Starting phenix.real_space_refine (version: dev) on Mon May 16 15:28:41 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rn3_4941/05_2022/6rn3_4941_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rn3_4941/05_2022/6rn3_4941.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rn3_4941/05_2022/6rn3_4941.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rn3_4941/05_2022/6rn3_4941.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rn3_4941/05_2022/6rn3_4941_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rn3_4941/05_2022/6rn3_4941_updated.pdb" } resolution = 4.0 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= 0.001 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral 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 "A ARG 550": "NH1" <-> "NH2" Residue "A TYR 653": "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 "B TYR 653": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 332": "NH1" <-> "NH2" Residue "F ARG 528": "NH1" <-> "NH2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 32871 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 5406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 684, 5406 Classifications: {'peptide': 684} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 23, 'TRANS': 659, 'PCIS': 1} Chain breaks: 4 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: 5430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 689, 5430 Classifications: {'peptide': 689} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 22, 'TRANS': 664, 'PCIS': 2} 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: "C" Number of atoms: 5430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 689, 5430 Classifications: {'peptide': 689} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 23, 'TRANS': 664, 'PCIS': 1} 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: 5406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 684, 5406 Classifications: {'peptide': 684} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 23, 'TRANS': 659, 'PCIS': 1} Chain breaks: 4 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: 5406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 684, 5406 Classifications: {'peptide': 684} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 22, 'TRANS': 659, 'PCIS': 2} 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: 5340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 675, 5340 Classifications: {'peptide': 675} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 22, 'TRANS': 651, 'PCIS': 1} Chain breaks: 5 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: {'AGS': 1, 'ADP': 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: 18.05, per 1000 atoms: 0.55 Number of scatterers: 32871 At special positions: 0 Unit cell: (144.56, 182, 166.4, 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 127 16.00 P 31 15.00 O 6295 8.00 N 5933 7.00 C 20485 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=19, symmetry=0 Number of additional bonds: simple=19, symmetry=0 Coordination: Other bonds: Time building additional restraints: 14.05 Conformation dependent library (CDL) restraints added in 5.6 seconds 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7680 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 187 helices and 24 sheets defined 55.6% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.07 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 194 Processing helix chain 'A' and resid 212 through 225 Processing helix chain 'A' and resid 242 through 248 removed outlier: 3.596A pdb=" N LEU A 245 " --> pdb=" O MET A 242 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL A 246 " --> pdb=" O GLY A 243 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N ALA A 247 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLY A 248 " --> pdb=" O LEU A 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 242 through 248' Processing helix chain 'A' and resid 255 through 269 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 359 removed outlier: 4.830A pdb=" N LEU A 359 " --> pdb=" O GLU A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 380 Processing helix chain 'A' and resid 388 through 405 Processing helix chain 'A' and resid 410 through 429 Processing helix chain 'A' and resid 444 through 492 Processing helix chain 'A' and resid 495 through 523 removed outlier: 4.007A pdb=" N SER A 499 " --> pdb=" O LEU A 495 " (cutoff:3.500A) Proline residue: A 507 - end of helix 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 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 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 805 Processing helix chain 'A' and resid 815 through 824 Processing helix chain 'A' and resid 828 through 834 Processing helix chain 'B' and resid 161 through 164 No H-bonds generated for 'chain 'B' and resid 161 through 164' 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 230 through 232 No H-bonds generated for 'chain 'B' and resid 230 through 232' Processing helix chain 'B' and resid 254 through 266 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 331 Processing helix chain 'B' and resid 343 through 360 Processing helix chain 'B' and resid 367 through 380 Processing helix chain 'B' and resid 388 through 405 Processing helix chain 'B' and resid 411 through 429 Processing helix chain 'B' and resid 444 through 492 Processing helix chain 'B' and resid 496 through 523 Proline residue: B 507 - end of helix Processing helix chain 'B' and resid 533 through 544 Processing helix chain 'B' and resid 553 through 569 Processing helix chain 'B' and resid 574 through 589 Processing helix chain 'B' and resid 611 through 622 removed outlier: 3.590A pdb=" N CYS B 615 " --> pdb=" O LYS B 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 647 removed outlier: 4.044A pdb=" N VAL B 647 " --> pdb=" O SER B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 658 removed outlier: 4.402A pdb=" N GLU B 657 " --> pdb=" O VAL B 654 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLU B 658 " --> pdb=" O GLY B 655 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 654 through 658' Processing helix chain 'B' and resid 662 through 668 Processing helix chain 'B' and resid 688 through 696 Processing helix chain 'B' and resid 720 through 728 removed outlier: 4.407A pdb=" N ASP B 723 " --> pdb=" O LEU B 720 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU B 724 " --> pdb=" O GLY B 721 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE B 725 " --> pdb=" O SER B 722 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG B 728 " --> pdb=" O ILE B 725 " (cutoff:3.500A) 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 806 Processing helix chain 'B' and resid 815 through 834 Proline residue: B 828 - end of helix Processing helix chain 'C' and resid 160 through 163 No H-bonds generated for 'chain 'C' and resid 160 through 163' Processing helix chain 'C' and resid 169 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 230 through 232 No H-bonds generated for 'chain 'C' and resid 230 through 232' Processing helix chain 'C' and resid 242 through 248 removed outlier: 3.691A pdb=" N ALA C 247 " --> pdb=" O GLY C 243 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N GLY C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 269 removed outlier: 4.004A pdb=" N GLN C 269 " --> pdb=" O ASP C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 283 No H-bonds generated for 'chain 'C' and resid 280 through 283' Processing helix chain 'C' and resid 300 through 304 Processing helix chain 'C' and resid 317 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 Processing helix chain 'C' and resid 367 through 379 Processing helix chain 'C' and resid 388 through 406 Processing helix chain 'C' and resid 411 through 429 Processing helix chain 'C' and resid 444 through 492 Processing helix chain 'C' and resid 495 through 523 removed outlier: 4.269A pdb=" N SER C 499 " --> pdb=" O LEU C 495 " (cutoff:3.500A) Proline residue: C 507 - end of helix 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 567 Processing helix chain 'C' and resid 574 through 589 Processing helix chain 'C' and resid 611 through 622 Processing helix chain 'C' and resid 640 through 646 Processing helix chain 'C' and resid 662 through 668 Processing helix chain 'C' and resid 679 through 681 No H-bonds generated for 'chain 'C' and resid 679 through 681' Processing helix chain 'C' and resid 684 through 686 No H-bonds generated for 'chain 'C' and resid 684 through 686' Processing helix chain 'C' and resid 689 through 696 Processing helix chain 'C' and resid 722 through 728 Processing helix chain 'C' and resid 734 through 748 Processing helix chain 'C' and resid 768 through 789 Processing helix chain 'C' and resid 797 through 807 Processing helix chain 'C' and resid 815 through 833 Proline residue: C 828 - end of helix 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 230 through 232 No H-bonds generated for 'chain 'D' and resid 230 through 232' Processing helix chain 'D' and resid 242 through 247 Processing helix chain 'D' and resid 254 through 269 Processing helix chain 'D' and resid 280 through 284 Processing helix chain 'D' and resid 296 through 304 removed outlier: 3.683A pdb=" N LYS D 300 " --> pdb=" O GLY D 296 " (cutoff:3.500A) Proline residue: D 301 - end of helix Processing helix chain 'D' and resid 316 through 321 removed outlier: 3.592A pdb=" N ARG D 320 " --> pdb=" O LEU D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 332 removed outlier: 4.936A pdb=" N ARG D 332 " --> pdb=" O ALA D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 360 Processing helix chain 'D' and resid 367 through 379 Processing helix chain 'D' and resid 388 through 406 Processing helix chain 'D' and resid 411 through 429 Processing helix chain 'D' and resid 444 through 492 Processing helix chain 'D' and resid 495 through 523 removed outlier: 3.980A pdb=" N SER D 499 " --> pdb=" O LEU D 495 " (cutoff:3.500A) Proline residue: D 507 - end of helix 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 589 Processing helix chain 'D' and resid 611 through 623 Processing helix chain 'D' and resid 640 through 643 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 667 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 756 removed outlier: 3.515A pdb=" N ARG D 756 " --> pdb=" O GLU D 752 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 789 Processing helix chain 'D' and resid 797 through 806 Processing helix chain 'D' and resid 815 through 833 Proline residue: D 828 - end of helix Processing helix chain 'E' and resid 160 through 162 No H-bonds generated for 'chain 'E' and resid 160 through 162' Processing helix chain 'E' and resid 168 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 243 through 248 removed outlier: 4.309A pdb=" N GLY E 248 " --> pdb=" O ALA E 244 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 269 Processing helix chain 'E' and resid 280 through 284 Processing helix chain 'E' and resid 300 through 305 removed outlier: 4.501A pdb=" N ALA E 304 " --> pdb=" O LYS E 300 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ARG E 305 " --> pdb=" O PRO E 301 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 300 through 305' Processing helix chain 'E' and resid 316 through 322 Processing helix chain 'E' and resid 327 through 329 No H-bonds generated for 'chain 'E' and resid 327 through 329' Processing helix chain 'E' and resid 343 through 357 removed outlier: 4.055A pdb=" N GLY E 352 " --> pdb=" O ALA E 348 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N GLU E 355 " --> pdb=" O ARG E 351 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ARG E 356 " --> pdb=" O GLY E 352 " (cutoff:3.500A) Processing helix chain 'E' and resid 367 through 380 Processing helix chain 'E' and resid 388 through 405 Processing helix chain 'E' and resid 411 through 429 Processing helix chain 'E' and resid 444 through 492 Processing helix chain 'E' and resid 496 through 523 Proline residue: E 507 - end of helix Processing helix chain 'E' and resid 533 through 541 Processing helix chain 'E' and resid 553 through 560 Processing helix chain 'E' and resid 562 through 569 Processing helix chain 'E' and resid 574 through 588 Processing helix chain 'E' and resid 612 through 622 Processing helix chain 'E' and resid 642 through 646 Processing helix chain 'E' and resid 654 through 656 No H-bonds generated for 'chain 'E' and resid 654 through 656' Processing helix chain 'E' and resid 662 through 665 No H-bonds generated for 'chain 'E' and resid 662 through 665' 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 685 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 756 removed outlier: 3.850A pdb=" N ARG E 756 " --> pdb=" O GLU E 752 " (cutoff:3.500A) 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 835 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 224 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 243 through 245 No H-bonds generated for 'chain 'F' and resid 243 through 245' Processing helix chain 'F' and resid 254 through 268 Processing helix chain 'F' and resid 280 through 284 Processing helix chain 'F' and resid 316 through 322 Processing helix chain 'F' and resid 343 through 353 removed outlier: 3.926A pdb=" N GLY F 352 " --> pdb=" O ALA F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 356 through 359 No H-bonds generated for 'chain 'F' and resid 356 through 359' Processing helix chain 'F' and resid 367 through 379 Processing helix chain 'F' and resid 388 through 406 Processing helix chain 'F' and resid 410 through 429 Processing helix chain 'F' and resid 444 through 492 Processing helix chain 'F' and resid 495 through 523 removed outlier: 3.990A pdb=" N SER F 499 " --> pdb=" O LEU F 495 " (cutoff:3.500A) Proline residue: F 507 - end of helix Processing helix chain 'F' and resid 533 through 542 Processing helix chain 'F' and resid 555 through 568 Processing helix chain 'F' and resid 574 through 587 Processing helix chain 'F' and resid 611 through 622 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 Processing helix chain 'F' and resid 721 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 835 Proline residue: F 828 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 334 through 337 removed outlier: 6.491A pdb=" N GLY A 312 " --> pdb=" O LEU A 204 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 236 through 240 Processing sheet with id= C, first strand: chain 'A' and resid 600 through 603 removed outlier: 7.103A pdb=" N VAL A 714 " --> pdb=" O PHE A 601 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N PHE A 603 " --> pdb=" O VAL A 714 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N MET A 716 " --> pdb=" O PHE A 603 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N THR A 717 " --> pdb=" O LEU A 676 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 792 through 795 Processing sheet with id= E, first strand: chain 'B' and resid 165 through 167 Processing sheet with id= F, first strand: chain 'B' and resid 311 through 314 removed outlier: 7.725A pdb=" N THR B 314 " --> pdb=" O PRO B 202 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N LEU B 204 " --> pdb=" O THR B 314 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N GLN B 334 " --> pdb=" O VAL B 203 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ILE B 205 " --> pdb=" O GLN B 334 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N VAL B 336 " --> pdb=" O ILE B 205 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'B' and resid 759 through 761 removed outlier: 3.954A pdb=" N VAL B 714 " --> pdb=" O GLY B 599 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 698 through 700 Processing sheet with id= I, first strand: chain 'B' and resid 792 through 795 Processing sheet with id= J, first strand: chain 'C' and resid 165 through 167 Processing sheet with id= K, first strand: chain 'C' and resid 334 through 337 removed outlier: 6.708A pdb=" N GLY C 312 " --> pdb=" O LEU C 204 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 599 through 603 removed outlier: 6.514A pdb=" N VAL C 630 " --> pdb=" O LEU C 675 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N ASP C 677 " --> pdb=" O VAL C 630 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N ILE C 632 " --> pdb=" O ASP C 677 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 793 through 795 removed outlier: 6.030A pdb=" N ILE C 844 " --> pdb=" O HIS C 794 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'D' and resid 165 through 167 removed outlier: 5.300A pdb=" N ASP D 278 " --> pdb=" O LEU D 240 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N THR D 314 " --> pdb=" O PRO D 202 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N LEU D 204 " --> pdb=" O THR D 314 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 630 through 633 Processing sheet with id= P, first strand: chain 'D' and resid 792 through 795 removed outlier: 3.587A pdb=" N ARG D 845 " --> pdb=" O VAL D 856 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 165 through 167 removed outlier: 3.547A pdb=" N LEU E 238 " --> pdb=" O ILE E 274 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU E 240 " --> pdb=" O PHE E 276 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ASP E 278 " --> pdb=" O LEU E 240 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N VAL E 311 " --> pdb=" O ILE E 277 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY E 206 " --> pdb=" O THR E 314 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 601 through 603 removed outlier: 6.218A pdb=" N VAL E 630 " --> pdb=" O LEU E 675 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N ASP E 677 " --> pdb=" O VAL E 630 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ILE E 632 " --> pdb=" O ASP E 677 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 698 through 700 removed outlier: 3.619A pdb=" N VAL E 707 " --> pdb=" O LEU E 699 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 793 through 795 removed outlier: 5.954A pdb=" N ILE E 844 " --> pdb=" O HIS E 794 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'F' and resid 165 through 167 Processing sheet with id= V, first strand: chain 'F' and resid 334 through 337 removed outlier: 6.784A pdb=" N GLY F 312 " --> pdb=" O LEU F 204 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'F' and resid 759 through 762 removed outlier: 3.805A pdb=" N LEU F 602 " --> pdb=" O GLU F 759 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU F 604 " --> pdb=" O VAL F 761 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ILE F 674 " --> pdb=" O ILE F 715 " (cutoff:3.500A) removed outlier: 9.098A pdb=" N THR F 717 " --> pdb=" O ILE F 674 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N LEU F 676 " --> pdb=" O THR F 717 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'F' and resid 792 through 795 removed outlier: 3.809A pdb=" N ARG F 845 " --> pdb=" O VAL F 856 " (cutoff:3.500A) 1604 hydrogen bonds defined for protein. 4770 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: 11.45 Time building geometry restraints manager: 14.96 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: 11712 1.36 - 1.51: 9837 1.51 - 1.66: 11539 1.66 - 1.80: 211 1.80 - 1.95: 22 Bond restraints: 33321 Sorted by residual: bond pdb=" CA SER C 600 " pdb=" CB SER C 600 " ideal model delta sigma weight residual 1.528 1.427 0.101 2.61e-02 1.47e+03 1.51e+01 bond pdb=" C ALA E 814 " pdb=" N ARG E 815 " ideal model delta sigma weight residual 1.332 1.298 0.034 1.09e-02 8.42e+03 9.48e+00 bond pdb=" CG ARG E 815 " pdb=" CD ARG E 815 " ideal model delta sigma weight residual 1.520 1.431 0.089 3.00e-02 1.11e+03 8.81e+00 bond pdb=" CA SER D 600 " pdb=" CB SER D 600 " ideal model delta sigma weight residual 1.522 1.486 0.036 1.27e-02 6.20e+03 7.84e+00 bond pdb=" CA ALA B 628 " pdb=" CB ALA B 628 " ideal model delta sigma weight residual 1.526 1.485 0.041 1.51e-02 4.39e+03 7.23e+00 ... (remaining 33316 not shown) Histogram of bond angle deviations from ideal: 96.42 - 106.74: 1063 106.74 - 117.06: 22723 117.06 - 127.38: 20917 127.38 - 137.70: 264 137.70 - 148.02: 3 Bond angle restraints: 44970 Sorted by residual: angle pdb=" C SER B 407 " pdb=" N PRO B 409 " pdb=" CA PRO B 409 " ideal model delta sigma weight residual 127.00 148.02 -21.02 2.40e+00 1.74e-01 7.67e+01 angle pdb=" C SER E 407 " pdb=" N PRO E 409 " pdb=" CA PRO E 409 " ideal model delta sigma weight residual 127.00 147.50 -20.50 2.40e+00 1.74e-01 7.30e+01 angle pdb=" C SER B 407 " pdb=" N PRO B 409 " pdb=" CD PRO B 409 " ideal model delta sigma weight residual 120.60 103.18 17.42 2.20e+00 2.07e-01 6.27e+01 angle pdb=" C SER E 407 " pdb=" N PRO E 409 " pdb=" CD PRO E 409 " ideal model delta sigma weight residual 120.60 103.33 17.27 2.20e+00 2.07e-01 6.16e+01 angle pdb=" N LEU E 444 " pdb=" CA LEU E 444 " pdb=" C LEU E 444 " ideal model delta sigma weight residual 113.50 106.47 7.03 1.23e+00 6.61e-01 3.26e+01 ... (remaining 44965 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.42: 20108 26.42 - 52.85: 412 52.85 - 79.27: 33 79.27 - 105.70: 5 105.70 - 132.12: 2 Dihedral angle restraints: 20560 sinusoidal: 8676 harmonic: 11884 Sorted by residual: dihedral pdb=" CA GLU C 207 " pdb=" C GLU C 207 " pdb=" N PRO C 208 " pdb=" CA PRO C 208 " ideal model delta harmonic sigma weight residual 180.00 -146.01 -33.99 0 5.00e+00 4.00e-02 4.62e+01 dihedral pdb=" CA HIS E 568 " pdb=" C HIS E 568 " pdb=" N ARG E 569 " pdb=" CA ARG E 569 " ideal model delta harmonic sigma weight residual 180.00 146.55 33.45 0 5.00e+00 4.00e-02 4.47e+01 dihedral pdb=" CA LEU F 245 " pdb=" C LEU F 245 " pdb=" N VAL F 246 " pdb=" CA VAL F 246 " ideal model delta harmonic sigma weight residual -180.00 -147.73 -32.27 0 5.00e+00 4.00e-02 4.17e+01 ... (remaining 20557 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 3464 0.057 - 0.114: 1286 0.114 - 0.172: 294 0.172 - 0.229: 41 0.229 - 0.286: 8 Chirality restraints: 5093 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 -2.34 -0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" PA AGS D1002 " pdb=" O2A AGS D1002 " pdb=" O3A AGS D1002 " pdb=" O5' AGS D1002 " both_signs ideal model delta sigma weight residual True 3.18 -2.91 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CA ARG D 815 " pdb=" N ARG D 815 " pdb=" C ARG D 815 " pdb=" CB ARG D 815 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.61e+00 ... (remaining 5090 not shown) Planarity restraints: 5872 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' ADP A1002 " 0.019 2.00e-02 2.50e+03 2.14e-02 1.26e+01 pdb=" C2 ADP A1002 " 0.009 2.00e-02 2.50e+03 pdb=" C4 ADP A1002 " -0.056 2.00e-02 2.50e+03 pdb=" C5 ADP A1002 " -0.000 2.00e-02 2.50e+03 pdb=" C6 ADP A1002 " -0.001 2.00e-02 2.50e+03 pdb=" C8 ADP A1002 " 0.003 2.00e-02 2.50e+03 pdb=" N1 ADP A1002 " -0.003 2.00e-02 2.50e+03 pdb=" N3 ADP A1002 " 0.026 2.00e-02 2.50e+03 pdb=" N6 ADP A1002 " 0.001 2.00e-02 2.50e+03 pdb=" N7 ADP A1002 " 0.020 2.00e-02 2.50e+03 pdb=" N9 ADP A1002 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B 300 " 0.057 5.00e-02 4.00e+02 8.57e-02 1.18e+01 pdb=" N PRO B 301 " -0.148 5.00e-02 4.00e+02 pdb=" CA PRO B 301 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 301 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 683 " 0.052 5.00e-02 4.00e+02 7.81e-02 9.77e+00 pdb=" N PRO A 684 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO A 684 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 684 " 0.043 5.00e-02 4.00e+02 ... (remaining 5869 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3709 2.74 - 3.28: 31749 3.28 - 3.82: 54243 3.82 - 4.36: 63534 4.36 - 4.90: 107187 Nonbonded interactions: 260422 Sorted by model distance: nonbonded pdb=" O1B AGS B1001 " pdb=" O2G AGS B1001 " model vdw 2.198 2.440 nonbonded pdb=" O1B AGS E1002 " pdb=" O2A AGS E1002 " model vdw 2.199 2.440 nonbonded pdb=" O1B AGS C1001 " pdb=" O2G AGS C1001 " model vdw 2.220 2.440 nonbonded pdb=" O1B AGS C1002 " pdb=" O2G AGS C1002 " model vdw 2.232 2.440 nonbonded pdb=" O1B AGS B1002 " pdb=" O2G AGS B1002 " model vdw 2.235 2.440 ... (remaining 260417 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 543 or resid 553 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 543 or resid 553 thro \ ugh 858)) selection = (chain 'D' and (resid 159 through 543 or resid 553 through 858)) selection = (chain 'E' and (resid 159 through 543 or resid 553 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 127 5.16 5 C 20485 2.51 5 N 5933 2.21 5 O 6295 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: 0.010 Normalize map: mean=0, sd=1: 1.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 7.150 Check model and map are aligned: 0.530 Convert atoms to be neutral: 0.290 Process input model: 84.230 Find NCS groups from input model: 3.430 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 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 : 0.010 0.109 33321 Z= 0.685 Angle : 1.151 21.024 44970 Z= 0.615 Chirality : 0.061 0.286 5093 Planarity : 0.008 0.086 5872 Dihedral : 10.838 132.121 12880 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.97 % Favored : 91.98 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.71 % Twisted General : 0.08 % 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: -3.79 (0.11), residues: 4053 helix: -2.10 (0.08), residues: 2310 sheet: -3.11 (0.23), residues: 374 loop : -2.76 (0.15), residues: 1369 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1150 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 1138 time to evaluate : 3.838 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 outliers start: 12 outliers final: 0 residues processed: 1149 average time/residue: 0.5045 time to fit residues: 888.2826 Evaluate side-chains 587 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 587 time to evaluate : 4.389 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.2571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 345 optimal weight: 1.9990 chunk 310 optimal weight: 6.9990 chunk 172 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 209 optimal weight: 2.9990 chunk 165 optimal weight: 20.0000 chunk 320 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 194 optimal weight: 0.4980 chunk 238 optimal weight: 20.0000 chunk 371 optimal weight: 20.0000 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 ASN A 361 HIS ** A 747 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 827 ASN A 849 ASN A 858 HIS B 195 GLN B 281 HIS B 334 GLN B 454 GLN B 620 ASN ** B 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 748 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 794 HIS B 823 GLN ** B 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 512 GLN C 641 HIS ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 747 HIS ** C 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 831 GLN D 195 GLN D 281 HIS D 567 HIS D 595 ASN D 692 GLN ** D 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 806 ASN ** D 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 857 GLN D 858 HIS ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 201 ASN E 281 HIS E 309 HIS ** E 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 512 GLN E 567 HIS E 641 HIS E 755 ASN E 806 ASN E 823 GLN E 857 GLN F 269 GLN ** F 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 321 GLN F 361 HIS F 421 GLN ** F 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 512 GLN ** F 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 770 HIS ** F 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 849 ASN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.121 33321 Z= 0.238 Angle : 0.720 10.059 44970 Z= 0.369 Chirality : 0.045 0.255 5093 Planarity : 0.006 0.113 5872 Dihedral : 8.355 117.756 4642 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.53 % Favored : 94.45 % Rotamer Outliers : 2.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.71 % 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: -2.09 (0.12), residues: 4053 helix: -0.53 (0.10), residues: 2307 sheet: -2.68 (0.23), residues: 418 loop : -2.27 (0.16), residues: 1328 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 758 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 659 time to evaluate : 4.144 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 outliers start: 99 outliers final: 54 residues processed: 721 average time/residue: 0.4471 time to fit residues: 521.5682 Evaluate side-chains 571 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 517 time to evaluate : 3.823 Switching outliers to nearest non-outliers outliers start: 54 outliers final: 0 residues processed: 54 average time/residue: 0.3186 time to fit residues: 37.7859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 206 optimal weight: 0.0570 chunk 115 optimal weight: 0.7980 chunk 309 optimal weight: 0.0570 chunk 252 optimal weight: 5.9990 chunk 102 optimal weight: 6.9990 chunk 372 optimal weight: 0.9980 chunk 401 optimal weight: 0.9990 chunk 331 optimal weight: 5.9990 chunk 368 optimal weight: 5.9990 chunk 126 optimal weight: 4.9990 chunk 298 optimal weight: 30.0000 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 747 HIS A 770 HIS ** B 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 512 GLN B 620 ASN B 641 HIS B 711 ASN B 747 HIS ** B 748 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 822 GLN ** B 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 264 ASN ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 747 HIS ** C 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 692 GLN D 748 ASN ** D 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 823 GLN F 192 GLN ** F 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 473 GLN F 688 ASN F 831 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.4053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.108 33321 Z= 0.190 Angle : 0.675 17.916 44970 Z= 0.338 Chirality : 0.043 0.170 5093 Planarity : 0.005 0.077 5872 Dihedral : 7.865 142.155 4642 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer Outliers : 1.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.71 % 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: -1.16 (0.13), residues: 4053 helix: 0.27 (0.11), residues: 2285 sheet: -2.16 (0.24), residues: 432 loop : -2.00 (0.16), residues: 1336 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 639 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 576 time to evaluate : 4.017 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: 63 outliers final: 28 residues processed: 619 average time/residue: 0.4367 time to fit residues: 445.1702 Evaluate side-chains 504 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 476 time to evaluate : 4.008 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.3491 time to fit residues: 22.6583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 367 optimal weight: 3.9990 chunk 279 optimal weight: 20.0000 chunk 193 optimal weight: 2.9990 chunk 41 optimal weight: 0.3980 chunk 177 optimal weight: 0.8980 chunk 249 optimal weight: 5.9990 chunk 373 optimal weight: 3.9990 chunk 395 optimal weight: 9.9990 chunk 195 optimal weight: 1.9990 chunk 353 optimal weight: 10.0000 chunk 106 optimal weight: 9.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 334 GLN B 454 GLN B 620 ASN ** B 748 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 822 GLN B 823 GLN ** B 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 858 HIS C 454 GLN ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 747 HIS C 822 GLN D 269 GLN D 641 HIS D 692 GLN ** D 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 192 GLN E 806 ASN E 823 GLN E 824 GLN F 849 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.4782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.150 33321 Z= 0.235 Angle : 0.662 12.933 44970 Z= 0.335 Chirality : 0.043 0.233 5093 Planarity : 0.005 0.106 5872 Dihedral : 7.632 151.831 4642 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer Outliers : 2.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.71 % 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: -0.65 (0.13), residues: 4053 helix: 0.69 (0.11), residues: 2291 sheet: -1.96 (0.25), residues: 438 loop : -1.79 (0.17), residues: 1324 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 602 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 520 time to evaluate : 4.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 82 outliers final: 47 residues processed: 567 average time/residue: 0.4258 time to fit residues: 402.9688 Evaluate side-chains 484 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 437 time to evaluate : 4.034 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 47 outliers final: 1 residues processed: 47 average time/residue: 0.3090 time to fit residues: 32.6535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 329 optimal weight: 2.9990 chunk 224 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 294 optimal weight: 5.9990 chunk 163 optimal weight: 4.9990 chunk 337 optimal weight: 1.9990 chunk 273 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 201 optimal weight: 1.9990 chunk 354 optimal weight: 0.9980 chunk 99 optimal weight: 30.0000 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 620 ASN B 747 HIS B 822 GLN ** B 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 747 HIS D 688 ASN ** D 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 192 GLN E 806 ASN E 824 GLN ** E 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 770 HIS F 831 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.5282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.157 33321 Z= 0.224 Angle : 0.632 14.641 44970 Z= 0.319 Chirality : 0.043 0.271 5093 Planarity : 0.005 0.105 5872 Dihedral : 7.462 151.109 4642 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer Outliers : 1.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.71 % 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: -0.39 (0.14), residues: 4053 helix: 0.92 (0.11), residues: 2297 sheet: -1.98 (0.24), residues: 438 loop : -1.67 (0.17), residues: 1318 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 475 time to evaluate : 3.726 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 outliers start: 56 outliers final: 28 residues processed: 517 average time/residue: 0.4110 time to fit residues: 357.9856 Evaluate side-chains 456 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 428 time to evaluate : 4.087 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 28 outliers final: 1 residues processed: 28 average time/residue: 0.3142 time to fit residues: 21.8092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 133 optimal weight: 2.9990 chunk 356 optimal weight: 20.0000 chunk 78 optimal weight: 0.9980 chunk 232 optimal weight: 20.0000 chunk 97 optimal weight: 10.0000 chunk 395 optimal weight: 8.9990 chunk 328 optimal weight: 3.9990 chunk 183 optimal weight: 1.9990 chunk 32 optimal weight: 20.0000 chunk 130 optimal weight: 8.9990 chunk 207 optimal weight: 4.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 GLN ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 620 ASN B 822 GLN ** B 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 GLN C 334 GLN ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 747 HIS ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 688 ASN D 822 GLN ** D 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 806 ASN E 824 GLN E 849 ASN ** F 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.5819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.215 33321 Z= 0.279 Angle : 0.674 15.720 44970 Z= 0.339 Chirality : 0.044 0.221 5093 Planarity : 0.005 0.080 5872 Dihedral : 7.440 153.593 4642 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer Outliers : 1.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.71 % 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: -0.32 (0.14), residues: 4053 helix: 0.99 (0.11), residues: 2309 sheet: -1.98 (0.24), residues: 459 loop : -1.68 (0.17), residues: 1285 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 459 time to evaluate : 4.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 65 outliers final: 37 residues processed: 499 average time/residue: 0.4299 time to fit residues: 361.2993 Evaluate side-chains 453 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 416 time to evaluate : 4.033 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 0 residues processed: 37 average time/residue: 0.3330 time to fit residues: 29.0096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 381 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 chunk 225 optimal weight: 3.9990 chunk 288 optimal weight: 7.9990 chunk 223 optimal weight: 5.9990 chunk 333 optimal weight: 6.9990 chunk 220 optimal weight: 8.9990 chunk 394 optimal weight: 0.0050 chunk 246 optimal weight: 2.9990 chunk 240 optimal weight: 0.9980 chunk 182 optimal weight: 2.9990 overall best weight: 1.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 512 GLN ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 192 GLN ** B 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 711 ASN B 822 GLN ** B 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 692 GLN ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 736 HIS ** E 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 806 ASN E 824 GLN ** F 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 755 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.6137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.321 33321 Z= 0.218 Angle : 0.647 19.402 44970 Z= 0.325 Chirality : 0.043 0.221 5093 Planarity : 0.004 0.076 5872 Dihedral : 7.401 168.146 4642 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer Outliers : 1.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.71 % 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: -0.15 (0.14), residues: 4053 helix: 1.13 (0.11), residues: 2302 sheet: -1.92 (0.24), residues: 447 loop : -1.60 (0.17), residues: 1304 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 443 time to evaluate : 4.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 21 residues processed: 468 average time/residue: 0.4258 time to fit residues: 338.7948 Evaluate side-chains 420 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 399 time to evaluate : 4.072 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.3084 time to fit residues: 17.9147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 243 optimal weight: 10.0000 chunk 157 optimal weight: 10.0000 chunk 235 optimal weight: 9.9990 chunk 118 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 chunk 76 optimal weight: 0.9990 chunk 250 optimal weight: 0.0980 chunk 268 optimal weight: 0.7980 chunk 194 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 309 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 GLN ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 620 ASN B 822 GLN ** B 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 192 GLN C 201 ASN ** C 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 747 HIS ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 281 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.6236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.535 33321 Z= 0.219 Angle : 0.778 73.898 44970 Z= 0.360 Chirality : 0.044 0.433 5093 Planarity : 0.004 0.073 5872 Dihedral : 7.402 170.196 4642 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer Outliers : 0.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.71 % 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: -0.05 (0.14), residues: 4053 helix: 1.20 (0.11), residues: 2291 sheet: -1.81 (0.24), residues: 443 loop : -1.54 (0.18), residues: 1319 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 424 time to evaluate : 3.925 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 outliers start: 24 outliers final: 12 residues processed: 437 average time/residue: 0.4083 time to fit residues: 303.8710 Evaluate side-chains 412 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 400 time to evaluate : 4.088 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.3780 time to fit residues: 13.5516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 358 optimal weight: 7.9990 chunk 377 optimal weight: 10.0000 chunk 344 optimal weight: 0.9980 chunk 367 optimal weight: 7.9990 chunk 221 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 288 optimal weight: 9.9990 chunk 112 optimal weight: 0.9990 chunk 331 optimal weight: 7.9990 chunk 347 optimal weight: 4.9990 chunk 366 optimal weight: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 822 GLN ** B 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 692 GLN ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 736 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.6263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.535 33321 Z= 0.219 Angle : 0.778 73.898 44970 Z= 0.360 Chirality : 0.044 0.433 5093 Planarity : 0.004 0.073 5872 Dihedral : 7.402 170.196 4642 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 16.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.71 % 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: -0.05 (0.14), residues: 4053 helix: 1.20 (0.11), residues: 2291 sheet: -1.81 (0.24), residues: 443 loop : -1.54 (0.18), residues: 1319 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 401 time to evaluate : 4.139 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: 2 outliers final: 1 residues processed: 401 average time/residue: 0.4246 time to fit residues: 291.4401 Evaluate side-chains 395 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 394 time to evaluate : 4.071 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3477 time to fit residues: 6.5890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 241 optimal weight: 10.0000 chunk 388 optimal weight: 6.9990 chunk 237 optimal weight: 6.9990 chunk 184 optimal weight: 0.6980 chunk 270 optimal weight: 9.9990 chunk 407 optimal weight: 10.0000 chunk 375 optimal weight: 0.4980 chunk 324 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 250 optimal weight: 4.9990 chunk 198 optimal weight: 20.0000 overall best weight: 2.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 822 GLN ** B 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 692 GLN ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.6267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.535 33321 Z= 0.219 Angle : 0.778 73.878 44970 Z= 0.360 Chirality : 0.044 0.433 5093 Planarity : 0.004 0.073 5872 Dihedral : 7.402 170.195 4642 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 17.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.71 % 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: -0.05 (0.14), residues: 4053 helix: 1.20 (0.11), residues: 2291 sheet: -1.81 (0.24), residues: 443 loop : -1.54 (0.18), residues: 1319 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 394 time to evaluate : 3.995 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: 1 outliers final: 0 residues processed: 394 average time/residue: 0.4329 time to fit residues: 292.8192 Evaluate side-chains 393 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 393 time to evaluate : 3.972 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.5318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 257 optimal weight: 0.6980 chunk 345 optimal weight: 0.7980 chunk 99 optimal weight: 9.9990 chunk 299 optimal weight: 7.9990 chunk 47 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 324 optimal weight: 1.9990 chunk 136 optimal weight: 9.9990 chunk 333 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 822 GLN ** B 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 692 GLN ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.137437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.104215 restraints weight = 68599.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.106536 restraints weight = 40612.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.108135 restraints weight = 28283.656| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.6271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.535 33321 Z= 0.219 Angle : 0.778 73.878 44970 Z= 0.360 Chirality : 0.044 0.433 5093 Planarity : 0.004 0.073 5872 Dihedral : 7.402 170.195 4642 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 17.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.71 % 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: -0.05 (0.14), residues: 4053 helix: 1.20 (0.11), residues: 2291 sheet: -1.81 (0.24), residues: 443 loop : -1.54 (0.18), residues: 1319 =============================================================================== Job complete usr+sys time: 7276.28 seconds wall clock time: 132 minutes 26.47 seconds (7946.47 seconds total)