Starting phenix.real_space_refine (version: 1.21rc1) on Thu Jul 6 04:22:57 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jd0_36171/07_2023/8jd0_36171_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jd0_36171/07_2023/8jd0_36171.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jd0_36171/07_2023/8jd0_36171.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jd0_36171/07_2023/8jd0_36171.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jd0_36171/07_2023/8jd0_36171_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jd0_36171/07_2023/8jd0_36171_updated.pdb" } resolution = 3.3 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= 0.002 sd= 0.065 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 68 5.16 5 C 7210 2.51 5 N 1927 2.21 5 O 2056 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "2 GLU 100": "OE1" <-> "OE2" Residue "2 PHE 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 231": "OE1" <-> "OE2" Residue "3 ASP 279": "OD1" <-> "OD2" Residue "3 ASP 461": "OD1" <-> "OD2" Residue "3 PHE 630": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 11264 Number of models: 1 Model: "" Number of chains: 4 Chain: "2" Number of atoms: 5377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 766, 5377 Classifications: {'peptide': 766} Incomplete info: {'truncation_to_alanine': 162} Link IDs: {'PTRANS': 37, 'TRANS': 728} Chain breaks: 2 Unresolved non-hydrogen bonds: 625 Unresolved non-hydrogen angles: 800 Unresolved non-hydrogen dihedrals: 515 Unresolved non-hydrogen chiralities: 64 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 2, 'TYR:plan': 8, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 15, 'GLU:plan': 12, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 364 Chain: "3" Number of atoms: 5567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 765, 5567 Classifications: {'peptide': 765} Incomplete info: {'truncation_to_alanine': 135} Link IDs: {'PTRANS': 30, 'TRANS': 734} Chain breaks: 2 Unresolved non-hydrogen bonds: 518 Unresolved non-hydrogen angles: 657 Unresolved non-hydrogen dihedrals: 438 Unresolved non-hydrogen chiralities: 46 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 9, 'ASN:plan1': 10, 'TRP:plan': 2, 'ASP:plan': 7, 'PHE:plan': 9, 'GLU:plan': 9, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 277 Chain: "2" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 156 Unusual residues: {'CLR': 4, 'J9R': 1, 'NAG': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "3" Number of atoms: 164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 164 Unusual residues: {'CLR': 5, 'NAG': 1} Classifications: {'peptide': 1, 'undetermined': 6} Modifications used: {'COO': 1} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.93, per 1000 atoms: 0.53 Number of scatterers: 11264 At special positions: 0 Unit cell: (85.68, 116.739, 184.212, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 68 16.00 F 3 9.00 O 2056 8.00 N 1927 7.00 C 7210 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 21101 " - " ASN 2 203 " " NAG 31002 " - " ASN 3 209 " Time building additional restraints: 4.44 Conformation dependent library (CDL) restraints added in 1.8 seconds 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2876 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 46 helices and 7 sheets defined 44.1% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.44 Creating SS restraints... Processing helix chain '2' and resid 60 through 73 Processing helix chain '2' and resid 95 through 109 removed outlier: 3.823A pdb=" N ASP 2 104 " --> pdb=" O GLU 2 100 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N PHE 2 105 " --> pdb=" O GLN 2 101 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL 2 106 " --> pdb=" O ALA 2 102 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER 2 109 " --> pdb=" O PHE 2 105 " (cutoff:3.500A) Processing helix chain '2' and resid 145 through 156 removed outlier: 3.573A pdb=" N ILE 2 149 " --> pdb=" O SER 2 145 " (cutoff:3.500A) Processing helix chain '2' and resid 171 through 173 No H-bonds generated for 'chain '2' and resid 171 through 173' Processing helix chain '2' and resid 188 through 201 removed outlier: 3.718A pdb=" N GLN 2 191 " --> pdb=" O ASP 2 188 " (cutoff:3.500A) Processing helix chain '2' and resid 215 through 230 removed outlier: 5.002A pdb=" N ALA 2 223 " --> pdb=" O THR 2 219 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU 2 226 " --> pdb=" O GLU 2 222 " (cutoff:3.500A) Processing helix chain '2' and resid 247 through 258 Processing helix chain '2' and resid 272 through 285 Processing helix chain '2' and resid 301 through 304 No H-bonds generated for 'chain '2' and resid 301 through 304' Processing helix chain '2' and resid 327 through 332 Processing helix chain '2' and resid 343 through 352 removed outlier: 4.135A pdb=" N ARG 2 346 " --> pdb=" O PRO 2 343 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG 2 352 " --> pdb=" O TRP 2 349 " (cutoff:3.500A) Processing helix chain '2' and resid 376 through 399 removed outlier: 4.204A pdb=" N MET 2 379 " --> pdb=" O SER 2 376 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N PHE 2 380 " --> pdb=" O LYS 2 377 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA 2 398 " --> pdb=" O MET 2 395 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU 2 399 " --> pdb=" O HIS 2 396 " (cutoff:3.500A) Processing helix chain '2' and resid 408 through 410 No H-bonds generated for 'chain '2' and resid 408 through 410' Processing helix chain '2' and resid 415 through 420 Processing helix chain '2' and resid 423 through 425 No H-bonds generated for 'chain '2' and resid 423 through 425' Processing helix chain '2' and resid 517 through 519 No H-bonds generated for 'chain '2' and resid 517 through 519' Processing helix chain '2' and resid 565 through 567 No H-bonds generated for 'chain '2' and resid 565 through 567' Processing helix chain '2' and resid 569 through 591 Processing helix chain '2' and resid 595 through 599 removed outlier: 3.759A pdb=" N LYS 2 599 " --> pdb=" O THR 2 595 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 595 through 599' Processing helix chain '2' and resid 603 through 622 Processing helix chain '2' and resid 629 through 660 removed outlier: 3.923A pdb=" N GLY 2 640 " --> pdb=" O ARG 2 636 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N PHE 2 643 " --> pdb=" O LEU 2 639 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU 2 650 " --> pdb=" O CYS 2 646 " (cutoff:3.500A) Processing helix chain '2' and resid 676 through 699 removed outlier: 4.615A pdb=" N VAL 2 680 " --> pdb=" O PRO 2 676 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ALA 2 681 " --> pdb=" O ALA 2 677 " (cutoff:3.500A) Processing helix chain '2' and resid 725 through 747 removed outlier: 3.784A pdb=" N SER 2 731 " --> pdb=" O SER 2 727 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N TYR 2 734 " --> pdb=" O GLY 2 730 " (cutoff:3.500A) Processing helix chain '2' and resid 756 through 784 removed outlier: 3.632A pdb=" N LYS 2 760 " --> pdb=" O PHE 2 756 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLY 2 763 " --> pdb=" O ALA 2 759 " (cutoff:3.500A) Proline residue: 2 778 - end of helix Processing helix chain '2' and resid 788 through 819 removed outlier: 4.120A pdb=" N ALA 2 811 " --> pdb=" O GLY 2 807 " (cutoff:3.500A) Proline residue: 2 812 - end of helix Processing helix chain '3' and resid 66 through 80 Processing helix chain '3' and resid 102 through 112 removed outlier: 3.869A pdb=" N LEU 3 110 " --> pdb=" O LEU 3 106 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N GLU 3 111 " --> pdb=" O GLU 3 107 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N PHE 3 112 " --> pdb=" O GLN 3 108 " (cutoff:3.500A) Processing helix chain '3' and resid 114 through 116 No H-bonds generated for 'chain '3' and resid 114 through 116' Processing helix chain '3' and resid 151 through 164 removed outlier: 4.209A pdb=" N LEU 3 163 " --> pdb=" O ASN 3 159 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N PHE 3 164 " --> pdb=" O LEU 3 160 " (cutoff:3.500A) Processing helix chain '3' and resid 194 through 207 Processing helix chain '3' and resid 221 through 236 removed outlier: 4.128A pdb=" N THR 3 225 " --> pdb=" O ASP 3 221 " (cutoff:3.500A) Processing helix chain '3' and resid 255 through 264 Processing helix chain '3' and resid 278 through 290 removed outlier: 3.868A pdb=" N GLU 3 283 " --> pdb=" O ASP 3 279 " (cutoff:3.500A) Processing helix chain '3' and resid 331 through 338 Processing helix chain '3' and resid 349 through 358 removed outlier: 3.969A pdb=" N ARG 3 352 " --> pdb=" O PRO 3 349 " (cutoff:3.500A) Processing helix chain '3' and resid 388 through 411 removed outlier: 4.089A pdb=" N MET 3 391 " --> pdb=" O SER 3 388 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N PHE 3 392 " --> pdb=" O LYS 3 389 " (cutoff:3.500A) Processing helix chain '3' and resid 427 through 433 Processing helix chain '3' and resid 578 through 602 removed outlier: 3.944A pdb=" N PHE 3 598 " --> pdb=" O VAL 3 594 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE 3 599 " --> pdb=" O VAL 3 595 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N LYS 3 600 " --> pdb=" O THR 3 596 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N HIS 3 601 " --> pdb=" O VAL 3 597 " (cutoff:3.500A) Processing helix chain '3' and resid 612 through 633 removed outlier: 3.501A pdb=" N GLY 3 621 " --> pdb=" O ILE 3 617 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N THR 3 629 " --> pdb=" O SER 3 625 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N PHE 3 630 " --> pdb=" O TYR 3 626 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N PHE 3 631 " --> pdb=" O CYS 3 627 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE 3 632 " --> pdb=" O MET 3 628 " (cutoff:3.500A) Processing helix chain '3' and resid 638 through 663 removed outlier: 3.810A pdb=" N ALA 3 642 " --> pdb=" O PRO 3 638 " (cutoff:3.500A) Processing helix chain '3' and resid 682 through 701 removed outlier: 3.818A pdb=" N SER 3 686 " --> pdb=" O PHE 3 682 " (cutoff:3.500A) Processing helix chain '3' and resid 705 through 708 No H-bonds generated for 'chain '3' and resid 705 through 708' Processing helix chain '3' and resid 729 through 754 removed outlier: 4.135A pdb=" N ILE 3 739 " --> pdb=" O SER 3 735 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU 3 747 " --> pdb=" O TYR 3 743 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL 3 748 " --> pdb=" O ASP 3 744 " (cutoff:3.500A) Processing helix chain '3' and resid 762 through 790 removed outlier: 3.882A pdb=" N PHE 3 765 " --> pdb=" O PRO 3 762 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N ASN 3 766 " --> pdb=" O GLU 3 763 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR 3 777 " --> pdb=" O THR 3 774 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N CYS 3 779 " --> pdb=" O TYR 3 776 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE 3 780 " --> pdb=" O THR 3 777 " (cutoff:3.500A) Proline residue: 3 787 - end of helix removed outlier: 3.539A pdb=" N TYR 3 790 " --> pdb=" O PRO 3 787 " (cutoff:3.500A) Processing helix chain '3' and resid 799 through 818 removed outlier: 3.845A pdb=" N ILE 3 805 " --> pdb=" O THR 3 801 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N SER 3 806 " --> pdb=" O THR 3 802 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N VAL 3 807 " --> pdb=" O MET 3 803 " (cutoff:3.500A) Processing helix chain '3' and resid 820 through 827 removed outlier: 3.506A pdb=" N ILE 3 825 " --> pdb=" O PRO 3 821 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE 3 826 " --> pdb=" O LYS 3 822 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain '2' and resid 84 through 90 removed outlier: 6.580A pdb=" N LEU 2 32 " --> pdb=" O GLY 2 85 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N HIS 2 87 " --> pdb=" O LEU 2 32 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N LEU 2 34 " --> pdb=" O HIS 2 87 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N LEU 2 89 " --> pdb=" O LEU 2 34 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N GLY 2 36 " --> pdb=" O LEU 2 89 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N GLY 2 35 " --> pdb=" O THR 2 137 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N VAL 2 139 " --> pdb=" O GLY 2 35 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N LEU 2 37 " --> pdb=" O VAL 2 139 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain '2' and resid 162 through 164 Processing sheet with id= C, first strand: chain '2' and resid 265 through 268 removed outlier: 4.856A pdb=" N VAL 2 265 " --> pdb=" O TYR 2 206 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N CYS 2 234 " --> pdb=" O VAL 2 207 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N THR 2 209 " --> pdb=" O CYS 2 234 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N ALA 2 236 " --> pdb=" O THR 2 209 " (cutoff:3.500A) removed outlier: 11.753A pdb=" N ALA 2 211 " --> pdb=" O ALA 2 236 " (cutoff:3.500A) removed outlier: 9.440A pdb=" N SER 2 238 " --> pdb=" O ALA 2 211 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain '2' and resid 315 through 319 removed outlier: 3.937A pdb=" N ARG 2 467 " --> pdb=" O LEU 2 459 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain '3' and resid 91 through 97 removed outlier: 6.795A pdb=" N LEU 3 39 " --> pdb=" O GLY 3 92 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N HIS 3 94 " --> pdb=" O LEU 3 39 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N LEU 3 41 " --> pdb=" O HIS 3 94 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N LEU 3 96 " --> pdb=" O LEU 3 41 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N GLY 3 43 " --> pdb=" O LEU 3 96 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N GLY 3 42 " --> pdb=" O ALA 3 143 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N VAL 3 145 " --> pdb=" O GLY 3 42 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N LEU 3 44 " --> pdb=" O VAL 3 145 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain '3' and resid 244 through 247 removed outlier: 7.223A pdb=" N THR 3 215 " --> pdb=" O GLU 3 245 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N VAL 3 247 " --> pdb=" O THR 3 215 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ALA 3 217 " --> pdb=" O VAL 3 247 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER 3 214 " --> pdb=" O VAL 3 271 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL 3 216 " --> pdb=" O VAL 3 273 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE 3 275 " --> pdb=" O VAL 3 216 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N THR 3 296 " --> pdb=" O VAL 3 272 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N LEU 3 274 " --> pdb=" O THR 3 296 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL 3 298 " --> pdb=" O LEU 3 274 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain '3' and resid 321 through 325 removed outlier: 3.564A pdb=" N GLY 3 484 " --> pdb=" O VAL 3 468 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ASN 3 470 " --> pdb=" O LYS 3 482 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N LYS 3 482 " --> pdb=" O ASN 3 470 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N GLN 3 472 " --> pdb=" O TYR 3 480 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N TYR 3 480 " --> pdb=" O GLN 3 472 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL 3 474 " --> pdb=" O TYR 3 478 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N TYR 3 478 " --> pdb=" O VAL 3 474 " (cutoff:3.500A) 455 hydrogen bonds defined for protein. 1143 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: 3.05 Time building geometry restraints manager: 4.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1838 1.31 - 1.44: 3046 1.44 - 1.56: 6559 1.56 - 1.69: 1 1.69 - 1.81: 86 Bond restraints: 11530 Sorted by residual: bond pdb=" C10 J9R 21102 " pdb=" N3 J9R 21102 " ideal model delta sigma weight residual 1.448 1.261 0.187 2.00e-02 2.50e+03 8.70e+01 bond pdb=" C6 J9R 21102 " pdb=" N1 J9R 21102 " ideal model delta sigma weight residual 1.335 1.451 -0.116 2.00e-02 2.50e+03 3.38e+01 bond pdb=" C15 J9R 21102 " pdb=" N3 J9R 21102 " ideal model delta sigma weight residual 1.458 1.380 0.078 2.00e-02 2.50e+03 1.50e+01 bond pdb=" C2 J9R 21102 " pdb=" C3 J9R 21102 " ideal model delta sigma weight residual 1.459 1.526 -0.067 2.00e-02 2.50e+03 1.12e+01 bond pdb=" C11 J9R 21102 " pdb=" N3 J9R 21102 " ideal model delta sigma weight residual 1.448 1.385 0.063 2.00e-02 2.50e+03 1.01e+01 ... (remaining 11525 not shown) Histogram of bond angle deviations from ideal: 99.22 - 106.18: 321 106.18 - 113.15: 6365 113.15 - 120.11: 3782 120.11 - 127.07: 5205 127.07 - 134.04: 129 Bond angle restraints: 15802 Sorted by residual: angle pdb=" C CYS 2 500 " pdb=" CA CYS 2 500 " pdb=" CB CYS 2 500 " ideal model delta sigma weight residual 117.23 111.22 6.01 1.36e+00 5.41e-01 1.95e+01 angle pdb=" CA CYS 2 500 " pdb=" C CYS 2 500 " pdb=" N SER 2 501 " ideal model delta sigma weight residual 119.98 117.14 2.84 8.50e-01 1.38e+00 1.11e+01 angle pdb=" CA PRO 3 139 " pdb=" N PRO 3 139 " pdb=" CD PRO 3 139 " ideal model delta sigma weight residual 112.00 107.38 4.62 1.40e+00 5.10e-01 1.09e+01 angle pdb=" CA LEU 2 639 " pdb=" CB LEU 2 639 " pdb=" CG LEU 2 639 " ideal model delta sigma weight residual 116.30 126.36 -10.06 3.50e+00 8.16e-02 8.27e+00 angle pdb=" C GLU 2 222 " pdb=" N ALA 2 223 " pdb=" CA ALA 2 223 " ideal model delta sigma weight residual 121.54 127.00 -5.46 1.91e+00 2.74e-01 8.17e+00 ... (remaining 15797 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.99: 6150 18.99 - 37.99: 495 37.99 - 56.98: 86 56.98 - 75.98: 15 75.98 - 94.97: 11 Dihedral angle restraints: 6757 sinusoidal: 2313 harmonic: 4444 Sorted by residual: dihedral pdb=" CB CYS 2 525 " pdb=" SG CYS 2 525 " pdb=" SG CYS 2 537 " pdb=" CB CYS 2 537 " ideal model delta sinusoidal sigma weight residual 93.00 178.71 -85.71 1 1.00e+01 1.00e-02 8.88e+01 dihedral pdb=" CB CYS 3 412 " pdb=" SG CYS 3 412 " pdb=" SG CYS 3 419 " pdb=" CB CYS 3 419 " ideal model delta sinusoidal sigma weight residual 93.00 168.75 -75.75 1 1.00e+01 1.00e-02 7.24e+01 dihedral pdb=" CB CYS 2 632 " pdb=" SG CYS 2 632 " pdb=" SG CYS 2 721 " pdb=" CB CYS 2 721 " ideal model delta sinusoidal sigma weight residual 93.00 161.91 -68.91 1 1.00e+01 1.00e-02 6.15e+01 ... (remaining 6754 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1140 0.028 - 0.056: 457 0.056 - 0.084: 137 0.084 - 0.112: 95 0.112 - 0.140: 18 Chirality restraints: 1847 Sorted by residual: chirality pdb=" CA THR 2 595 " pdb=" N THR 2 595 " pdb=" C THR 2 595 " pdb=" CB THR 2 595 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.93e-01 chirality pdb=" CA ILE 2 523 " pdb=" N ILE 2 523 " pdb=" C ILE 2 523 " pdb=" CB ILE 2 523 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.49e-01 chirality pdb=" CA SER 3 684 " pdb=" N SER 3 684 " pdb=" C SER 3 684 " pdb=" CB SER 3 684 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.02e-01 ... (remaining 1844 not shown) Planarity restraints: 2009 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE 3 138 " -0.063 5.00e-02 4.00e+02 9.29e-02 1.38e+01 pdb=" N PRO 3 139 " 0.161 5.00e-02 4.00e+02 pdb=" CA PRO 3 139 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO 3 139 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA 2 223 " -0.012 2.00e-02 2.50e+03 2.47e-02 6.09e+00 pdb=" C ALA 2 223 " 0.043 2.00e-02 2.50e+03 pdb=" O ALA 2 223 " -0.016 2.00e-02 2.50e+03 pdb=" N PHE 2 224 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU 2 218 " 0.009 2.00e-02 2.50e+03 1.74e-02 3.04e+00 pdb=" C GLU 2 218 " -0.030 2.00e-02 2.50e+03 pdb=" O GLU 2 218 " 0.011 2.00e-02 2.50e+03 pdb=" N THR 2 219 " 0.010 2.00e-02 2.50e+03 ... (remaining 2006 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2949 2.80 - 3.33: 10874 3.33 - 3.85: 18409 3.85 - 4.38: 20372 4.38 - 4.90: 35781 Nonbonded interactions: 88385 Sorted by model distance: nonbonded pdb=" O TYR 3 212 " pdb=" OG1 THR 3 506 " model vdw 2.278 2.440 nonbonded pdb=" OG SER 3 151 " pdb=" O GLU 31001 " model vdw 2.303 2.440 nonbonded pdb=" OG SER 3 149 " pdb=" OE1 GLU 31001 " model vdw 2.329 2.440 nonbonded pdb=" O GLY 3 579 " pdb=" OG1 THR 3 582 " model vdw 2.355 2.440 nonbonded pdb=" O ASP 2 421 " pdb=" ND2 ASN 2 425 " model vdw 2.361 2.520 ... (remaining 88380 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: 2.260 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: 10.450 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 29.860 Find NCS groups from input model: 0.410 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6638 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.187 11530 Z= 0.247 Angle : 0.488 10.063 15802 Z= 0.242 Chirality : 0.039 0.140 1847 Planarity : 0.003 0.093 2007 Dihedral : 14.089 94.974 3827 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer Outliers : 0.10 % 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: 0.18 (0.22), residues: 1519 helix: 1.86 (0.20), residues: 677 sheet: -1.35 (0.46), residues: 147 loop : -1.35 (0.23), residues: 695 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 98 time to evaluate : 1.210 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 99 average time/residue: 0.1989 time to fit residues: 30.6411 Evaluate side-chains 91 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 90 time to evaluate : 1.188 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1339 time to fit residues: 1.8018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 0.0670 chunk 115 optimal weight: 0.5980 chunk 63 optimal weight: 10.0000 chunk 39 optimal weight: 0.3980 chunk 77 optimal weight: 1.9990 chunk 61 optimal weight: 8.9990 chunk 119 optimal weight: 1.9990 chunk 46 optimal weight: 30.0000 chunk 72 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 138 optimal weight: 7.9990 overall best weight: 0.8122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 345 ASN 3 369 HIS ** 3 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6852 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 11530 Z= 0.258 Angle : 0.524 8.357 15802 Z= 0.274 Chirality : 0.041 0.143 1847 Planarity : 0.005 0.061 2007 Dihedral : 5.042 78.500 1725 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer Outliers : 2.09 % 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: -0.23 (0.22), residues: 1519 helix: 1.34 (0.20), residues: 682 sheet: -1.36 (0.45), residues: 151 loop : -1.43 (0.23), residues: 686 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 92 time to evaluate : 1.223 Fit side-chains outliers start: 21 outliers final: 15 residues processed: 107 average time/residue: 0.2004 time to fit residues: 33.6155 Evaluate side-chains 100 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 85 time to evaluate : 1.243 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1104 time to fit residues: 5.0146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 76 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 93 optimal weight: 0.1980 chunk 38 optimal weight: 3.9990 chunk 138 optimal weight: 7.9990 chunk 149 optimal weight: 20.0000 chunk 123 optimal weight: 20.0000 chunk 137 optimal weight: 20.0000 chunk 47 optimal weight: 4.9990 chunk 110 optimal weight: 0.5980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 365 HIS 2 469 GLN 3 168 GLN 3 369 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.070 11530 Z= 0.482 Angle : 0.649 7.648 15802 Z= 0.338 Chirality : 0.045 0.275 1847 Planarity : 0.006 0.063 2007 Dihedral : 5.534 70.638 1725 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer Outliers : 2.69 % 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: -0.82 (0.21), residues: 1519 helix: 0.86 (0.20), residues: 684 sheet: -2.17 (0.43), residues: 147 loop : -1.63 (0.22), residues: 688 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 86 time to evaluate : 1.252 Fit side-chains outliers start: 27 outliers final: 17 residues processed: 109 average time/residue: 0.1949 time to fit residues: 33.9243 Evaluate side-chains 100 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 83 time to evaluate : 1.245 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1164 time to fit residues: 5.4276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 9.9990 chunk 103 optimal weight: 0.5980 chunk 71 optimal weight: 5.9990 chunk 15 optimal weight: 0.7980 chunk 65 optimal weight: 50.0000 chunk 92 optimal weight: 0.7980 chunk 138 optimal weight: 9.9990 chunk 146 optimal weight: 4.9990 chunk 72 optimal weight: 9.9990 chunk 131 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 602 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.063 11530 Z= 0.482 Angle : 0.644 10.097 15802 Z= 0.334 Chirality : 0.045 0.353 1847 Planarity : 0.006 0.069 2007 Dihedral : 5.848 61.956 1725 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer Outliers : 2.09 % 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: -1.12 (0.21), residues: 1519 helix: 0.69 (0.20), residues: 683 sheet: -2.87 (0.41), residues: 142 loop : -1.74 (0.22), residues: 694 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 87 time to evaluate : 1.250 Fit side-chains outliers start: 21 outliers final: 15 residues processed: 105 average time/residue: 0.2066 time to fit residues: 33.4731 Evaluate side-chains 96 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 81 time to evaluate : 1.237 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1020 time to fit residues: 4.4885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 60 optimal weight: 6.9990 chunk 125 optimal weight: 9.9990 chunk 101 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 131 optimal weight: 9.9990 chunk 37 optimal weight: 0.6980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 11530 Z= 0.287 Angle : 0.559 11.089 15802 Z= 0.284 Chirality : 0.041 0.193 1847 Planarity : 0.005 0.071 2007 Dihedral : 5.613 53.324 1725 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer Outliers : 1.29 % 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 (0.21), residues: 1519 helix: 0.73 (0.20), residues: 689 sheet: -2.87 (0.41), residues: 141 loop : -1.71 (0.22), residues: 689 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 88 time to evaluate : 1.284 Fit side-chains outliers start: 13 outliers final: 5 residues processed: 100 average time/residue: 0.2069 time to fit residues: 32.3460 Evaluate side-chains 89 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 84 time to evaluate : 1.268 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1231 time to fit residues: 2.8823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 7.9990 chunk 132 optimal weight: 20.0000 chunk 29 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 chunk 68 optimal weight: 9.9990 chunk 12 optimal weight: 0.8980 chunk 48 optimal weight: 10.0000 chunk 77 optimal weight: 0.7980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.070 11530 Z= 0.422 Angle : 0.614 10.867 15802 Z= 0.316 Chirality : 0.043 0.310 1847 Planarity : 0.005 0.073 2007 Dihedral : 5.707 58.222 1725 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer Outliers : 1.49 % 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: -1.15 (0.21), residues: 1519 helix: 0.74 (0.20), residues: 684 sheet: -3.14 (0.39), residues: 147 loop : -1.78 (0.22), residues: 688 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 82 time to evaluate : 1.172 Fit side-chains outliers start: 15 outliers final: 8 residues processed: 95 average time/residue: 0.2093 time to fit residues: 31.0898 Evaluate side-chains 89 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 81 time to evaluate : 1.149 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1686 time to fit residues: 3.7058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 9.9990 chunk 16 optimal weight: 2.9990 chunk 83 optimal weight: 0.5980 chunk 107 optimal weight: 1.9990 chunk 123 optimal weight: 20.0000 chunk 82 optimal weight: 1.9990 chunk 146 optimal weight: 5.9990 chunk 91 optimal weight: 0.6980 chunk 89 optimal weight: 0.6980 chunk 67 optimal weight: 30.0000 chunk 90 optimal weight: 0.5980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 11530 Z= 0.277 Angle : 0.559 11.268 15802 Z= 0.284 Chirality : 0.041 0.209 1847 Planarity : 0.005 0.073 2007 Dihedral : 5.521 55.196 1725 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer Outliers : 1.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.21), residues: 1519 helix: 0.78 (0.20), residues: 687 sheet: -3.06 (0.40), residues: 142 loop : -1.79 (0.22), residues: 690 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 82 time to evaluate : 1.158 Fit side-chains outliers start: 10 outliers final: 4 residues processed: 91 average time/residue: 0.2085 time to fit residues: 29.5378 Evaluate side-chains 85 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 81 time to evaluate : 1.373 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1052 time to fit residues: 2.5019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 9.9990 chunk 87 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 chunk 28 optimal weight: 0.2980 chunk 93 optimal weight: 2.9990 chunk 99 optimal weight: 0.5980 chunk 72 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 115 optimal weight: 0.9980 chunk 133 optimal weight: 0.9980 chunk 140 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6994 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 11530 Z= 0.228 Angle : 0.537 11.937 15802 Z= 0.272 Chirality : 0.041 0.340 1847 Planarity : 0.004 0.073 2007 Dihedral : 5.371 52.142 1725 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer Outliers : 1.19 % 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: -1.03 (0.22), residues: 1519 helix: 0.86 (0.20), residues: 682 sheet: -2.94 (0.40), residues: 146 loop : -1.76 (0.22), residues: 691 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 82 time to evaluate : 1.270 Fit side-chains outliers start: 12 outliers final: 6 residues processed: 86 average time/residue: 0.2072 time to fit residues: 28.2873 Evaluate side-chains 90 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 84 time to evaluate : 1.235 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1217 time to fit residues: 3.0187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 0.9990 chunk 136 optimal weight: 10.0000 chunk 140 optimal weight: 0.0170 chunk 82 optimal weight: 0.9990 chunk 59 optimal weight: 8.9990 chunk 107 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 123 optimal weight: 20.0000 chunk 129 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 144 optimal weight: 8.9990 overall best weight: 0.9424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 11530 Z= 0.287 Angle : 0.569 11.910 15802 Z= 0.290 Chirality : 0.042 0.320 1847 Planarity : 0.005 0.073 2007 Dihedral : 5.445 51.081 1725 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer Outliers : 0.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.21), residues: 1519 helix: 0.91 (0.20), residues: 677 sheet: -3.08 (0.40), residues: 141 loop : -1.76 (0.22), residues: 701 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 85 time to evaluate : 1.163 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 88 average time/residue: 0.1952 time to fit residues: 27.5081 Evaluate side-chains 84 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 82 time to evaluate : 1.316 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1286 time to fit residues: 2.4470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 88 optimal weight: 0.6980 chunk 68 optimal weight: 5.9990 chunk 100 optimal weight: 0.6980 chunk 151 optimal weight: 0.9980 chunk 139 optimal weight: 20.0000 chunk 120 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 93 optimal weight: 2.9990 chunk 73 optimal weight: 40.0000 chunk 95 optimal weight: 0.9980 chunk 128 optimal weight: 0.3980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 11530 Z= 0.227 Angle : 0.556 12.070 15802 Z= 0.281 Chirality : 0.040 0.206 1847 Planarity : 0.004 0.074 2007 Dihedral : 5.418 52.956 1725 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer Outliers : 0.40 % 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: -0.97 (0.22), residues: 1519 helix: 0.98 (0.20), residues: 673 sheet: -2.97 (0.39), residues: 151 loop : -1.75 (0.22), residues: 695 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 84 time to evaluate : 1.266 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 87 average time/residue: 0.2425 time to fit residues: 32.9070 Evaluate side-chains 82 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 1.863 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.3248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 36 optimal weight: 1.9990 chunk 111 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 120 optimal weight: 1.9990 chunk 50 optimal weight: 8.9990 chunk 124 optimal weight: 9.9990 chunk 15 optimal weight: 0.3980 chunk 22 optimal weight: 0.9980 chunk 106 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.200034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.150923 restraints weight = 13920.196| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 2.06 r_work: 0.3438 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 11530 Z= 0.205 Angle : 0.535 12.119 15802 Z= 0.269 Chirality : 0.040 0.145 1847 Planarity : 0.004 0.073 2007 Dihedral : 5.306 54.082 1725 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % 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: -0.94 (0.22), residues: 1519 helix: 1.01 (0.20), residues: 673 sheet: -2.83 (0.39), residues: 156 loop : -1.76 (0.22), residues: 690 =============================================================================== Job complete usr+sys time: 2228.14 seconds wall clock time: 41 minutes 8.62 seconds (2468.62 seconds total)