Starting phenix.real_space_refine (version: dev) on Fri Dec 16 07:25:13 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qs6_4624/12_2022/6qs6_4624_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qs6_4624/12_2022/6qs6_4624.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/6qs6_4624/12_2022/6qs6_4624.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qs6_4624/12_2022/6qs6_4624.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qs6_4624/12_2022/6qs6_4624_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qs6_4624/12_2022/6qs6_4624_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= 0.008 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 812 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 320": "NH1" <-> "NH2" Residue "A TYR 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 332": "NH1" <-> "NH2" Residue "A ARG 528": "NH1" <-> "NH2" Residue "A ARG 550": "NH1" <-> "NH2" Residue "A TYR 671": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 320": "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-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 28557 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 4538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4538 Classifications: {'peptide': 577} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 554} Chain breaks: 2 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: 4538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4538 Classifications: {'peptide': 577} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 554} Chain breaks: 2 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: 4538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4538 Classifications: {'peptide': 577} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 554} Chain breaks: 2 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: "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: 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} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 14.90, per 1000 atoms: 0.52 Number of scatterers: 28557 At special positions: 0 Unit cell: (123.9, 145.95, 150.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 109 16.00 P 31 15.00 O 5416 8.00 N 5179 7.00 C 17822 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=17, symmetry=0 Number of additional bonds: simple=17, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.83 Conformation dependent library (CDL) restraints added in 4.3 seconds 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6652 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 177 helices and 27 sheets defined 50.6% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.46 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 174 Processing helix chain 'A' and resid 184 through 195 Processing helix chain 'A' and resid 212 through 225 Processing helix chain 'A' and resid 243 through 245 No H-bonds generated for 'chain 'A' and resid 243 through 245' Processing helix chain 'A' and resid 255 through 268 Processing helix chain 'A' and resid 280 through 283 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 332 Processing helix chain 'A' and resid 343 through 358 Processing helix chain 'A' and resid 367 through 379 Processing helix chain 'A' and resid 388 through 405 Processing helix chain 'A' and resid 533 through 543 Processing helix chain 'A' and resid 555 through 560 Processing helix chain 'A' and resid 562 through 568 removed outlier: 3.755A pdb=" N HIS A 568 " --> pdb=" O GLN A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 588 Processing helix chain 'A' and resid 611 through 622 Processing helix chain 'A' and resid 634 through 636 No H-bonds generated for 'chain 'A' and resid 634 through 636' Processing helix chain 'A' and resid 640 through 647 Processing helix chain 'A' and resid 654 through 658 removed outlier: 4.574A pdb=" N GLU A 657 " --> pdb=" O VAL A 654 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU A 658 " --> pdb=" O GLY A 655 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 654 through 658' 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 728 Processing helix chain 'A' and resid 734 through 748 Processing helix chain 'A' and resid 751 through 755 Processing helix chain 'A' and resid 768 through 789 Processing helix chain 'A' and resid 797 through 806 Processing helix chain 'A' and resid 815 through 826 Processing helix chain 'A' and resid 828 through 833 Processing helix chain 'B' and resid 168 through 173 Processing helix chain 'B' and resid 184 through 194 Processing helix chain 'B' and resid 212 through 225 Processing helix chain 'B' and resid 242 through 245 No H-bonds generated for 'chain 'B' and resid 242 through 245' Processing helix chain 'B' and resid 254 through 267 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 Processing helix chain 'B' and resid 327 through 332 Processing helix chain 'B' and resid 343 through 361 Processing helix chain 'B' and resid 367 through 380 Processing helix chain 'B' and resid 388 through 407 Processing helix chain 'B' and resid 533 through 543 Processing helix chain 'B' and resid 553 through 569 Processing helix chain 'B' and resid 574 through 589 Processing helix chain 'B' and resid 612 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 640 through 647 removed outlier: 3.651A pdb=" N VAL B 643 " --> pdb=" O LYS B 640 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER B 644 " --> pdb=" O HIS B 641 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VAL B 647 " --> pdb=" O SER B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 661 through 668 Processing helix chain 'B' and resid 679 through 681 No H-bonds generated for 'chain 'B' and resid 679 through 681' 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 727 Processing helix chain 'B' and resid 734 through 748 Processing helix chain 'B' and resid 768 through 789 Processing helix chain 'B' and resid 797 through 805 Processing helix chain 'B' and resid 815 through 835 Proline residue: B 828 - end of helix Processing helix chain 'C' and resid 160 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 213 through 225 Processing helix chain 'C' and resid 242 through 246 Processing helix chain 'C' and resid 254 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 299 through 304 Processing helix chain 'C' and resid 316 through 322 Processing helix chain 'C' and resid 327 through 331 Processing helix chain 'C' and resid 343 through 361 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 588 Processing helix chain 'C' and resid 611 through 622 Processing helix chain 'C' and resid 640 through 647 removed outlier: 3.871A pdb=" N VAL C 643 " --> pdb=" O LYS C 640 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ARG C 645 " --> pdb=" O SER C 642 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL C 647 " --> pdb=" O SER C 644 " (cutoff:3.500A) 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 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 753 through 756 No H-bonds generated for 'chain 'C' and resid 753 through 756' Processing helix chain 'C' and resid 768 through 789 removed outlier: 3.819A pdb=" N GLU C 788 " --> pdb=" O LYS C 784 " (cutoff:3.500A) removed outlier: 4.057A 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 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 169 through 173 Processing helix chain 'D' and resid 184 through 194 Processing helix chain 'D' and resid 212 through 225 Processing helix chain 'D' and resid 242 through 248 removed outlier: 3.809A pdb=" N ALA D 247 " --> pdb=" O GLY D 243 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N GLY D 248 " --> pdb=" O ALA D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 268 Processing helix chain 'D' and resid 280 through 284 removed outlier: 3.751A pdb=" N VAL D 284 " --> pdb=" O LEU D 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 280 through 284' Processing helix chain 'D' and resid 300 through 305 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 379 Processing helix chain 'D' and resid 388 through 406 Processing helix chain 'D' and resid 410 through 426 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 567 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 645 Processing helix chain 'D' and resid 656 through 658 No H-bonds generated for 'chain 'D' and resid 656 through 658' 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 751 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 824 Processing helix chain 'D' and resid 826 through 834 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 243 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 299 through 305 Processing helix chain 'E' and resid 316 through 322 Processing helix chain 'E' and resid 343 through 361 Processing helix chain 'E' and resid 367 through 379 Processing helix chain 'E' and resid 388 through 406 Processing helix chain 'E' and resid 533 through 541 Processing helix chain 'E' and resid 554 through 560 Processing helix chain 'E' and resid 562 through 569 Processing helix chain 'E' and resid 574 through 589 Processing helix chain 'E' and resid 611 through 623 removed outlier: 3.921A pdb=" N CYS E 615 " --> pdb=" O LYS E 611 " (cutoff:3.500A) Processing helix chain 'E' and resid 634 through 636 No H-bonds generated for 'chain 'E' and resid 634 through 636' Processing helix chain 'E' and resid 641 through 646 Processing helix chain 'E' and resid 664 through 667 No H-bonds generated for 'chain 'E' and resid 664 through 667' 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 684 through 696 Processing helix chain 'E' and resid 722 through 728 Processing helix chain 'E' and resid 735 through 748 Processing helix chain 'E' and resid 751 through 755 Processing helix chain 'E' and resid 768 through 789 Processing helix chain 'E' and resid 797 through 806 Processing helix chain 'E' and resid 815 through 833 Proline residue: E 828 - end of helix Processing helix chain 'F' and resid 169 through 173 Processing helix chain 'F' and resid 184 through 195 Processing helix chain 'F' and resid 212 through 225 Processing helix chain 'F' and resid 242 through 247 Processing helix chain 'F' and resid 255 through 269 Processing helix chain 'F' and resid 280 through 284 Processing helix chain 'F' and resid 300 through 305 removed outlier: 3.679A pdb=" N ARG F 305 " --> pdb=" O PRO F 301 " (cutoff:3.500A) Processing helix chain 'F' and resid 316 through 322 Processing helix chain 'F' and resid 343 through 360 Processing helix chain 'F' and resid 367 through 380 Processing helix chain 'F' and resid 388 through 405 Processing helix chain 'F' and resid 533 through 542 Processing helix chain 'F' and resid 556 through 569 removed outlier: 3.529A pdb=" N HIS F 568 " --> pdb=" O GLN F 564 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG F 569 " --> pdb=" O GLU F 565 " (cutoff:3.500A) Processing helix chain 'F' and resid 574 through 589 Processing helix chain 'F' and resid 611 through 622 Processing helix chain 'F' and resid 640 through 645 Processing helix chain 'F' and resid 654 through 656 No H-bonds generated for 'chain 'F' and resid 654 through 656' Processing helix chain 'F' and resid 664 through 667 No H-bonds generated for 'chain 'F' and resid 664 through 667' 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 696 Processing helix chain 'F' and resid 722 through 726 Processing helix chain 'F' and resid 734 through 748 Processing helix chain 'F' and resid 751 through 756 Processing helix chain 'F' and resid 768 through 789 Processing helix chain 'F' and resid 797 through 807 Processing helix chain 'F' and resid 814 through 835 Proline residue: F 828 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 165 through 167 Processing sheet with id= B, first strand: chain 'A' and resid 311 through 314 removed outlier: 7.817A pdb=" N THR A 314 " --> pdb=" O PRO A 202 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N LEU A 204 " --> pdb=" O THR A 314 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N GLN A 334 " --> pdb=" O VAL A 203 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ILE A 205 " --> pdb=" O GLN A 334 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL A 336 " --> pdb=" O ILE A 205 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 759 through 762 removed outlier: 3.658A pdb=" N GLU A 759 " --> pdb=" O SER A 600 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU A 602 " --> pdb=" O GLU A 759 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU A 604 " --> pdb=" O VAL A 761 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLY A 599 " --> pdb=" O THR A 712 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N SER A 672 " --> pdb=" O VAL A 713 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N ILE A 715 " --> pdb=" O SER A 672 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ILE A 674 " --> pdb=" O ILE A 715 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N THR A 717 " --> pdb=" O ILE A 674 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N LEU A 676 " --> pdb=" O THR A 717 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 698 through 700 removed outlier: 3.561A pdb=" N LEU A 699 " --> pdb=" O VAL A 707 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 792 through 795 Processing sheet with id= F, first strand: chain 'B' and resid 165 through 167 removed outlier: 5.432A pdb=" N ASP B 278 " --> pdb=" O LEU B 240 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N VAL B 311 " --> pdb=" O ILE B 277 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N GLN B 334 " --> pdb=" O VAL B 203 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N ILE B 205 " --> pdb=" O GLN B 334 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N VAL B 336 " --> pdb=" O ILE B 205 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 601 through 603 removed outlier: 7.061A pdb=" N GLU B 759 " --> pdb=" O LEU B 602 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'B' and resid 630 through 633 removed outlier: 6.070A pdb=" N VAL B 713 " --> pdb=" O ILE B 674 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N LEU B 676 " --> pdb=" O VAL B 713 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ILE B 715 " --> pdb=" O LEU B 676 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 698 through 701 removed outlier: 3.868A pdb=" N ARG B 705 " --> pdb=" O ASP B 701 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 793 through 795 removed outlier: 6.330A pdb=" N ILE B 844 " --> pdb=" O HIS B 794 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'C' and resid 165 through 167 removed outlier: 4.850A pdb=" N ASP C 278 " --> pdb=" O LEU C 240 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N VAL C 311 " --> pdb=" O ILE C 277 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N THR C 314 " --> pdb=" O PRO C 202 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N LEU C 204 " --> pdb=" O THR C 314 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N GLN C 334 " --> pdb=" O VAL C 203 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ILE C 205 " --> pdb=" O GLN C 334 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N VAL C 336 " --> pdb=" O ILE C 205 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 759 through 762 removed outlier: 3.559A pdb=" N LEU C 602 " --> pdb=" O GLU C 759 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 698 through 700 Processing sheet with id= N, first strand: chain 'C' and resid 792 through 795 Processing sheet with id= O, first strand: chain 'D' and resid 165 through 167 removed outlier: 5.099A pdb=" N ASP D 278 " --> pdb=" O LEU D 240 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N VAL D 311 " --> pdb=" O ILE D 277 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 759 through 761 removed outlier: 3.507A pdb=" N GLU D 759 " --> pdb=" O SER D 600 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU D 602 " --> pdb=" O GLU D 759 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR D 717 " --> pdb=" O LEU D 676 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N VAL D 630 " --> pdb=" O LEU D 675 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ASP D 677 " --> pdb=" O VAL D 630 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE D 632 " --> pdb=" O ASP D 677 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 845 through 848 removed outlier: 3.693A pdb=" N ARG D 845 " --> pdb=" O VAL D 856 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 335 through 337 removed outlier: 6.579A pdb=" N VAL E 203 " --> pdb=" O VAL E 336 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ALA E 313 " --> pdb=" O ILE E 277 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 236 through 238 removed outlier: 3.585A pdb=" N LEU E 238 " --> pdb=" O ILE E 274 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 599 through 603 removed outlier: 3.697A pdb=" N THR E 717 " --> pdb=" O LEU E 676 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N VAL E 630 " --> pdb=" O LEU E 675 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N ASP E 677 " --> pdb=" O VAL E 630 " (cutoff:3.500A) removed outlier: 6.954A 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 792 through 795 removed outlier: 3.557A 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 Processing sheet with id= X, first strand: chain 'F' and resid 334 through 337 removed outlier: 6.937A pdb=" N GLY F 312 " --> pdb=" O LEU F 204 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N GLY F 206 " --> pdb=" O GLY F 312 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N THR F 314 " --> pdb=" O GLY F 206 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'F' and resid 599 through 603 removed outlier: 3.802A pdb=" N MET F 716 " --> pdb=" O PHE F 601 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'F' and resid 698 through 700 removed outlier: 3.501A pdb=" N VAL F 707 " --> pdb=" O LEU F 699 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'F' and resid 793 through 795 removed outlier: 6.238A pdb=" N ILE F 844 " --> pdb=" O HIS F 794 " (cutoff:3.500A) 1212 hydrogen bonds defined for protein. 3612 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: 10.34 Time building geometry restraints manager: 12.54 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: 10116 1.36 - 1.50: 8035 1.50 - 1.65: 10640 1.65 - 1.80: 152 1.80 - 1.94: 45 Bond restraints: 28988 Sorted by residual: bond pdb=" CB GLN C 692 " pdb=" CG GLN C 692 " ideal model delta sigma weight residual 1.520 1.424 0.096 3.00e-02 1.11e+03 1.02e+01 bond pdb=" CB VAL D 580 " pdb=" CG1 VAL D 580 " ideal model delta sigma weight residual 1.521 1.417 0.104 3.30e-02 9.18e+02 1.00e+01 bond pdb=" CG GLN C 692 " pdb=" CD GLN C 692 " ideal model delta sigma weight residual 1.516 1.440 0.076 2.50e-02 1.60e+03 9.23e+00 bond pdb=" CB LEU D 618 " pdb=" CG LEU D 618 " ideal model delta sigma weight residual 1.530 1.470 0.060 2.00e-02 2.50e+03 8.90e+00 bond pdb=" CB GLN B 692 " pdb=" CG GLN B 692 " ideal model delta sigma weight residual 1.520 1.439 0.081 3.00e-02 1.11e+03 7.37e+00 ... (remaining 28983 not shown) Histogram of bond angle deviations from ideal: 94.87 - 103.72: 415 103.72 - 112.58: 15252 112.58 - 121.44: 16808 121.44 - 130.29: 6571 130.29 - 139.15: 139 Bond angle restraints: 39185 Sorted by residual: angle pdb=" N VAL B 686 " pdb=" CA VAL B 686 " pdb=" C VAL B 686 " ideal model delta sigma weight residual 112.96 106.52 6.44 1.00e+00 1.00e+00 4.14e+01 angle pdb=" N VAL E 666 " pdb=" CA VAL E 666 " pdb=" C VAL E 666 " ideal model delta sigma weight residual 112.96 107.50 5.46 1.00e+00 1.00e+00 2.98e+01 angle pdb=" CB LYS B 199 " pdb=" CG LYS B 199 " pdb=" CD LYS B 199 " ideal model delta sigma weight residual 111.30 100.17 11.13 2.30e+00 1.89e-01 2.34e+01 angle pdb=" C LEU B 386 " pdb=" N PRO B 387 " pdb=" CA PRO B 387 " ideal model delta sigma weight residual 127.00 136.59 -9.59 2.40e+00 1.74e-01 1.60e+01 angle pdb=" N ARG D 815 " pdb=" CA ARG D 815 " pdb=" C ARG D 815 " ideal model delta sigma weight residual 109.81 118.48 -8.67 2.21e+00 2.05e-01 1.54e+01 ... (remaining 39180 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.10: 17558 32.10 - 64.19: 183 64.19 - 96.29: 17 96.29 - 128.39: 2 128.39 - 160.48: 2 Dihedral angle restraints: 17762 sinusoidal: 7445 harmonic: 10317 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 180.00 142.77 37.23 0 5.00e+00 4.00e-02 5.55e+01 dihedral pdb=" O1B ADP A1002 " pdb=" O3A ADP A1002 " pdb=" PB ADP A1002 " pdb=" PA ADP A1002 " ideal model delta sinusoidal sigma weight residual 300.00 139.51 160.48 1 2.00e+01 2.50e-03 4.66e+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 72.63 -132.62 1 2.00e+01 2.50e-03 4.03e+01 ... (remaining 17759 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 3330 0.067 - 0.134: 962 0.134 - 0.200: 133 0.200 - 0.267: 8 0.267 - 0.334: 3 Chirality restraints: 4436 Sorted by residual: chirality pdb=" CB ILE B 205 " pdb=" CA ILE B 205 " pdb=" CG1 ILE B 205 " pdb=" CG2 ILE B 205 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.79e+00 chirality pdb=" CB THR C 282 " pdb=" CA THR C 282 " pdb=" OG1 THR C 282 " pdb=" CG2 THR C 282 " both_signs ideal model delta sigma weight residual False 2.55 2.25 0.30 2.00e-01 2.50e+01 2.20e+00 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 1.98e+00 ... (remaining 4433 not shown) Planarity restraints: 5114 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS D 683 " 0.059 5.00e-02 4.00e+02 8.94e-02 1.28e+01 pdb=" N PRO D 684 " -0.155 5.00e-02 4.00e+02 pdb=" CA PRO D 684 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO D 684 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 763 " 0.018 2.00e-02 2.50e+03 2.42e-02 1.03e+01 pdb=" CG PHE C 763 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 PHE C 763 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 PHE C 763 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE C 763 " -0.017 2.00e-02 2.50e+03 pdb=" CE2 PHE C 763 " 0.010 2.00e-02 2.50e+03 pdb=" CZ PHE C 763 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ADP A1002 " 0.014 2.00e-02 2.50e+03 1.87e-02 9.58e+00 pdb=" C2 ADP A1002 " 0.009 2.00e-02 2.50e+03 pdb=" C4 ADP A1002 " -0.051 2.00e-02 2.50e+03 pdb=" C5 ADP A1002 " 0.002 2.00e-02 2.50e+03 pdb=" C6 ADP A1002 " -0.001 2.00e-02 2.50e+03 pdb=" C8 ADP A1002 " 0.013 2.00e-02 2.50e+03 pdb=" N1 ADP A1002 " 0.001 2.00e-02 2.50e+03 pdb=" N3 ADP A1002 " 0.020 2.00e-02 2.50e+03 pdb=" N6 ADP A1002 " -0.000 2.00e-02 2.50e+03 pdb=" N7 ADP A1002 " 0.009 2.00e-02 2.50e+03 pdb=" N9 ADP A1002 " -0.016 2.00e-02 2.50e+03 ... (remaining 5111 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 2520 2.73 - 3.27: 27663 3.27 - 3.81: 47126 3.81 - 4.36: 56622 4.36 - 4.90: 96502 Nonbonded interactions: 230433 Sorted by model distance: nonbonded pdb=" O2A AGS D 902 " pdb=" O2B AGS D 902 " model vdw 2.187 2.440 nonbonded pdb=" O1B AGS C1002 " pdb=" O2G AGS C1002 " model vdw 2.226 2.440 nonbonded pdb=" O1B AGS B1002 " pdb=" O2G AGS B1002 " model vdw 2.231 2.440 nonbonded pdb=" O2A AGS C1002 " pdb=" O2B AGS C1002 " model vdw 2.236 2.440 nonbonded pdb=" O1B AGS B1001 " pdb=" O2G AGS B1001 " model vdw 2.238 2.440 ... (remaining 230428 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 858)) selection = (chain 'C' and (resid 159 through 287 or resid 293 through 408 or resid 527 thro \ ugh 858)) selection = (chain 'D' and (resid 159 through 408 or resid 527 through 858)) selection = (chain 'E' and resid 159 through 858) selection = (chain 'F' and resid 159 through 858) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 31 5.49 5 S 109 5.16 5 C 17822 2.51 5 N 5179 2.21 5 O 5416 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 1.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.190 Construct map_model_manager: 0.030 Extract box with map and model: 8.120 Check model and map are aligned: 0.420 Convert atoms to be neutral: 0.240 Process input model: 71.450 Find NCS groups from input model: 2.110 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Set scattering table: 0.030 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4566 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 0.104 28988 Z= 0.704 Angle : 1.090 13.526 39185 Z= 0.578 Chirality : 0.061 0.334 4436 Planarity : 0.008 0.089 5114 Dihedral : 10.530 160.483 11110 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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: -4.07 (0.11), residues: 3532 helix: -2.38 (0.09), residues: 1931 sheet: -3.20 (0.24), residues: 372 loop : -2.74 (0.15), residues: 1229 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1028 residues out of total 2994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1026 time to evaluate : 3.205 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 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 1028 average time/residue: 0.4535 time to fit residues: 694.9074 Evaluate side-chains 577 residues out of total 2994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 577 time to evaluate : 3.429 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.9077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 300 optimal weight: 0.5980 chunk 269 optimal weight: 5.9990 chunk 149 optimal weight: 0.9990 chunk 92 optimal weight: 0.8980 chunk 182 optimal weight: 1.9990 chunk 144 optimal weight: 3.9990 chunk 279 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 169 optimal weight: 0.6980 chunk 207 optimal weight: 10.0000 chunk 323 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 GLN ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 ASN ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 362 HIS A 641 HIS ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 747 HIS A 794 HIS A 849 ASN B 195 GLN B 281 HIS B 297 ASN ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 778 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 822 GLN B 823 GLN ** B 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 ASN C 641 HIS ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 858 HIS D 192 GLN D 692 GLN D 806 ASN D 822 GLN E 309 HIS E 334 GLN ** E 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 567 HIS E 574 ASN E 688 ASN ** E 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 858 HIS F 195 GLN ** F 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 726 GLN F 849 ASN ** F 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5185 moved from start: 0.3859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.081 28988 Z= 0.253 Angle : 0.766 15.816 39185 Z= 0.381 Chirality : 0.048 0.276 4436 Planarity : 0.006 0.068 5114 Dihedral : 8.645 143.029 4064 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 18.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer Outliers : 2.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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: -2.57 (0.13), residues: 3532 helix: -0.94 (0.11), residues: 1927 sheet: -2.82 (0.24), residues: 395 loop : -2.33 (0.16), residues: 1210 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 712 residues out of total 2994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 627 time to evaluate : 3.484 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 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: 85 outliers final: 40 residues processed: 677 average time/residue: 0.4543 time to fit residues: 481.1239 Evaluate side-chains 518 residues out of total 2994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 478 time to evaluate : 3.278 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 0 residues processed: 40 average time/residue: 0.2666 time to fit residues: 24.8474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 179 optimal weight: 0.3980 chunk 100 optimal weight: 7.9990 chunk 269 optimal weight: 2.9990 chunk 220 optimal weight: 8.9990 chunk 89 optimal weight: 0.4980 chunk 323 optimal weight: 7.9990 chunk 349 optimal weight: 0.8980 chunk 288 optimal weight: 0.3980 chunk 321 optimal weight: 7.9990 chunk 110 optimal weight: 5.9990 chunk 259 optimal weight: 10.0000 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 174 GLN ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 778 GLN B 362 HIS ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 822 GLN ** B 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 159 GLN ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 HIS E 361 HIS E 806 ASN E 831 GLN E 849 ASN F 281 HIS ** F 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 692 GLN ** F 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5520 moved from start: 0.4999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 28988 Z= 0.219 Angle : 0.715 13.150 39185 Z= 0.354 Chirality : 0.045 0.185 4436 Planarity : 0.005 0.071 5114 Dihedral : 8.305 144.565 4064 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 18.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer Outliers : 2.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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: -1.86 (0.14), residues: 3532 helix: -0.34 (0.11), residues: 1940 sheet: -2.48 (0.25), residues: 400 loop : -2.10 (0.17), residues: 1192 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 2994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 544 time to evaluate : 3.481 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 75 outliers final: 30 residues processed: 591 average time/residue: 0.3984 time to fit residues: 374.3173 Evaluate side-chains 484 residues out of total 2994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 454 time to evaluate : 3.475 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.2825 time to fit residues: 20.2940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 319 optimal weight: 0.4980 chunk 243 optimal weight: 10.0000 chunk 168 optimal weight: 4.9990 chunk 35 optimal weight: 8.9990 chunk 154 optimal weight: 2.9990 chunk 217 optimal weight: 0.0870 chunk 325 optimal weight: 0.8980 chunk 344 optimal weight: 6.9990 chunk 169 optimal weight: 0.9990 chunk 308 optimal weight: 10.0000 chunk 92 optimal weight: 1.9990 overall best weight: 0.8962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 GLN ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 281 HIS A 297 ASN ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 281 HIS ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 221 GLN E 269 GLN ** E 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5767 moved from start: 0.5781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.063 28988 Z= 0.204 Angle : 0.685 12.837 39185 Z= 0.336 Chirality : 0.044 0.183 4436 Planarity : 0.005 0.081 5114 Dihedral : 8.058 146.564 4064 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 18.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer Outliers : 2.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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: -1.41 (0.14), residues: 3532 helix: 0.02 (0.12), residues: 1948 sheet: -2.22 (0.25), residues: 395 loop : -1.93 (0.17), residues: 1189 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 2994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 519 time to evaluate : 3.279 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 73 outliers final: 29 residues processed: 563 average time/residue: 0.3834 time to fit residues: 351.6712 Evaluate side-chains 470 residues out of total 2994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 441 time to evaluate : 3.622 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.2643 time to fit residues: 19.4198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 286 optimal weight: 6.9990 chunk 195 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 256 optimal weight: 0.5980 chunk 141 optimal weight: 10.0000 chunk 293 optimal weight: 0.9980 chunk 237 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 175 optimal weight: 2.9990 chunk 308 optimal weight: 10.0000 chunk 86 optimal weight: 5.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 GLN ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 806 ASN ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 281 HIS C 309 HIS ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 692 GLN E 824 GLN ** F 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 857 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6172 moved from start: 0.6787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.075 28988 Z= 0.229 Angle : 0.724 15.438 39185 Z= 0.354 Chirality : 0.046 0.277 4436 Planarity : 0.005 0.061 5114 Dihedral : 7.916 135.046 4064 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 17.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer Outliers : 2.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.14), residues: 3532 helix: 0.23 (0.12), residues: 1939 sheet: -1.91 (0.24), residues: 395 loop : -1.78 (0.17), residues: 1198 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 596 residues out of total 2994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 535 time to evaluate : 3.363 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: 61 outliers final: 26 residues processed: 570 average time/residue: 0.3893 time to fit residues: 358.9558 Evaluate side-chains 482 residues out of total 2994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 456 time to evaluate : 2.967 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.2954 time to fit residues: 18.6036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 115 optimal weight: 9.9990 chunk 309 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 202 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 344 optimal weight: 6.9990 chunk 285 optimal weight: 7.9990 chunk 159 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 113 optimal weight: 20.0000 chunk 180 optimal weight: 0.0570 overall best weight: 2.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 GLN ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 454 GLN ** D 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 573 GLN D 620 ASN D 703 GLN D 764 HIS ** D 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 574 ASN E 778 GLN E 857 GLN F 225 ASN ** F 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 688 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6897 moved from start: 0.8729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.103 28988 Z= 0.331 Angle : 0.840 19.314 39185 Z= 0.412 Chirality : 0.051 0.404 4436 Planarity : 0.006 0.072 5114 Dihedral : 8.187 132.607 4064 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 19.51 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.92 % Favored : 94.05 % Rotamer Outliers : 2.32 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.14), residues: 3532 helix: 0.06 (0.12), residues: 1927 sheet: -1.70 (0.25), residues: 394 loop : -1.52 (0.18), residues: 1211 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 633 residues out of total 2994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 564 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 outliers start: 69 outliers final: 31 residues processed: 605 average time/residue: 0.4002 time to fit residues: 387.7000 Evaluate side-chains 488 residues out of total 2994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 457 time to evaluate : 3.643 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.2637 time to fit residues: 19.9129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 332 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 196 optimal weight: 0.9980 chunk 251 optimal weight: 9.9990 chunk 194 optimal weight: 3.9990 chunk 289 optimal weight: 0.8980 chunk 192 optimal weight: 4.9990 chunk 343 optimal weight: 6.9990 chunk 214 optimal weight: 0.9980 chunk 209 optimal weight: 4.9990 chunk 158 optimal weight: 2.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 GLN A 595 ASN B 719 ASN ** B 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 GLN ** C 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 GLN ** D 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 620 ASN F 225 ASN F 688 ASN F 692 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 moved from start: 0.9466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.059 28988 Z= 0.238 Angle : 0.735 17.127 39185 Z= 0.361 Chirality : 0.046 0.206 4436 Planarity : 0.005 0.061 5114 Dihedral : 7.908 126.599 4064 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 19.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer Outliers : 1.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.14), residues: 3532 helix: 0.30 (0.12), residues: 1922 sheet: -1.39 (0.25), residues: 394 loop : -1.47 (0.18), residues: 1216 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 2994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 529 time to evaluate : 3.858 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: 48 outliers final: 18 residues processed: 551 average time/residue: 0.3948 time to fit residues: 357.2044 Evaluate side-chains 468 residues out of total 2994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 450 time to evaluate : 3.570 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.2593 time to fit residues: 13.5126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 212 optimal weight: 3.9990 chunk 137 optimal weight: 0.7980 chunk 204 optimal weight: 6.9990 chunk 103 optimal weight: 6.9990 chunk 67 optimal weight: 0.9980 chunk 66 optimal weight: 6.9990 chunk 218 optimal weight: 8.9990 chunk 233 optimal weight: 0.7980 chunk 169 optimal weight: 0.7980 chunk 31 optimal weight: 6.9990 chunk 269 optimal weight: 10.0000 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 HIS B 174 GLN B 806 ASN ** B 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 GLN ** C 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 620 ASN ** D 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 1.0077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 28988 Z= 0.236 Angle : 0.730 13.375 39185 Z= 0.357 Chirality : 0.046 0.198 4436 Planarity : 0.005 0.060 5114 Dihedral : 7.858 135.212 4064 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 20.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer Outliers : 1.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.14), residues: 3532 helix: 0.40 (0.12), residues: 1920 sheet: -1.30 (0.25), residues: 388 loop : -1.39 (0.18), residues: 1224 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 2994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 489 time to evaluate : 3.287 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: 36 outliers final: 12 residues processed: 503 average time/residue: 0.3810 time to fit residues: 313.1343 Evaluate side-chains 440 residues out of total 2994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 428 time to evaluate : 3.329 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2774 time to fit residues: 10.7409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 312 optimal weight: 4.9990 chunk 328 optimal weight: 20.0000 chunk 299 optimal weight: 6.9990 chunk 319 optimal weight: 0.9980 chunk 192 optimal weight: 6.9990 chunk 139 optimal weight: 6.9990 chunk 251 optimal weight: 5.9990 chunk 98 optimal weight: 0.9990 chunk 288 optimal weight: 6.9990 chunk 302 optimal weight: 0.9980 chunk 318 optimal weight: 6.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 711 ASN B 192 GLN B 719 ASN B 778 GLN ** B 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 GLN ** C 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 ASN C 334 GLN ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 GLN E 822 GLN F 159 GLN ** F 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 1.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.076 28988 Z= 0.331 Angle : 0.852 19.494 39185 Z= 0.420 Chirality : 0.051 0.374 4436 Planarity : 0.006 0.099 5114 Dihedral : 8.171 140.568 4064 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 22.63 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.54 % Favored : 93.43 % Rotamer Outliers : 1.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.14), residues: 3532 helix: 0.20 (0.12), residues: 1917 sheet: -1.34 (0.26), residues: 378 loop : -1.49 (0.18), residues: 1237 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 2994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 494 time to evaluate : 3.609 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 outliers start: 51 outliers final: 24 residues processed: 517 average time/residue: 0.4048 time to fit residues: 348.6128 Evaluate side-chains 446 residues out of total 2994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 422 time to evaluate : 3.060 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.2502 time to fit residues: 15.7616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 209 optimal weight: 6.9990 chunk 338 optimal weight: 20.0000 chunk 206 optimal weight: 8.9990 chunk 160 optimal weight: 5.9990 chunk 235 optimal weight: 0.0980 chunk 354 optimal weight: 20.0000 chunk 326 optimal weight: 5.9990 chunk 282 optimal weight: 9.9990 chunk 29 optimal weight: 0.8980 chunk 218 optimal weight: 6.9990 chunk 173 optimal weight: 3.9990 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 GLN B 726 GLN B 806 ASN C 195 GLN C 281 HIS ** C 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 192 GLN ** D 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 683 HIS E 195 GLN E 641 HIS ** F 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 688 ASN ** F 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 1.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.078 28988 Z= 0.346 Angle : 0.860 19.558 39185 Z= 0.428 Chirality : 0.051 0.291 4436 Planarity : 0.006 0.106 5114 Dihedral : 8.249 147.889 4064 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 22.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer Outliers : 0.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.14), residues: 3532 helix: 0.04 (0.12), residues: 1925 sheet: -1.43 (0.26), residues: 389 loop : -1.41 (0.18), residues: 1218 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 2994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 488 time to evaluate : 3.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 7 residues processed: 492 average time/residue: 0.3808 time to fit residues: 309.3366 Evaluate side-chains 428 residues out of total 2994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 421 time to evaluate : 3.380 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 7 average time/residue: 0.2605 time to fit residues: 7.9632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 224 optimal weight: 1.9990 chunk 300 optimal weight: 0.8980 chunk 86 optimal weight: 10.0000 chunk 260 optimal weight: 5.9990 chunk 41 optimal weight: 0.0170 chunk 78 optimal weight: 0.8980 chunk 282 optimal weight: 5.9990 chunk 118 optimal weight: 0.9980 chunk 290 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 overall best weight: 0.7618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 806 ASN B 857 GLN C 195 GLN C 201 ASN C 334 GLN C 726 GLN C 778 GLN ** C 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 688 ASN E 822 GLN ** F 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 824 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.123527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.098961 restraints weight = 71274.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.101272 restraints weight = 40434.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.102751 restraints weight = 27141.263| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 1.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.093 28988 Z= 0.224 Angle : 0.791 17.255 39185 Z= 0.385 Chirality : 0.047 0.393 4436 Planarity : 0.005 0.059 5114 Dihedral : 7.984 147.380 4064 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 21.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer Outliers : 0.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.14), residues: 3532 helix: 0.35 (0.12), residues: 1899 sheet: -1.34 (0.25), residues: 400 loop : -1.35 (0.18), residues: 1233 =============================================================================== Job complete usr+sys time: 6829.46 seconds wall clock time: 123 minutes 46.40 seconds (7426.40 seconds total)