Starting phenix.real_space_refine (version: 1.21rc1) on Fri May 12 23:43:55 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qs8_4627/05_2023/6qs8_4627_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qs8_4627/05_2023/6qs8_4627.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qs8_4627/05_2023/6qs8_4627.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qs8_4627/05_2023/6qs8_4627.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qs8_4627/05_2023/6qs8_4627_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qs8_4627/05_2023/6qs8_4627_updated.pdb" } resolution = 3.9 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= 0.004 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 "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: 3 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: 14.85, per 1000 atoms: 0.51 Number of scatterers: 28875 At special positions: 0 Unit cell: (119.7, 143.85, 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=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.34 Conformation dependent library (CDL) restraints added in 4.7 seconds 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 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 25 sheets defined 50.4% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.61 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 193 Processing helix chain 'A' and resid 212 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 282 No H-bonds generated for 'chain 'A' and resid 280 through 282' 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 407 Processing helix chain 'A' and resid 533 through 542 Processing helix chain 'A' and resid 555 through 560 Processing helix chain 'A' and resid 562 through 567 Processing helix chain 'A' and resid 574 through 588 Processing helix chain 'A' and resid 611 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 735 through 748 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 213 through 225 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 304 Proline residue: B 301 - end of helix removed outlier: 3.761A pdb=" N ALA B 304 " --> pdb=" O LYS B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 322 Processing helix chain 'B' and resid 327 through 331 Processing helix chain 'B' and resid 343 through 352 Processing helix chain 'B' and resid 354 through 361 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 544 Processing helix chain 'B' and resid 553 through 560 Processing helix chain 'B' and resid 562 through 567 Processing helix chain 'B' and resid 574 through 589 Processing helix chain 'B' and resid 611 through 623 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 640 through 647 removed outlier: 3.675A pdb=" N VAL B 643 " --> pdb=" O LYS B 640 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N VAL B 647 " --> pdb=" O SER B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 658 No H-bonds generated for 'chain 'B' and resid 656 through 658' Processing helix chain 'B' and resid 661 through 668 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 688 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 753 through 756 No H-bonds generated for 'chain 'B' and resid 753 through 756' Processing helix chain 'B' and resid 768 through 789 Processing helix chain 'B' and resid 797 through 806 Processing helix chain 'B' and resid 815 through 833 Proline residue: B 828 - end of helix 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: 3.579A 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 254 through 269 removed outlier: 3.584A pdb=" N GLN C 269 " --> pdb=" O ASP C 265 " (cutoff:3.500A) 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 318 through 322 Processing helix chain 'C' and resid 327 through 330 No H-bonds generated for 'chain 'C' and resid 327 through 330' Processing helix chain 'C' and resid 343 through 361 removed outlier: 3.872A pdb=" N GLY C 352 " --> pdb=" O ALA C 348 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N GLU C 355 " --> pdb=" O ARG C 351 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N ARG C 356 " --> pdb=" O GLY C 352 " (cutoff:3.500A) removed outlier: 3.615A 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 623 Processing helix chain 'C' and resid 642 through 647 Processing helix chain 'C' and resid 661 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 787 Processing helix chain 'C' and resid 799 through 806 Processing helix chain 'C' and resid 815 through 833 Proline residue: C 828 - end of helix Processing helix chain 'D' and resid 161 through 164 No H-bonds generated for 'chain 'D' and resid 161 through 164' Processing helix chain 'D' and resid 168 through 173 Processing helix chain 'D' and resid 184 through 194 Processing helix chain 'D' and resid 213 through 225 Processing helix chain 'D' and resid 242 through 248 Processing helix chain 'D' and resid 254 through 269 Processing helix chain 'D' and resid 280 through 283 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 318 through 322 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 380 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 560 Processing helix chain 'D' and resid 562 through 566 Processing helix chain 'D' and resid 574 through 588 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 685 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 805 Processing helix chain 'D' and resid 815 through 834 Proline residue: D 828 - end of helix Processing helix chain 'E' and resid 161 through 164 No H-bonds generated for 'chain 'E' and resid 161 through 164' Processing helix chain 'E' and resid 169 through 173 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 245 No H-bonds generated for 'chain 'E' and resid 242 through 245' 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: 3.831A pdb=" N GLU E 330 " --> pdb=" O ALA E 327 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ARG E 331 " --> pdb=" O ALA E 328 " (cutoff:3.500A) Processing helix chain 'E' and resid 343 through 361 removed outlier: 4.550A pdb=" N LEU E 359 " --> pdb=" O GLU E 355 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N HIS E 360 " --> pdb=" O ARG E 356 " (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 544 Processing helix chain 'E' and resid 553 through 566 Processing helix chain 'E' and resid 574 through 588 Processing helix chain 'E' and resid 611 through 623 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 768 through 787 Processing helix chain 'E' and resid 799 through 806 Processing helix chain 'E' and resid 815 through 834 Proline residue: E 828 - end of helix Processing helix chain 'F' and resid 161 through 164 No H-bonds generated for 'chain 'F' and resid 161 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 225 removed outlier: 3.807A 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 303 Proline residue: F 301 - end of helix 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 352 Processing helix chain 'F' and resid 354 through 361 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: 4.487A pdb=" N HIS F 567 " --> pdb=" O GLU F 563 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N HIS F 568 " --> pdb=" O GLN F 564 " (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 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: 4.401A pdb=" N ASN F 688 " --> pdb=" O PRO F 684 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N ILE F 689 " --> pdb=" O ASP F 685 " (cutoff:3.500A) Processing helix chain 'F' and resid 722 through 728 Processing helix chain 'F' and resid 735 through 748 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: 4.610A pdb=" N ASP A 278 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N VAL A 311 " --> pdb=" O ILE A 277 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N GLN A 334 " --> pdb=" O VAL A 203 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ILE A 205 " --> pdb=" O GLN A 334 " (cutoff:3.500A) removed outlier: 6.370A 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: 6.506A pdb=" N VAL A 630 " --> pdb=" O LEU A 675 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ASP A 677 " --> pdb=" O VAL A 630 " (cutoff:3.500A) removed outlier: 6.319A 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: 6.172A 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: 5.385A pdb=" N ASP B 278 " --> pdb=" O LEU B 240 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N VAL B 311 " --> pdb=" O ILE B 277 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLY B 206 " --> pdb=" O THR B 314 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N GLN B 334 " --> pdb=" O VAL B 203 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ILE B 205 " --> pdb=" O GLN B 334 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N VAL B 336 " --> pdb=" O ILE B 205 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 759 through 762 removed outlier: 3.571A pdb=" N GLU B 759 " --> pdb=" O SER B 600 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY B 599 " --> pdb=" O THR B 712 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N SER B 672 " --> pdb=" O VAL B 713 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N ILE B 715 " --> pdb=" O SER B 672 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ILE B 674 " --> pdb=" O ILE B 715 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N THR B 717 " --> pdb=" O ILE B 674 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N LEU B 676 " --> pdb=" O THR B 717 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL B 630 " --> pdb=" O LEU B 675 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N ASP B 677 " --> pdb=" O VAL B 630 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ILE B 632 " --> pdb=" O ASP B 677 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 698 through 700 Processing sheet with id= H, first strand: chain 'B' and resid 793 through 795 removed outlier: 5.870A pdb=" N ILE B 844 " --> pdb=" O HIS B 794 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG B 845 " --> pdb=" O VAL B 856 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 165 through 167 removed outlier: 4.987A pdb=" N ASP C 278 " --> pdb=" O LEU C 240 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL C 311 " --> pdb=" O ILE C 277 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 202 through 205 removed outlier: 5.703A pdb=" N GLN C 334 " --> pdb=" O VAL C 203 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ILE C 205 " --> pdb=" O GLN C 334 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N VAL C 336 " --> pdb=" O ILE C 205 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'C' and resid 759 through 762 removed outlier: 3.561A pdb=" N GLU C 759 " --> pdb=" O SER C 600 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL C 630 " --> pdb=" O LEU C 675 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N ASP C 677 " --> pdb=" O VAL C 630 " (cutoff:3.500A) removed outlier: 6.926A 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 792 through 795 removed outlier: 3.635A 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: 5.303A pdb=" N ASP D 278 " --> pdb=" O LEU D 240 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLY D 206 " --> pdb=" O THR D 314 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N GLN D 334 " --> pdb=" O VAL D 203 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ILE D 205 " --> pdb=" O GLN D 334 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N VAL D 336 " --> pdb=" O ILE D 205 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 759 through 762 removed outlier: 3.627A pdb=" N GLU D 759 " --> pdb=" O SER D 600 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY D 599 " --> pdb=" O THR D 712 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N SER D 672 " --> pdb=" O VAL D 713 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N ILE D 715 " --> pdb=" O SER D 672 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ILE D 674 " --> pdb=" O ILE D 715 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N THR D 717 " --> pdb=" O ILE D 674 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU D 676 " --> pdb=" O THR D 717 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N VAL D 630 " --> pdb=" O LEU D 675 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N ASP D 677 " --> pdb=" O VAL D 630 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ILE D 632 " --> pdb=" O ASP D 677 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 698 through 700 Processing sheet with id= Q, first strand: chain 'D' and resid 792 through 795 Processing sheet with id= R, first strand: chain 'E' and resid 165 through 167 removed outlier: 3.648A pdb=" N LEU E 238 " --> pdb=" O ILE E 274 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 333 through 337 removed outlier: 7.587A pdb=" N ASN E 201 " --> pdb=" O GLN E 334 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N VAL E 336 " --> pdb=" O ASN E 201 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL E 203 " --> pdb=" O VAL E 336 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ALA E 313 " --> pdb=" O ILE E 277 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 759 through 762 removed outlier: 3.738A pdb=" N LEU E 602 " --> pdb=" O GLU E 759 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL E 630 " --> pdb=" O LEU E 675 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N ASP E 677 " --> pdb=" O VAL E 630 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ILE E 632 " --> pdb=" O ASP E 677 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 698 through 700 Processing sheet with id= V, first strand: chain 'E' and resid 844 through 848 removed outlier: 3.933A pdb=" N ARG E 845 " --> pdb=" O VAL E 856 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'F' and resid 165 through 167 removed outlier: 3.619A pdb=" N LEU F 238 " --> pdb=" O ILE F 274 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU F 240 " --> pdb=" O PHE F 276 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N ASP F 278 " --> pdb=" O LEU F 240 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N VAL F 311 " --> pdb=" O ILE F 277 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N THR F 314 " --> pdb=" O PRO F 202 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N LEU F 204 " --> pdb=" O THR F 314 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'F' and resid 599 through 604 removed outlier: 3.727A pdb=" N GLY F 599 " --> pdb=" O THR F 712 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE F 601 " --> pdb=" O VAL F 714 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N SER F 672 " --> pdb=" O VAL F 713 " (cutoff:3.500A) removed outlier: 8.649A pdb=" N ILE F 715 " --> pdb=" O SER F 672 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ILE F 674 " --> pdb=" O ILE F 715 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N THR F 717 " --> pdb=" O ILE F 674 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N LEU F 676 " --> pdb=" O THR F 717 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL F 630 " --> pdb=" O LEU F 675 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N ASP F 677 " --> pdb=" O VAL F 630 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ILE F 632 " --> pdb=" O ASP F 677 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'F' and resid 792 through 795 1208 hydrogen bonds defined for protein. 3603 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: 9.58 Time building geometry restraints manager: 13.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 10263 1.36 - 1.51: 8656 1.51 - 1.65: 10184 1.65 - 1.80: 174 1.80 - 1.95: 20 Bond restraints: 29297 Sorted by residual: bond pdb=" CG1 ILE B 584 " pdb=" CD1 ILE B 584 " ideal model delta sigma weight residual 1.513 1.380 0.133 3.90e-02 6.57e+02 1.16e+01 bond pdb=" CG1 ILE D 584 " pdb=" CD1 ILE D 584 " ideal model delta sigma weight residual 1.513 1.381 0.132 3.90e-02 6.57e+02 1.15e+01 bond pdb=" CG1 ILE C 584 " pdb=" CD1 ILE C 584 " ideal model delta sigma weight residual 1.513 1.391 0.122 3.90e-02 6.57e+02 9.77e+00 bond pdb=" CB GLU B 752 " pdb=" CG GLU B 752 " ideal model delta sigma weight residual 1.520 1.430 0.090 3.00e-02 1.11e+03 8.97e+00 bond pdb=" CB PRO B 650 " pdb=" CG PRO B 650 " ideal model delta sigma weight residual 1.492 1.352 0.140 5.00e-02 4.00e+02 7.81e+00 ... (remaining 29292 not shown) Histogram of bond angle deviations from ideal: 96.23 - 104.11: 435 104.11 - 112.00: 14014 112.00 - 119.89: 12455 119.89 - 127.77: 12464 127.77 - 135.66: 226 Bond angle restraints: 39594 Sorted by residual: angle pdb=" C LEU A 299 " pdb=" N LYS A 300 " pdb=" CA LYS A 300 " ideal model delta sigma weight residual 120.09 126.79 -6.70 1.25e+00 6.40e-01 2.87e+01 angle pdb=" C SER C 644 " pdb=" N ARG C 645 " pdb=" CA ARG C 645 " ideal model delta sigma weight residual 121.58 112.42 9.16 1.95e+00 2.63e-01 2.21e+01 angle pdb=" CB LYS B 199 " pdb=" CG LYS B 199 " pdb=" CD LYS B 199 " ideal model delta sigma weight residual 111.30 100.76 10.54 2.30e+00 1.89e-01 2.10e+01 angle pdb=" C ALA C 247 " pdb=" N GLY C 248 " pdb=" CA GLY C 248 " ideal model delta sigma weight residual 121.82 111.65 10.17 2.30e+00 1.89e-01 1.95e+01 angle pdb=" CA LEU D 646 " pdb=" CB LEU D 646 " pdb=" CG LEU D 646 " ideal model delta sigma weight residual 116.30 131.25 -14.95 3.50e+00 8.16e-02 1.82e+01 ... (remaining 39589 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.36: 17590 26.36 - 52.72: 333 52.72 - 79.09: 26 79.09 - 105.45: 4 105.45 - 131.81: 2 Dihedral angle restraints: 17955 sinusoidal: 7533 harmonic: 10422 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 180.00 141.73 38.27 0 5.00e+00 4.00e-02 5.86e+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 300.00 168.19 131.81 1 2.00e+01 2.50e-03 4.00e+01 dihedral pdb=" CA ASP A 624 " pdb=" C ASP A 624 " pdb=" N SER A 625 " pdb=" CA SER A 625 " ideal model delta harmonic sigma weight residual -180.00 -148.79 -31.21 0 5.00e+00 4.00e-02 3.90e+01 ... (remaining 17952 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 3441 0.070 - 0.141: 928 0.141 - 0.211: 103 0.211 - 0.281: 4 0.281 - 0.351: 3 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 -2.28 -0.35 2.00e-01 2.50e+01 3.08e+00 chirality pdb=" CB VAL C 679 " pdb=" CA VAL C 679 " pdb=" CG1 VAL C 679 " pdb=" CG2 VAL C 679 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.71e+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 -2.30 -0.29 2.00e-01 2.50e+01 2.13e+00 ... (remaining 4476 not shown) Planarity restraints: 5168 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE D 763 " 0.020 2.00e-02 2.50e+03 2.52e-02 1.11e+01 pdb=" CG PHE D 763 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 PHE D 763 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 PHE D 763 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE D 763 " -0.015 2.00e-02 2.50e+03 pdb=" CE2 PHE D 763 " 0.013 2.00e-02 2.50e+03 pdb=" CZ PHE D 763 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 763 " 0.019 2.00e-02 2.50e+03 2.51e-02 1.10e+01 pdb=" CG PHE B 763 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 PHE B 763 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 PHE B 763 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE B 763 " -0.015 2.00e-02 2.50e+03 pdb=" CE2 PHE B 763 " 0.014 2.00e-02 2.50e+03 pdb=" CZ PHE B 763 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 763 " 0.018 2.00e-02 2.50e+03 2.38e-02 9.88e+00 pdb=" CG PHE C 763 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 PHE C 763 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 PHE C 763 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE C 763 " -0.016 2.00e-02 2.50e+03 pdb=" CE2 PHE C 763 " 0.012 2.00e-02 2.50e+03 pdb=" CZ PHE C 763 " 0.005 2.00e-02 2.50e+03 ... (remaining 5165 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 270 2.59 - 3.17: 23431 3.17 - 3.75: 44444 3.75 - 4.32: 63078 4.32 - 4.90: 103385 Nonbonded interactions: 234608 Sorted by model distance: nonbonded pdb=" O1B AGS D 902 " pdb="MG MG D 904 " model vdw 2.018 2.170 nonbonded pdb=" O2G AGS E1002 " pdb="MG MG E1003 " model vdw 2.024 2.170 nonbonded pdb=" OG1 THR E 612 " pdb="MG MG E1003 " model vdw 2.045 2.170 nonbonded pdb=" O1B AGS C1001 " pdb="MG MG C1003 " model vdw 2.062 2.170 nonbonded pdb=" O1B AGS D 901 " pdb="MG MG D 903 " model vdw 2.066 2.170 ... (remaining 234603 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: 1.040 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: 7.910 Check model and map are aligned: 0.420 Set scattering table: 0.240 Process input model: 71.410 Find NCS groups from input model: 2.240 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 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 0.140 29297 Z= 0.728 Angle : 1.047 14.947 39594 Z= 0.565 Chirality : 0.061 0.351 4479 Planarity : 0.008 0.072 5168 Dihedral : 10.417 131.810 11231 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -3.91 (0.11), residues: 3561 helix: -2.48 (0.08), residues: 1986 sheet: -2.65 (0.24), residues: 352 loop : -2.38 (0.16), residues: 1223 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 917 residues out of total 3026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 912 time to evaluate : 3.856 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 0 residues processed: 916 average time/residue: 0.5187 time to fit residues: 695.6485 Evaluate side-chains 426 residues out of total 3026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 426 time to evaluate : 3.606 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.9128 ------------------------------------------------------------------------------- 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: 0.7980 chunk 272 optimal weight: 0.9980 chunk 151 optimal weight: 2.9990 chunk 93 optimal weight: 8.9990 chunk 184 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 282 optimal weight: 3.9990 chunk 109 optimal weight: 5.9990 chunk 171 optimal weight: 7.9990 chunk 210 optimal weight: 0.4980 chunk 326 optimal weight: 9.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 281 HIS ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 GLN ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 719 ASN A 726 GLN ** A 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 GLN B 195 GLN B 297 ASN B 360 HIS ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 747 HIS B 849 ASN B 858 HIS C 201 ASN C 297 ASN C 334 GLN C 421 GLN ** C 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 159 GLN ** D 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 641 HIS ** D 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 692 GLN D 748 ASN D 806 ASN D 822 GLN E 192 GLN E 641 HIS E 683 HIS E 692 GLN E 703 GLN F 281 HIS F 309 HIS F 378 HIS F 573 GLN F 711 ASN F 726 GLN F 747 HIS F 794 HIS F 831 GLN F 849 ASN F 858 HIS Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 29297 Z= 0.241 Angle : 0.682 9.986 39594 Z= 0.343 Chirality : 0.045 0.222 4479 Planarity : 0.005 0.056 5168 Dihedral : 7.449 93.968 4097 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer Outliers : 2.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -2.07 (0.13), residues: 3561 helix: -0.80 (0.11), residues: 1956 sheet: -2.33 (0.24), residues: 382 loop : -1.74 (0.17), residues: 1223 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 3026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 467 time to evaluate : 3.647 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 outliers start: 81 outliers final: 45 residues processed: 517 average time/residue: 0.4200 time to fit residues: 336.7683 Evaluate side-chains 405 residues out of total 3026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 360 time to evaluate : 2.787 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 0 residues processed: 45 average time/residue: 0.2256 time to fit residues: 22.9559 ------------------------------------------------------------------------------- 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: 0.5980 chunk 101 optimal weight: 4.9990 chunk 272 optimal weight: 5.9990 chunk 222 optimal weight: 0.7980 chunk 90 optimal weight: 0.9980 chunk 327 optimal weight: 0.9980 chunk 353 optimal weight: 0.0770 chunk 291 optimal weight: 1.9990 chunk 324 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 262 optimal weight: 2.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 ASN A 297 ASN ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 GLN ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 747 HIS C 195 GLN C 421 GLN C 426 GLN C 445 ASN C 641 HIS ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 748 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 195 GLN ** D 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 748 ASN D 806 ASN D 822 GLN ** E 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 427 GLN E 567 HIS ** F 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 378 HIS ** F 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.3925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 29297 Z= 0.180 Angle : 0.616 10.060 39594 Z= 0.306 Chirality : 0.043 0.213 4479 Planarity : 0.005 0.061 5168 Dihedral : 6.957 80.550 4097 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer Outliers : 1.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.13 (0.14), residues: 3561 helix: 0.08 (0.11), residues: 1938 sheet: -2.22 (0.23), residues: 400 loop : -1.40 (0.17), residues: 1223 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 3026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 411 time to evaluate : 3.688 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: 48 outliers final: 20 residues processed: 441 average time/residue: 0.4355 time to fit residues: 303.2693 Evaluate side-chains 360 residues out of total 3026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 340 time to evaluate : 3.323 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.2913 time to fit residues: 15.5603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 323 optimal weight: 0.0070 chunk 246 optimal weight: 7.9990 chunk 169 optimal weight: 8.9990 chunk 36 optimal weight: 5.9990 chunk 156 optimal weight: 1.9990 chunk 219 optimal weight: 7.9990 chunk 328 optimal weight: 10.0000 chunk 347 optimal weight: 6.9990 chunk 171 optimal weight: 10.0000 chunk 311 optimal weight: 6.9990 chunk 93 optimal weight: 0.0170 overall best weight: 3.0042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 HIS A 360 HIS A 567 HIS ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 858 HIS B 159 GLN B 620 ASN ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 747 HIS ** B 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 445 ASN ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 747 HIS C 822 GLN ** D 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 748 ASN D 822 GLN D 831 GLN D 857 GLN ** E 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 427 GLN E 574 ASN ** E 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 378 HIS F 823 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.4372 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: