nonbonded pdb=" O MET 3 593 " pdb=" OG1 THR 3 596 " model vdw 2.286 2.440 ... (remaining 85033 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.770 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: 11.070 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 30.250 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.050 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:12.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.086 10942 Z= 0.144 Angle : 0.437 7.049 14937 Z= 0.233 Chirality : 0.040 0.309 1742 Planarity : 0.004 0.104 1958 Dihedral : 13.328 89.017 3659 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer Outliers : 0.20 % 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: -0.38 (0.22), residues: 1483 helix: 1.38 (0.21), residues: 624 sheet: -0.85 (0.40), residues: 172 loop : -1.69 (0.23), residues: 687 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 111 time to evaluate : 1.130 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 112 average time/residue: 1.1156 time to fit residues: 136.3821 Evaluate side-chains 109 residues out of total 1275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 1.178 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 125 optimal weight: 10.0000 chunk 112 optimal weight: 2.9990 chunk 62 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 76 optimal weight: 0.0970 chunk 60 optimal weight: 8.9990 chunk 116 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 71 optimal weight: 0.0040 chunk 86 optimal weight: 1.9990 chunk 135 optimal weight: 10.0000 overall best weight: 1.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 283 GLN 3 470 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.069 10942 Z= 0.391 Angle : 0.610 7.614 14937 Z= 0.325 Chirality : 0.046 0.226 1742 Planarity : 0.005 0.051 1958 Dihedral : 4.503 36.241 1604 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer Outliers : 2.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.22), residues: 1483 helix: 1.31 (0.20), residues: 635 sheet: -1.23 (0.36), residues: 194 loop : -1.96 (0.23), residues: 654 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 116 time to evaluate : 1.185 Fit side-chains outliers start: 23 outliers final: 12 residues processed: 132 average time/residue: 1.1335 time to fit residues: 163.2499 Evaluate side-chains 118 residues out of total 1275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 106 time to evaluate : 1.159 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 10 residues processed: 2 average time/residue: 0.1625 time to fit residues: 2.1082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 75 optimal weight: 0.8980 chunk 41 optimal weight: 0.5980 chunk 112 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 135 optimal weight: 6.9990 chunk 146 optimal weight: 20.0000 chunk 120 optimal weight: 4.9990 chunk 134 optimal weight: 0.9980 chunk 46 optimal weight: 7.9990 chunk 108 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 338 ASN 3 485 HIS 3 495 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 10942 Z= 0.239 Angle : 0.506 8.031 14937 Z= 0.266 Chirality : 0.042 0.235 1742 Planarity : 0.004 0.039 1958 Dihedral : 4.213 33.646 1604 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer Outliers : 3.03 % 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: -0.47 (0.22), residues: 1483 helix: 1.58 (0.21), residues: 642 sheet: -1.23 (0.36), residues: 189 loop : -2.04 (0.23), residues: 652 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 109 time to evaluate : 1.288 Fit side-chains outliers start: 30 outliers final: 17 residues processed: 132 average time/residue: 1.2409 time to fit residues: 177.3896 Evaluate side-chains 123 residues out of total 1275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 106 time to evaluate : 1.140 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 14 residues processed: 3 average time/residue: 0.1915 time to fit residues: 2.4494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 133 optimal weight: 10.0000 chunk 101 optimal weight: 0.6980 chunk 70 optimal weight: 6.9990 chunk 15 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 chunk 91 optimal weight: 0.5980 chunk 136 optimal weight: 2.9990 chunk 144 optimal weight: 6.9990 chunk 71 optimal weight: 7.9990 chunk 128 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 390 HIS 3 485 HIS 3 495 ASN 3 508 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.061 10942 Z= 0.384 Angle : 0.584 7.832 14937 Z= 0.306 Chirality : 0.045 0.223 1742 Planarity : 0.004 0.038 1958 Dihedral : 4.593 38.025 1604 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer Outliers : 3.64 % 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: -0.59 (0.22), residues: 1483 helix: 1.52 (0.21), residues: 639 sheet: -1.31 (0.35), residues: 189 loop : -2.14 (0.23), residues: 655 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 112 time to evaluate : 1.176 Fit side-chains outliers start: 36 outliers final: 23 residues processed: 139 average time/residue: 1.1339 time to fit residues: 171.8485 Evaluate side-chains 131 residues out of total 1275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 108 time to evaluate : 1.250 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 18 residues processed: 5 average time/residue: 0.2024 time to fit residues: 3.1530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 119 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 59 optimal weight: 20.0000 chunk 122 optimal weight: 0.8980 chunk 99 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 73 optimal weight: 7.9990 chunk 129 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 360 GLN 3 473 ASN 3 485 HIS 3 495 ASN 3 508 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.051 10942 Z= 0.315 Angle : 0.551 7.325 14937 Z= 0.289 Chirality : 0.044 0.231 1742 Planarity : 0.004 0.037 1958 Dihedral : 4.508 35.861 1604 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer Outliers : 4.55 % 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: -0.57 (0.22), residues: 1483 helix: 1.50 (0.21), residues: 647 sheet: -1.29 (0.35), residues: 189 loop : -2.13 (0.23), residues: 647 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 108 time to evaluate : 1.169 Fit side-chains outliers start: 45 outliers final: 29 residues processed: 141 average time/residue: 1.0796 time to fit residues: 166.2884 Evaluate side-chains 138 residues out of total 1275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 109 time to evaluate : 1.189 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 23 residues processed: 6 average time/residue: 0.4951 time to fit residues: 5.1828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 48 optimal weight: 3.9990 chunk 129 optimal weight: 7.9990 chunk 28 optimal weight: 0.7980 chunk 84 optimal weight: 0.0050 chunk 35 optimal weight: 3.9990 chunk 144 optimal weight: 8.9990 chunk 119 optimal weight: 0.7980 chunk 66 optimal weight: 6.9990 chunk 11 optimal weight: 0.7980 chunk 47 optimal weight: 0.0000 chunk 75 optimal weight: 0.8980 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 414 ASN 3 473 ASN 3 485 HIS 3 495 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 10942 Z= 0.175 Angle : 0.480 7.359 14937 Z= 0.251 Chirality : 0.041 0.241 1742 Planarity : 0.003 0.038 1958 Dihedral : 4.169 30.991 1604 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer Outliers : 3.54 % 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: -0.31 (0.22), residues: 1483 helix: 1.80 (0.21), residues: 644 sheet: -1.04 (0.37), residues: 182 loop : -2.11 (0.23), residues: 657 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 113 time to evaluate : 1.200 Fit side-chains outliers start: 35 outliers final: 31 residues processed: 143 average time/residue: 1.0841 time to fit residues: 170.1008 Evaluate side-chains 138 residues out of total 1275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 107 time to evaluate : 1.176 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 26 residues processed: 5 average time/residue: 0.1949 time to fit residues: 3.0884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 138 optimal weight: 0.0370 chunk 16 optimal weight: 2.9990 chunk 82 optimal weight: 0.0370 chunk 105 optimal weight: 0.6980 chunk 81 optimal weight: 0.9980 chunk 121 optimal weight: 6.9990 chunk 80 optimal weight: 0.9990 chunk 143 optimal weight: 0.0570 chunk 89 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 66 optimal weight: 20.0000 overall best weight: 0.3654 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 414 ASN 3 473 ASN 3 485 HIS 3 495 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 10942 Z= 0.155 Angle : 0.469 7.166 14937 Z= 0.244 Chirality : 0.041 0.235 1742 Planarity : 0.003 0.038 1958 Dihedral : 3.968 27.949 1604 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer Outliers : 3.64 % 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: -0.17 (0.22), residues: 1483 helix: 1.95 (0.21), residues: 644 sheet: -0.94 (0.38), residues: 182 loop : -2.10 (0.23), residues: 657 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 117 time to evaluate : 1.211 Fit side-chains revert: symmetry clash outliers start: 36 outliers final: 28 residues processed: 146 average time/residue: 0.9857 time to fit residues: 158.6131 Evaluate side-chains 142 residues out of total 1275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 114 time to evaluate : 1.075 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 23 residues processed: 5 average time/residue: 0.1794 time to fit residues: 2.8087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 88 optimal weight: 0.1980 chunk 57 optimal weight: 10.0000 chunk 85 optimal weight: 1.9990 chunk 43 optimal weight: 0.0050 chunk 28 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 97 optimal weight: 0.5980 chunk 71 optimal weight: 0.4980 chunk 13 optimal weight: 0.6980 chunk 112 optimal weight: 0.8980 overall best weight: 0.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 414 ASN 3 473 ASN 3 485 HIS 3 495 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 10942 Z= 0.159 Angle : 0.471 7.116 14937 Z= 0.245 Chirality : 0.041 0.233 1742 Planarity : 0.003 0.038 1958 Dihedral : 3.945 27.450 1604 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer Outliers : 3.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.22), residues: 1483 helix: 2.02 (0.21), residues: 644 sheet: -0.83 (0.38), residues: 180 loop : -2.08 (0.23), residues: 659 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 115 time to evaluate : 1.229 Fit side-chains revert: symmetry clash outliers start: 33 outliers final: 26 residues processed: 145 average time/residue: 1.0383 time to fit residues: 165.4911 Evaluate side-chains 138 residues out of total 1275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 112 time to evaluate : 1.250 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 25 residues processed: 1 average time/residue: 0.1605 time to fit residues: 1.9189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 130 optimal weight: 20.0000 chunk 137 optimal weight: 10.0000 chunk 125 optimal weight: 0.9990 chunk 133 optimal weight: 0.0770 chunk 80 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 120 optimal weight: 0.2980 chunk 126 optimal weight: 10.0000 chunk 87 optimal weight: 0.9990 overall best weight: 0.6542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 414 ASN 3 473 ASN 3 485 HIS 3 495 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 10942 Z= 0.212 Angle : 0.499 6.945 14937 Z= 0.261 Chirality : 0.042 0.223 1742 Planarity : 0.004 0.042 1958 Dihedral : 4.097 30.386 1604 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer Outliers : 3.54 % 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: -0.11 (0.22), residues: 1483 helix: 1.99 (0.21), residues: 645 sheet: -0.84 (0.38), residues: 180 loop : -2.08 (0.23), residues: 658 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 108 time to evaluate : 1.150 Fit side-chains revert: symmetry clash outliers start: 35 outliers final: 29 residues processed: 137 average time/residue: 1.0327 time to fit residues: 155.4075 Evaluate side-chains 138 residues out of total 1275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 109 time to evaluate : 1.157 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 25 residues processed: 4 average time/residue: 0.1820 time to fit residues: 2.8068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 141 optimal weight: 7.9990 chunk 86 optimal weight: 0.5980 chunk 67 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 chunk 148 optimal weight: 6.9990 chunk 136 optimal weight: 10.0000 chunk 118 optimal weight: 0.0070 chunk 12 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 72 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 overall best weight: 1.3204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 439 ASN 3 315 HIS 3 414 ASN 3 473 ASN 3 485 HIS 3 495 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.058 10942 Z= 0.361 Angle : 0.574 6.774 14937 Z= 0.302 Chirality : 0.045 0.210 1742 Planarity : 0.005 0.084 1958 Dihedral : 4.491 36.907 1604 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer Outliers : 3.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.22), residues: 1483 helix: 1.75 (0.21), residues: 650 sheet: -1.06 (0.36), residues: 189 loop : -2.13 (0.23), residues: 644 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 107 time to evaluate : 1.147 Fit side-chains outliers start: 33 outliers final: 28 residues processed: 134 average time/residue: 1.1431 time to fit residues: 167.6692 Evaluate side-chains 133 residues out of total 1275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 105 time to evaluate : 1.231 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 24 residues processed: 4 average time/residue: 0.1976 time to fit residues: 2.8594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 125 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 108 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 118 optimal weight: 0.4980 chunk 49 optimal weight: 20.0000 chunk 121 optimal weight: 7.9990 chunk 14 optimal weight: 0.9990 chunk 21 optimal weight: 0.3980 chunk 103 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 439 ASN 3 360 GLN 3 414 ASN 3 473 ASN 3 485 HIS 3 495 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.211726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.135699 restraints weight = 10893.160| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.27 r_work: 0.3170 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 10942 Z= 0.196 Angle : 0.500 7.081 14937 Z= 0.262 Chirality : 0.042 0.224 1742 Planarity : 0.004 0.042 1958 Dihedral : 4.215 32.643 1604 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer Outliers : 2.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.22), residues: 1483 helix: 1.88 (0.21), residues: 649 sheet: -0.91 (0.37), residues: 186 loop : -2.08 (0.23), residues: 648 =============================================================================== Job complete usr+sys time: 3745.69 seconds wall clock time: 67 minutes 47.33 seconds (4067.33 seconds total)