Starting phenix.real_space_refine (version: 1.21rc1) on Fri May 12 23:41:03 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qs7_4626/05_2023/6qs7_4626_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qs7_4626/05_2023/6qs7_4626.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qs7_4626/05_2023/6qs7_4626.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qs7_4626/05_2023/6qs7_4626.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qs7_4626/05_2023/6qs7_4626_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qs7_4626/05_2023/6qs7_4626_updated.pdb" } resolution = 3.8 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= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1218 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians P 32 5.49 5 Mg 8 5.21 5 S 108 5.16 5 C 18010 2.51 5 N 5230 2.21 5 O 5487 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 320": "NH1" <-> "NH2" Residue "A ARG 332": "NH1" <-> "NH2" Residue "A ARG 528": "NH1" <-> "NH2" Residue "B ARG 252": "NH1" <-> "NH2" Residue "B ARG 332": "NH1" <-> "NH2" Residue "B ARG 528": "NH1" <-> "NH2" Residue "B ARG 550": "NH1" <-> "NH2" Residue "C ARG 252": "NH1" <-> "NH2" Residue "C ARG 332": "NH1" <-> "NH2" Residue "C ARG 528": "NH1" <-> "NH2" Residue "C ARG 550": "NH1" <-> "NH2" Residue "D ARG 332": "NH1" <-> "NH2" Residue "D ARG 528": "NH1" <-> "NH2" Residue "D ARG 550": "NH1" <-> "NH2" Residue "E ARG 332": "NH1" <-> "NH2" Residue "E ARG 528": "NH1" <-> "NH2" Residue "E ARG 550": "NH1" <-> "NH2" Residue "E PHE 637": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 252": "NH1" <-> "NH2" Residue "F ARG 332": "NH1" <-> "NH2" Residue "F ARG 528": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/chem_data/mon_lib" Total number of atoms: 28875 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 4472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 568, 4472 Classifications: {'peptide': 568} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 546} Chain breaks: 3 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 4562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 582, 4562 Classifications: {'peptide': 582} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 559} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 4976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 630, 4976 Classifications: {'peptide': 630} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 606} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 4952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 625, 4952 Classifications: {'peptide': 625} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 601} Chain breaks: 3 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 4952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 625, 4952 Classifications: {'peptide': 625} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 601} Chain breaks: 3 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 4496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4496 Classifications: {'peptide': 573} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 551} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "S" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 120 Classifications: {'peptide': 24} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'TRANS': 23} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'UNK:plan-1': 24} Unresolved non-hydrogen planarities: 24 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'AGS': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 14.35, per 1000 atoms: 0.50 Number of scatterers: 28875 At special positions: 0 Unit cell: (124.95, 144.9, 157.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 108 16.00 P 32 15.00 Mg 8 11.99 O 5487 8.00 N 5230 7.00 C 18010 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=9, symmetry=0 Number of additional bonds: simple=9, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.70 Conformation dependent library (CDL) restraints added in 4.0 seconds 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6724 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 178 helices and 26 sheets defined 51.1% alpha, 8.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.29 Creating SS restraints... Processing helix chain 'A' and resid 161 through 164 No H-bonds generated for 'chain 'A' and resid 161 through 164' Processing helix chain 'A' and resid 168 through 173 Processing helix chain 'A' and resid 184 through 195 removed outlier: 3.613A pdb=" N GLN A 195 " --> pdb=" O ILE A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 225 Processing helix chain 'A' and resid 242 through 245 No H-bonds generated for 'chain 'A' and resid 242 through 245' Processing helix chain 'A' and resid 255 through 268 Processing helix chain 'A' and resid 280 through 284 removed outlier: 3.818A pdb=" N VAL A 284 " --> pdb=" O HIS A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 304 Proline residue: A 301 - end of helix Processing helix chain 'A' and resid 316 through 322 Processing helix chain 'A' and resid 327 through 331 Processing helix chain 'A' and resid 343 through 352 Processing helix chain 'A' and resid 354 through 360 Processing helix chain 'A' and resid 367 through 380 Processing helix chain 'A' and resid 388 through 405 Processing helix chain 'A' and resid 533 through 542 Processing helix chain 'A' and resid 555 through 566 removed outlier: 3.787A pdb=" N ARG A 561 " --> pdb=" O GLU A 557 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N GLU A 563 " --> pdb=" O LEU A 559 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLN A 564 " --> pdb=" O LEU A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 589 Processing helix chain 'A' and resid 612 through 622 Processing helix chain 'A' and resid 640 through 647 Processing helix chain 'A' and resid 662 through 668 Processing helix chain 'A' and resid 679 through 681 No H-bonds generated for 'chain 'A' and resid 679 through 681' Processing helix chain 'A' and resid 686 through 696 Processing helix chain 'A' and resid 722 through 726 Processing helix chain 'A' and resid 734 through 748 Processing helix chain 'A' and resid 751 through 754 No H-bonds generated for 'chain 'A' and resid 751 through 754' Processing helix chain 'A' and resid 768 through 789 Processing helix chain 'A' and resid 797 through 804 Processing helix chain 'A' and resid 814 through 826 Processing helix chain 'A' and resid 828 through 834 Processing helix chain 'B' and resid 168 through 174 Processing helix chain 'B' and resid 184 through 194 Processing helix chain 'B' and resid 212 through 225 removed outlier: 4.094A pdb=" N VAL B 216 " --> pdb=" O LYS B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 232 No H-bonds generated for 'chain 'B' and resid 230 through 232' Processing helix chain 'B' and resid 242 through 246 Processing helix chain 'B' and resid 255 through 268 Processing helix chain 'B' and resid 280 through 284 Processing helix chain 'B' and resid 295 through 303 Proline residue: B 301 - end of helix Processing helix chain 'B' and resid 316 through 322 removed outlier: 4.046A pdb=" N ARG B 320 " --> pdb=" O LEU B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 331 Processing helix chain 'B' and resid 343 through 361 removed outlier: 5.247A pdb=" N GLU B 355 " --> pdb=" O ARG B 351 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N ARG B 356 " --> pdb=" O GLY B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 379 Processing helix chain 'B' and resid 388 through 406 Processing helix chain 'B' and resid 533 through 543 Processing helix chain 'B' and resid 553 through 560 Processing helix chain 'B' and resid 562 through 566 Processing helix chain 'B' and resid 574 through 588 Processing helix chain 'B' and resid 611 through 622 Processing helix chain 'B' and resid 634 through 636 No H-bonds generated for 'chain 'B' and resid 634 through 636' Processing helix chain 'B' and resid 642 through 647 Processing helix chain 'B' and resid 661 through 667 Processing helix chain 'B' and resid 684 through 686 No H-bonds generated for 'chain 'B' and resid 684 through 686' Processing helix chain 'B' and resid 689 through 696 Processing helix chain 'B' and resid 722 through 728 Processing helix chain 'B' and resid 734 through 748 Processing helix chain 'B' and resid 751 through 754 No H-bonds generated for 'chain 'B' and resid 751 through 754' Processing helix chain 'B' and resid 768 through 789 Processing helix chain 'B' and resid 797 through 806 Processing helix chain 'B' and resid 813 through 833 Proline residue: B 816 - end of helix removed outlier: 3.580A pdb=" N ARG B 819 " --> pdb=" O PRO B 816 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN B 823 " --> pdb=" O ALA B 820 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN B 824 " --> pdb=" O ILE B 821 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE B 825 " --> pdb=" O GLN B 822 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N ASN B 827 " --> pdb=" O GLN B 824 " (cutoff:3.500A) Proline residue: B 828 - end of helix removed outlier: 3.796A pdb=" N ILE B 833 " --> pdb=" O ALA B 830 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 164 No H-bonds generated for 'chain 'C' and resid 161 through 164' Processing helix chain 'C' and resid 168 through 173 Processing helix chain 'C' and resid 184 through 194 Processing helix chain 'C' and resid 212 through 225 removed outlier: 3.895A pdb=" N VAL C 216 " --> pdb=" O LYS C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 247 Processing helix chain 'C' and resid 255 through 268 Processing helix chain 'C' and resid 280 through 282 No H-bonds generated for 'chain 'C' and resid 280 through 282' Processing helix chain 'C' and resid 300 through 304 Processing helix chain 'C' and resid 317 through 322 Processing helix chain 'C' and resid 343 through 361 removed outlier: 4.300A pdb=" N GLY C 352 " --> pdb=" O ALA C 348 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N GLU C 355 " --> pdb=" O ARG C 351 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N ARG C 356 " --> pdb=" O GLY C 352 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR C 357 " --> pdb=" O LEU C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 380 Processing helix chain 'C' and resid 388 through 406 Processing helix chain 'C' and resid 410 through 428 Processing helix chain 'C' and resid 445 through 464 Processing helix chain 'C' and resid 533 through 543 Processing helix chain 'C' and resid 553 through 560 Processing helix chain 'C' and resid 562 through 566 Processing helix chain 'C' and resid 574 through 589 Processing helix chain 'C' and resid 611 through 622 Processing helix chain 'C' and resid 634 through 636 No H-bonds generated for 'chain 'C' and resid 634 through 636' Processing helix chain 'C' and resid 642 through 647 Processing helix chain 'C' and resid 654 through 656 No H-bonds generated for 'chain 'C' and resid 654 through 656' Processing helix chain 'C' and resid 662 through 668 Processing helix chain 'C' and resid 679 through 681 No H-bonds generated for 'chain 'C' and resid 679 through 681' Processing helix chain 'C' and resid 684 through 686 No H-bonds generated for 'chain 'C' and resid 684 through 686' Processing helix chain 'C' and resid 689 through 696 Processing helix chain 'C' and resid 722 through 728 Processing helix chain 'C' and resid 734 through 748 Processing helix chain 'C' and resid 768 through 789 removed outlier: 3.726A pdb=" N GLU C 788 " --> pdb=" O LYS C 784 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ARG C 789 " --> pdb=" O ARG C 785 " (cutoff:3.500A) Processing helix chain 'C' and resid 797 through 806 Processing helix chain 'C' and resid 815 through 834 Proline residue: C 828 - end of helix Processing helix chain 'D' and resid 160 through 164 Processing helix chain 'D' and resid 169 through 173 Processing helix chain 'D' and resid 184 through 194 Processing helix chain 'D' and resid 214 through 224 Processing helix chain 'D' and resid 242 through 248 Processing helix chain 'D' and resid 254 through 269 removed outlier: 3.562A pdb=" N GLN D 269 " --> pdb=" O ASP D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 282 No H-bonds generated for 'chain 'D' and resid 280 through 282' Processing helix chain 'D' and resid 297 through 303 Proline residue: D 301 - end of helix No H-bonds generated for 'chain 'D' and resid 297 through 303' Processing helix chain 'D' and resid 316 through 322 removed outlier: 4.002A pdb=" N ARG D 320 " --> pdb=" O LEU D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 331 Processing helix chain 'D' and resid 343 through 361 Processing helix chain 'D' and resid 367 through 379 Processing helix chain 'D' and resid 388 through 406 Processing helix chain 'D' and resid 410 through 428 Processing helix chain 'D' and resid 445 through 464 Processing helix chain 'D' and resid 533 through 543 Processing helix chain 'D' and resid 553 through 565 removed outlier: 5.868A pdb=" N GLU D 563 " --> pdb=" O LEU D 559 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N GLN D 564 " --> pdb=" O LEU D 560 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 589 Processing helix chain 'D' and resid 611 through 623 Processing helix chain 'D' and resid 634 through 636 No H-bonds generated for 'chain 'D' and resid 634 through 636' Processing helix chain 'D' and resid 642 through 646 Processing helix chain 'D' and resid 654 through 656 No H-bonds generated for 'chain 'D' and resid 654 through 656' Processing helix chain 'D' and resid 662 through 668 Processing helix chain 'D' and resid 679 through 681 No H-bonds generated for 'chain 'D' and resid 679 through 681' Processing helix chain 'D' and resid 684 through 696 Processing helix chain 'D' and resid 722 through 728 Processing helix chain 'D' and resid 734 through 748 Processing helix chain 'D' and resid 753 through 755 No H-bonds generated for 'chain 'D' and resid 753 through 755' Processing helix chain 'D' and resid 768 through 789 Processing helix chain 'D' and resid 797 through 806 Processing helix chain 'D' and resid 815 through 833 Proline residue: D 828 - end of helix Processing helix chain 'E' and resid 168 through 174 Processing helix chain 'E' and resid 184 through 194 Processing helix chain 'E' and resid 212 through 225 Processing helix chain 'E' and resid 230 through 232 No H-bonds generated for 'chain 'E' and resid 230 through 232' Processing helix chain 'E' and resid 242 through 247 removed outlier: 3.590A pdb=" N VAL E 246 " --> pdb=" O MET E 242 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA E 247 " --> pdb=" O GLY E 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 242 through 247' Processing helix chain 'E' and resid 254 through 269 Processing helix chain 'E' and resid 280 through 284 Processing helix chain 'E' and resid 296 through 303 Proline residue: E 301 - end of helix Processing helix chain 'E' and resid 316 through 322 Processing helix chain 'E' and resid 327 through 332 removed outlier: 3.847A pdb=" N GLU E 330 " --> pdb=" O ALA E 327 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ARG E 331 " --> pdb=" O ALA E 328 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG E 332 " --> pdb=" O LEU E 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 327 through 332' Processing helix chain 'E' and resid 343 through 359 removed outlier: 4.551A pdb=" N LEU E 359 " --> pdb=" O GLU E 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 367 through 380 Processing helix chain 'E' and resid 388 through 406 Processing helix chain 'E' and resid 410 through 428 Processing helix chain 'E' and resid 445 through 465 Processing helix chain 'E' and resid 533 through 543 Processing helix chain 'E' and resid 553 through 569 Processing helix chain 'E' and resid 574 through 588 Processing helix chain 'E' and resid 612 through 622 Processing helix chain 'E' and resid 642 through 646 Processing helix chain 'E' and resid 662 through 668 Processing helix chain 'E' and resid 679 through 681 No H-bonds generated for 'chain 'E' and resid 679 through 681' Processing helix chain 'E' and resid 687 through 696 Processing helix chain 'E' and resid 722 through 728 Processing helix chain 'E' and resid 734 through 748 Processing helix chain 'E' and resid 751 through 754 No H-bonds generated for 'chain 'E' and resid 751 through 754' Processing helix chain 'E' and resid 768 through 787 Processing helix chain 'E' and resid 797 through 806 Processing helix chain 'E' and resid 815 through 834 Proline residue: E 828 - end of helix Processing helix chain 'F' and resid 160 through 164 Processing helix chain 'F' and resid 168 through 173 Processing helix chain 'F' and resid 184 through 194 Processing helix chain 'F' and resid 212 through 224 removed outlier: 3.949A pdb=" N VAL F 216 " --> pdb=" O LYS F 212 " (cutoff:3.500A) Processing helix chain 'F' and resid 230 through 232 No H-bonds generated for 'chain 'F' and resid 230 through 232' Processing helix chain 'F' and resid 242 through 245 No H-bonds generated for 'chain 'F' and resid 242 through 245' Processing helix chain 'F' and resid 255 through 269 Processing helix chain 'F' and resid 280 through 284 Processing helix chain 'F' and resid 296 through 305 Proline residue: F 301 - end of helix removed outlier: 3.774A pdb=" N ALA F 304 " --> pdb=" O LYS F 300 " (cutoff:3.500A) Processing helix chain 'F' and resid 316 through 322 Processing helix chain 'F' and resid 328 through 331 No H-bonds generated for 'chain 'F' and resid 328 through 331' Processing helix chain 'F' and resid 343 through 361 removed outlier: 4.875A pdb=" N GLU F 355 " --> pdb=" O ARG F 351 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N ARG F 356 " --> pdb=" O GLY F 352 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR F 357 " --> pdb=" O LEU F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 367 through 380 Processing helix chain 'F' and resid 388 through 406 Processing helix chain 'F' and resid 533 through 542 Processing helix chain 'F' and resid 555 through 569 removed outlier: 4.699A pdb=" N HIS F 567 " --> pdb=" O GLU F 563 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N HIS F 568 " --> pdb=" O GLN F 564 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ARG F 569 " --> pdb=" O GLU F 565 " (cutoff:3.500A) Processing helix chain 'F' and resid 574 through 588 Processing helix chain 'F' and resid 611 through 622 Processing helix chain 'F' and resid 643 through 646 No H-bonds generated for 'chain 'F' and resid 643 through 646' Processing helix chain 'F' and resid 655 through 658 Processing helix chain 'F' and resid 663 through 668 Processing helix chain 'F' and resid 679 through 681 No H-bonds generated for 'chain 'F' and resid 679 through 681' Processing helix chain 'F' and resid 684 through 695 removed outlier: 3.965A pdb=" N ASN F 688 " --> pdb=" O PRO F 684 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N ILE F 689 " --> pdb=" O ASP F 685 " (cutoff:3.500A) Processing helix chain 'F' and resid 720 through 728 removed outlier: 4.341A pdb=" N ASP F 723 " --> pdb=" O LEU F 720 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG F 728 " --> pdb=" O ILE F 725 " (cutoff:3.500A) Processing helix chain 'F' and resid 735 through 748 Processing helix chain 'F' and resid 751 through 756 removed outlier: 4.101A pdb=" N ARG F 756 " --> pdb=" O GLU F 752 " (cutoff:3.500A) Processing helix chain 'F' and resid 769 through 789 Processing helix chain 'F' and resid 797 through 807 Processing helix chain 'F' and resid 815 through 833 Proline residue: F 828 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 165 through 167 removed outlier: 4.468A pdb=" N ASP A 278 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N VAL A 311 " --> pdb=" O ILE A 277 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY A 206 " --> pdb=" O THR A 314 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N GLN A 334 " --> pdb=" O VAL A 203 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N ILE A 205 " --> pdb=" O GLN A 334 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N VAL A 336 " --> pdb=" O ILE A 205 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 599 through 603 removed outlier: 3.641A pdb=" N PHE A 601 " --> pdb=" O VAL A 714 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL A 630 " --> pdb=" O LEU A 675 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N ASP A 677 " --> pdb=" O VAL A 630 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE A 632 " --> pdb=" O ASP A 677 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 698 through 700 Processing sheet with id= D, first strand: chain 'A' and resid 793 through 795 removed outlier: 5.936A pdb=" N ILE A 844 " --> pdb=" O HIS A 794 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 165 through 167 removed outlier: 5.365A pdb=" N ASP B 278 " --> pdb=" O LEU B 240 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL B 311 " --> pdb=" O ILE B 277 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 202 through 206 removed outlier: 5.947A pdb=" N GLN B 334 " --> pdb=" O VAL B 203 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ILE B 205 " --> pdb=" O GLN B 334 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N VAL B 336 " --> pdb=" O ILE B 205 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'B' and resid 599 through 604 removed outlier: 6.589A pdb=" N ILE B 674 " --> pdb=" O ILE B 715 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N THR B 717 " --> pdb=" O ILE B 674 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N LEU B 676 " --> pdb=" O THR B 717 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL B 630 " --> pdb=" O LEU B 675 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ASP B 677 " --> pdb=" O VAL B 630 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ILE B 632 " --> pdb=" O ASP B 677 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 698 through 700 removed outlier: 3.544A pdb=" N LEU B 699 " --> pdb=" O VAL B 707 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 793 through 795 removed outlier: 5.880A pdb=" N ILE B 844 " --> pdb=" O HIS B 794 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 165 through 167 removed outlier: 5.094A pdb=" N ASP C 278 " --> pdb=" O LEU C 240 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N VAL C 311 " --> pdb=" O ILE C 277 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 599 through 602 removed outlier: 6.547A pdb=" N VAL C 630 " --> pdb=" O LEU C 675 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N ASP C 677 " --> pdb=" O VAL C 630 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ILE C 632 " --> pdb=" O ASP C 677 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 698 through 700 Processing sheet with id= M, first strand: chain 'C' and resid 844 through 848 removed outlier: 3.821A pdb=" N ARG C 845 " --> pdb=" O VAL C 856 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 165 through 167 removed outlier: 4.893A pdb=" N ASP D 278 " --> pdb=" O LEU D 240 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N VAL D 311 " --> pdb=" O ILE D 277 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLY D 206 " --> pdb=" O THR D 314 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N GLN D 334 " --> pdb=" O VAL D 203 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ILE D 205 " --> pdb=" O GLN D 334 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N VAL D 336 " --> pdb=" O ILE D 205 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 601 through 604 removed outlier: 6.814A pdb=" N GLU D 759 " --> pdb=" O LEU D 602 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N LEU D 604 " --> pdb=" O GLU D 759 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N VAL D 761 " --> pdb=" O LEU D 604 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'D' and resid 630 through 633 removed outlier: 6.197A pdb=" N VAL D 713 " --> pdb=" O ILE D 674 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N LEU D 676 " --> pdb=" O VAL D 713 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ILE D 715 " --> pdb=" O LEU D 676 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 698 through 700 Processing sheet with id= R, first strand: chain 'D' and resid 844 through 848 Processing sheet with id= S, first strand: chain 'E' and resid 165 through 167 removed outlier: 3.618A pdb=" N LEU E 238 " --> pdb=" O ILE E 274 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 333 through 337 removed outlier: 7.619A pdb=" N ASN E 201 " --> pdb=" O GLN E 334 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N VAL E 336 " --> pdb=" O ASN E 201 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL E 203 " --> pdb=" O VAL E 336 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ALA E 313 " --> pdb=" O ILE E 277 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 759 through 762 removed outlier: 3.652A pdb=" N LEU E 602 " --> pdb=" O GLU E 759 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N VAL E 630 " --> pdb=" O LEU E 675 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ASP E 677 " --> pdb=" O VAL E 630 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ILE E 632 " --> pdb=" O ASP E 677 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 698 through 700 removed outlier: 3.525A pdb=" N LEU E 699 " --> pdb=" O VAL E 707 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 846 through 848 Processing sheet with id= X, first strand: chain 'F' and resid 165 through 167 removed outlier: 5.822A pdb=" N ASP F 278 " --> pdb=" O LEU F 240 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL F 311 " --> pdb=" O ILE F 277 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N THR F 314 " --> pdb=" O PRO F 202 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N LEU F 204 " --> pdb=" O THR F 314 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N GLN F 334 " --> pdb=" O VAL F 203 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N ILE F 205 " --> pdb=" O GLN F 334 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N VAL F 336 " --> pdb=" O ILE F 205 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'F' and resid 759 through 763 removed outlier: 3.860A pdb=" N LEU F 602 " --> pdb=" O GLU F 759 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL F 761 " --> pdb=" O LEU F 602 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER F 718 " --> pdb=" O PHE F 603 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY F 605 " --> pdb=" O SER F 718 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N VAL F 630 " --> pdb=" O LEU F 675 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ASP F 677 " --> pdb=" O VAL F 630 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE F 632 " --> pdb=" O ASP F 677 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'F' and resid 792 through 795 1196 hydrogen bonds defined for protein. 3540 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: 9.65 Time building geometry restraints manager: 12.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.34: 10032 1.34 - 1.50: 7639 1.50 - 1.65: 11433 1.65 - 1.80: 160 1.80 - 1.95: 34 Bond restraints: 29298 Sorted by residual: bond pdb=" CA MET C 634 " pdb=" C MET C 634 " ideal model delta sigma weight residual 1.522 1.435 0.087 1.72e-02 3.38e+03 2.56e+01 bond pdb=" C GLY A 253 " pdb=" N GLU A 254 " ideal model delta sigma weight residual 1.332 1.264 0.068 1.40e-02 5.10e+03 2.36e+01 bond pdb=" C ALA D 682 " pdb=" N HIS D 683 " ideal model delta sigma weight residual 1.333 1.224 0.108 2.74e-02 1.33e+03 1.56e+01 bond pdb=" C PHE C 749 " pdb=" N ARG C 750 " ideal model delta sigma weight residual 1.333 1.246 0.086 2.74e-02 1.33e+03 9.90e+00 bond pdb=" CB GLN D 692 " pdb=" CG GLN D 692 " ideal model delta sigma weight residual 1.520 1.431 0.089 3.00e-02 1.11e+03 8.85e+00 ... (remaining 29293 not shown) Histogram of bond angle deviations from ideal: 96.50 - 104.38: 473 104.38 - 112.26: 14694 112.26 - 120.14: 12985 120.14 - 128.02: 11239 128.02 - 135.89: 207 Bond angle restraints: 39598 Sorted by residual: angle pdb=" C SER C 644 " pdb=" N ARG C 645 " pdb=" CA ARG C 645 " ideal model delta sigma weight residual 121.58 112.48 9.10 1.95e+00 2.63e-01 2.18e+01 angle pdb=" C GLY F 730 " pdb=" N GLU F 731 " pdb=" CA GLU F 731 " ideal model delta sigma weight residual 122.08 128.02 -5.94 1.47e+00 4.63e-01 1.63e+01 angle pdb=" C ALA C 247 " pdb=" N GLY C 248 " pdb=" CA GLY C 248 " ideal model delta sigma weight residual 122.46 111.80 10.66 2.70e+00 1.37e-01 1.56e+01 angle pdb=" N GLY C 296 " pdb=" CA GLY C 296 " pdb=" C GLY C 296 " ideal model delta sigma weight residual 113.18 104.14 9.04 2.37e+00 1.78e-01 1.46e+01 angle pdb=" CA LEU E 646 " pdb=" CB LEU E 646 " pdb=" CG LEU E 646 " ideal model delta sigma weight residual 116.30 129.49 -13.19 3.50e+00 8.16e-02 1.42e+01 ... (remaining 39593 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.96: 17537 23.96 - 47.93: 381 47.93 - 71.89: 28 71.89 - 95.85: 8 95.85 - 119.82: 2 Dihedral angle restraints: 17956 sinusoidal: 7533 harmonic: 10423 Sorted by residual: dihedral pdb=" CA MET C 293 " pdb=" C MET C 293 " pdb=" N ASP C 294 " pdb=" CA ASP C 294 " ideal model delta harmonic sigma weight residual 180.00 147.92 32.08 0 5.00e+00 4.00e-02 4.12e+01 dihedral pdb=" C5' ADP F1001 " pdb=" O5' ADP F1001 " pdb=" PA ADP F1001 " pdb=" O2A ADP F1001 " ideal model delta sinusoidal sigma weight residual -60.00 -179.81 119.82 1 2.00e+01 2.50e-03 3.59e+01 dihedral pdb=" O1B ADP F1001 " pdb=" O3A ADP F1001 " pdb=" PB ADP F1001 " pdb=" PA ADP F1001 " ideal model delta sinusoidal sigma weight residual -60.00 -176.25 116.25 1 2.00e+01 2.50e-03 3.46e+01 ... (remaining 17953 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 3091 0.057 - 0.113: 1107 0.113 - 0.170: 252 0.170 - 0.226: 24 0.226 - 0.283: 5 Chirality restraints: 4479 Sorted by residual: chirality pdb=" CB VAL B 679 " pdb=" CA VAL B 679 " pdb=" CG1 VAL B 679 " pdb=" CG2 VAL B 679 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CG LEU B 694 " pdb=" CB LEU B 694 " pdb=" CD1 LEU B 694 " pdb=" CD2 LEU B 694 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CB VAL D 679 " pdb=" CA VAL D 679 " pdb=" CG1 VAL D 679 " pdb=" CG2 VAL D 679 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.53e+00 ... (remaining 4476 not shown) Planarity restraints: 5170 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 300 " 0.049 5.00e-02 4.00e+02 7.45e-02 8.88e+00 pdb=" N PRO B 301 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO B 301 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 301 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 763 " 0.013 2.00e-02 2.50e+03 2.18e-02 8.30e+00 pdb=" CG PHE C 763 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 PHE C 763 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 PHE C 763 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE C 763 " -0.016 2.00e-02 2.50e+03 pdb=" CE2 PHE C 763 " 0.010 2.00e-02 2.50e+03 pdb=" CZ PHE C 763 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 823 " 0.014 2.00e-02 2.50e+03 2.77e-02 7.69e+00 pdb=" C GLN C 823 " -0.048 2.00e-02 2.50e+03 pdb=" O GLN C 823 " 0.018 2.00e-02 2.50e+03 pdb=" N GLN C 824 " 0.016 2.00e-02 2.50e+03 ... (remaining 5167 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 360 2.61 - 3.18: 24582 3.18 - 3.76: 44605 3.76 - 4.33: 61982 4.33 - 4.90: 101448 Nonbonded interactions: 232977 Sorted by model distance: nonbonded pdb=" OG1 THR E 612 " pdb="MG MG E1003 " model vdw 2.041 2.170 nonbonded pdb=" O1B AGS C1001 " pdb="MG MG C1003 " model vdw 2.046 2.170 nonbonded pdb=" OG1 THR C 612 " pdb="MG MG C1004 " model vdw 2.062 2.170 nonbonded pdb=" OG1 THR D 612 " pdb="MG MG D1004 " model vdw 2.067 2.170 nonbonded pdb=" O1B AGS D1001 " pdb="MG MG D1003 " model vdw 2.067 2.170 ... (remaining 232972 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 159 through 858) selection = (chain 'B' and (resid 159 through 287 or resid 293 through 543 or resid 553 thro \ ugh 858)) selection = (chain 'C' and (resid 159 through 287 or resid 293 through 408 or resid 527 thro \ ugh 543 or resid 553 through 858)) selection = (chain 'D' and (resid 159 through 408 or resid 527 through 543 or resid 553 thro \ ugh 858)) selection = (chain 'E' and (resid 159 through 408 or resid 527 through 543 or resid 553 thro \ ugh 858)) selection = (chain 'F' and (resid 159 through 287 or resid 293 through 858)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.160 Construct map_model_manager: 0.020 Extract box with map and model: 8.050 Check model and map are aligned: 0.410 Set scattering table: 0.230 Process input model: 69.170 Find NCS groups from input model: 2.270 Set up NCS constraints: 0.110 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: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 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 : 0.011 0.147 29298 Z= 0.681 Angle : 1.053 14.039 39598 Z= 0.564 Chirality : 0.059 0.283 4479 Planarity : 0.008 0.074 5170 Dihedral : 10.389 119.815 11232 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer Outliers : 0.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.83 (0.11), residues: 3563 helix: -2.30 (0.09), residues: 1903 sheet: -2.75 (0.25), residues: 339 loop : -2.58 (0.15), residues: 1321 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 936 residues out of total 3026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 930 time to evaluate : 3.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 936 average time/residue: 0.5015 time to fit residues: 685.6485 Evaluate side-chains 444 residues out of total 3026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 443 time to evaluate : 3.457 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2360 time to fit residues: 5.1408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 303 optimal weight: 8.9990 chunk 272 optimal weight: 0.9990 chunk 151 optimal weight: 0.9990 chunk 93 optimal weight: 6.9990 chunk 184 optimal weight: 0.7980 chunk 145 optimal weight: 0.9990 chunk 282 optimal weight: 0.9980 chunk 109 optimal weight: 4.9990 chunk 171 optimal weight: 0.9990 chunk 210 optimal weight: 1.9990 chunk 326 optimal weight: 9.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 GLN ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 404 GLN ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 726 GLN ** A 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 827 ASN ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 620 ASN B 641 HIS ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 747 HIS B 748 ASN ** B 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 794 HIS ** C 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 822 GLN D 192 GLN D 201 ASN D 567 HIS D 620 ASN D 641 HIS ** D 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 726 GLN D 748 ASN D 822 GLN E 297 ASN E 309 HIS E 334 GLN E 426 GLN E 568 HIS E 620 ASN E 641 HIS F 281 HIS F 309 HIS ** F 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 770 HIS F 776 GLN F 849 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 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 0.037 29298 Z= 0.207 Angle : 0.684 13.557 39598 Z= 0.338 Chirality : 0.044 0.223 4479 Planarity : 0.005 0.052 5170 Dihedral : 7.777 96.841 4098 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer Outliers : 2.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.13), residues: 3563 helix: -0.85 (0.11), residues: 1908 sheet: -2.44 (0.25), residues: 383 loop : -2.02 (0.17), residues: 1272 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 3026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 531 time to evaluate : 3.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 82 outliers final: 41 residues processed: 584 average time/residue: 0.4286 time to fit residues: 391.2746 Evaluate side-chains 433 residues out of total 3026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 392 time to evaluate : 3.234 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 0 residues processed: 41 average time/residue: 0.2170 time to fit residues: 20.4171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 181 optimal weight: 8.9990 chunk 101 optimal weight: 0.9990 chunk 272 optimal weight: 5.9990 chunk 222 optimal weight: 0.8980 chunk 90 optimal weight: 5.9990 chunk 327 optimal weight: 10.0000 chunk 353 optimal weight: 9.9990 chunk 291 optimal weight: 5.9990 chunk 324 optimal weight: 10.0000 chunk 111 optimal weight: 1.9990 chunk 262 optimal weight: 0.8980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: