Starting phenix.real_space_refine on Sat Aug 10 11:27:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qs4_4621/08_2024/6qs4_4621.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qs4_4621/08_2024/6qs4_4621.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qs4_4621/08_2024/6qs4_4621.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qs4_4621/08_2024/6qs4_4621.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qs4_4621/08_2024/6qs4_4621.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qs4_4621/08_2024/6qs4_4621.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 31 5.49 5 S 107 5.16 5 C 17996 2.51 5 N 5225 2.21 5 O 5480 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 320": "NH1" <-> "NH2" Residue "A ARG 332": "NH1" <-> "NH2" Residue "A ARG 528": "NH1" <-> "NH2" Residue "B ARG 252": "NH1" <-> "NH2" Residue "B ARG 332": "NH1" <-> "NH2" Residue "B ARG 528": "NH1" <-> "NH2" Residue "B ARG 550": "NH1" <-> "NH2" Residue "C ARG 252": "NH1" <-> "NH2" Residue "C ARG 332": "NH1" <-> "NH2" Residue "C ARG 528": "NH1" <-> "NH2" Residue "C ARG 550": "NH1" <-> "NH2" Residue "D ARG 332": "NH1" <-> "NH2" Residue "D ARG 528": "NH1" <-> "NH2" Residue "D ARG 550": "NH1" <-> "NH2" Residue "E ARG 332": "NH1" <-> "NH2" Residue "E ARG 528": "NH1" <-> "NH2" Residue "E ARG 550": "NH1" <-> "NH2" Residue "F ARG 252": "NH1" <-> "NH2" Residue "F ARG 332": "NH1" <-> "NH2" Residue "F ARG 528": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 28839 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 4472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 568, 4472 Classifications: {'peptide': 568} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 546} Chain breaks: 3 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 4562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 582, 4562 Classifications: {'peptide': 582} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 559} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 4976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 630, 4976 Classifications: {'peptide': 630} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 606} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 4952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 625, 4952 Classifications: {'peptide': 625} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 601} Chain breaks: 3 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 4952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 625, 4952 Classifications: {'peptide': 625} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 601} Chain breaks: 3 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 4472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 568, 4472 Classifications: {'peptide': 568} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 546} Chain breaks: 3 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "S" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 120 Classifications: {'peptide': 24} Link IDs: {'TRANS': 23} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "B" 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: "C" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 93 Unusual residues: {'AGS': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 93 Unusual residues: {'AGS': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 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: 14.34, per 1000 atoms: 0.50 Number of scatterers: 28839 At special positions: 0 Unit cell: (117.6, 142.8, 156.45, 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 107 16.00 P 31 15.00 O 5480 8.00 N 5225 7.00 C 17996 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=10, symmetry=0 Number of additional bonds: simple=10, symmetry=0 Coordination: Other bonds: Time building additional restraints: 10.68 Conformation dependent library (CDL) restraints added in 4.7 seconds 7156 Ramachandran restraints generated. 3578 Oldfield, 0 Emsley, 3578 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6716 Finding SS restraints... Secondary structure from input PDB file: 183 helices and 27 sheets defined 59.4% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.06 Creating SS restraints... Processing helix chain 'A' and resid 160 through 165 removed outlier: 3.597A pdb=" N TYR A 164 " --> pdb=" O ALA A 160 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR A 165 " --> pdb=" O LEU A 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 160 through 165' Processing helix chain 'A' and resid 167 through 174 removed outlier: 4.356A pdb=" N ARG A 171 " --> pdb=" O ASP A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 195 Processing helix chain 'A' and resid 211 through 225 Processing helix chain 'A' and resid 254 through 269 Processing helix chain 'A' and resid 279 through 285 removed outlier: 3.762A pdb=" N MET A 283 " --> pdb=" O ALA A 279 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY A 285 " --> pdb=" O HIS A 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 279 through 285' Processing helix chain 'A' and resid 295 through 306 Proline residue: A 301 - end of helix Processing helix chain 'A' and resid 315 through 323 Processing helix chain 'A' and resid 326 through 331 Processing helix chain 'A' and resid 342 through 362 removed outlier: 4.733A pdb=" N GLU A 355 " --> pdb=" O ARG A 351 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N ARG A 356 " --> pdb=" O GLY A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 381 removed outlier: 3.782A pdb=" N ILE A 381 " --> pdb=" O SER A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 406 Processing helix chain 'A' and resid 532 through 543 Processing helix chain 'A' and resid 555 through 561 Processing helix chain 'A' and resid 561 through 567 Processing helix chain 'A' and resid 573 through 590 removed outlier: 3.840A pdb=" N GLY A 590 " --> pdb=" O ARG A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 623 Processing helix chain 'A' and resid 639 through 647 removed outlier: 3.888A pdb=" N VAL A 643 " --> pdb=" O GLU A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 669 Processing helix chain 'A' and resid 679 through 682 Processing helix chain 'A' and resid 683 through 684 No H-bonds generated for 'chain 'A' and resid 683 through 684' Processing helix chain 'A' and resid 685 through 697 removed outlier: 3.615A pdb=" N ILE A 689 " --> pdb=" O ASP A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 727 removed outlier: 3.656A pdb=" N ILE A 725 " --> pdb=" O GLY A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 749 removed outlier: 3.653A pdb=" N MET A 737 " --> pdb=" O ASP A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 757 removed outlier: 3.696A pdb=" N ARG A 756 " --> pdb=" O GLU A 752 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE A 757 " --> pdb=" O PHE A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 767 through 790 Processing helix chain 'A' and resid 796 through 805 Processing helix chain 'A' and resid 814 through 835 removed outlier: 4.194A pdb=" N ASN A 827 " --> pdb=" O GLN A 823 " (cutoff:3.500A) Proline residue: A 828 - end of helix removed outlier: 3.620A pdb=" N GLN A 831 " --> pdb=" O ASN A 827 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER A 835 " --> pdb=" O GLN A 831 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 164 Processing helix chain 'B' and resid 168 through 174 Processing helix chain 'B' and resid 183 through 195 Processing helix chain 'B' and resid 211 through 225 removed outlier: 3.703A pdb=" N VAL B 216 " --> pdb=" O LYS B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 233 Processing helix chain 'B' and resid 242 through 247 removed outlier: 3.570A pdb=" N ALA B 247 " --> pdb=" O GLY B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 269 Processing helix chain 'B' and resid 279 through 285 removed outlier: 3.949A pdb=" N GLY B 285 " --> pdb=" O HIS B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 304 Proline residue: B 301 - end of helix removed outlier: 4.081A pdb=" N ALA B 304 " --> pdb=" O LYS B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 323 Processing helix chain 'B' and resid 326 through 331 Processing helix chain 'B' and resid 342 through 353 Processing helix chain 'B' and resid 353 through 362 removed outlier: 3.699A pdb=" N TYR B 357 " --> pdb=" O LEU B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 380 Processing helix chain 'B' and resid 387 through 408 removed outlier: 4.094A pdb=" N LYS B 408 " --> pdb=" O GLN B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 544 Processing helix chain 'B' and resid 552 through 561 Processing helix chain 'B' and resid 561 through 567 Processing helix chain 'B' and resid 573 through 589 removed outlier: 3.803A pdb=" N VAL B 577 " --> pdb=" O GLN B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 610 through 624 Processing helix chain 'B' and resid 635 through 638 removed outlier: 4.024A pdb=" N MET B 638 " --> pdb=" O SER B 635 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 635 through 638' Processing helix chain 'B' and resid 642 through 648 Processing helix chain 'B' and resid 655 through 659 removed outlier: 3.817A pdb=" N GLU B 658 " --> pdb=" O GLY B 655 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY B 659 " --> pdb=" O TYR B 656 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 655 through 659' Processing helix chain 'B' and resid 660 through 669 removed outlier: 3.976A pdb=" N ARG B 669 " --> pdb=" O ALA B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 687 removed outlier: 3.515A pdb=" N PHE B 687 " --> pdb=" O PRO B 684 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 697 Processing helix chain 'B' and resid 721 through 729 Processing helix chain 'B' and resid 733 through 749 removed outlier: 3.560A pdb=" N MET B 737 " --> pdb=" O ASP B 733 " (cutoff:3.500A) Processing helix chain 'B' and resid 750 through 756 removed outlier: 3.639A pdb=" N ARG B 756 " --> pdb=" O GLU B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 767 through 790 Processing helix chain 'B' and resid 796 through 807 Processing helix chain 'B' and resid 814 through 827 Processing helix chain 'B' and resid 827 through 835 Processing helix chain 'C' and resid 160 through 164 Processing helix chain 'C' and resid 168 through 174 Processing helix chain 'C' and resid 183 through 195 Processing helix chain 'C' and resid 211 through 226 Processing helix chain 'C' and resid 229 through 233 Processing helix chain 'C' and resid 241 through 247 Processing helix chain 'C' and resid 253 through 269 Processing helix chain 'C' and resid 280 through 283 Processing helix chain 'C' and resid 295 through 305 removed outlier: 3.653A pdb=" N LEU C 299 " --> pdb=" O ALA C 295 " (cutoff:3.500A) Proline residue: C 301 - end of helix removed outlier: 3.677A pdb=" N ARG C 305 " --> pdb=" O PRO C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 323 removed outlier: 3.561A pdb=" N GLN C 321 " --> pdb=" O ASP C 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 331 removed outlier: 3.618A pdb=" N ARG C 331 " --> pdb=" O ALA C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 362 removed outlier: 3.658A pdb=" N THR C 346 " --> pdb=" O SER C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 380 Processing helix chain 'C' and resid 387 through 407 removed outlier: 3.704A pdb=" N ILE C 391 " --> pdb=" O PRO C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 428 Processing helix chain 'C' and resid 444 through 465 Processing helix chain 'C' and resid 532 through 542 Processing helix chain 'C' and resid 552 through 561 removed outlier: 3.800A pdb=" N ARG C 561 " --> pdb=" O GLU C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 561 through 567 removed outlier: 3.720A pdb=" N HIS C 567 " --> pdb=" O GLU C 563 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 590 removed outlier: 3.587A pdb=" N VAL C 577 " --> pdb=" O GLN C 573 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY C 590 " --> pdb=" O ARG C 586 " (cutoff:3.500A) Processing helix chain 'C' and resid 610 through 624 Processing helix chain 'C' and resid 633 through 637 Processing helix chain 'C' and resid 642 through 648 Processing helix chain 'C' and resid 655 through 659 removed outlier: 3.736A pdb=" N GLU C 658 " --> pdb=" O GLY C 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 660 through 668 Processing helix chain 'C' and resid 687 through 696 Processing helix chain 'C' and resid 721 through 729 Processing helix chain 'C' and resid 733 through 749 Processing helix chain 'C' and resid 750 through 755 removed outlier: 3.504A pdb=" N ASN C 755 " --> pdb=" O PRO C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 767 through 790 removed outlier: 4.117A pdb=" N GLU C 788 " --> pdb=" O LYS C 784 " (cutoff:3.500A) Processing helix chain 'C' and resid 796 through 806 removed outlier: 3.658A pdb=" N LYS C 801 " --> pdb=" O ASP C 797 " (cutoff:3.500A) Processing helix chain 'C' and resid 814 through 834 Proline residue: C 828 - end of helix Processing helix chain 'D' and resid 168 through 174 Processing helix chain 'D' and resid 183 through 195 removed outlier: 3.612A pdb=" N ILE D 187 " --> pdb=" O ARG D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 226 removed outlier: 3.793A pdb=" N VAL D 216 " --> pdb=" O LYS D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 233 Processing helix chain 'D' and resid 241 through 249 removed outlier: 3.684A pdb=" N LEU D 245 " --> pdb=" O ASP D 241 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA D 249 " --> pdb=" O LEU D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 267 Processing helix chain 'D' and resid 280 through 283 Processing helix chain 'D' and resid 298 through 304 removed outlier: 4.508A pdb=" N ALA D 302 " --> pdb=" O MET D 298 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ALA D 304 " --> pdb=" O LYS D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 323 removed outlier: 3.821A pdb=" N ARG D 320 " --> pdb=" O LEU D 316 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLN D 321 " --> pdb=" O ASP D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 331 Processing helix chain 'D' and resid 342 through 362 Processing helix chain 'D' and resid 366 through 380 removed outlier: 3.830A pdb=" N ILE D 370 " --> pdb=" O THR D 366 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 407 Processing helix chain 'D' and resid 409 through 429 Processing helix chain 'D' and resid 444 through 465 Processing helix chain 'D' and resid 532 through 544 removed outlier: 3.712A pdb=" N ILE D 536 " --> pdb=" O THR D 532 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 561 removed outlier: 3.618A pdb=" N ARG D 561 " --> pdb=" O GLU D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 561 through 567 Processing helix chain 'D' and resid 573 through 589 Processing helix chain 'D' and resid 610 through 623 Processing helix chain 'D' and resid 633 through 637 Processing helix chain 'D' and resid 642 through 647 Processing helix chain 'D' and resid 655 through 659 removed outlier: 3.502A pdb=" N GLU D 658 " --> pdb=" O GLY D 655 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY D 659 " --> pdb=" O TYR D 656 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 655 through 659' Processing helix chain 'D' and resid 661 through 669 Processing helix chain 'D' and resid 678 through 682 removed outlier: 3.650A pdb=" N LYS D 681 " --> pdb=" O ALA D 678 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA D 682 " --> pdb=" O VAL D 679 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 678 through 682' Processing helix chain 'D' and resid 685 through 697 Processing helix chain 'D' and resid 721 through 729 Processing helix chain 'D' and resid 733 through 749 Processing helix chain 'D' and resid 767 through 790 Processing helix chain 'D' and resid 796 through 806 removed outlier: 3.648A pdb=" N LEU D 800 " --> pdb=" O SER D 796 " (cutoff:3.500A) Processing helix chain 'D' and resid 814 through 835 removed outlier: 3.624A pdb=" N LYS D 818 " --> pdb=" O ALA D 814 " (cutoff:3.500A) Proline residue: D 828 - end of helix Processing helix chain 'E' and resid 160 through 164 Processing helix chain 'E' and resid 168 through 174 Processing helix chain 'E' and resid 183 through 195 Processing helix chain 'E' and resid 211 through 226 Processing helix chain 'E' and resid 229 through 233 removed outlier: 3.582A pdb=" N LYS E 233 " --> pdb=" O GLU E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 241 through 247 removed outlier: 3.867A pdb=" N VAL E 246 " --> pdb=" O MET E 242 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 269 Processing helix chain 'E' and resid 295 through 304 Proline residue: E 301 - end of helix Processing helix chain 'E' and resid 315 through 322 Processing helix chain 'E' and resid 326 through 331 removed outlier: 3.694A pdb=" N GLU E 330 " --> pdb=" O ASP E 326 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ARG E 331 " --> pdb=" O ALA E 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 326 through 331' Processing helix chain 'E' and resid 342 through 362 Processing helix chain 'E' and resid 366 through 380 Processing helix chain 'E' and resid 387 through 407 Processing helix chain 'E' and resid 409 through 428 Processing helix chain 'E' and resid 444 through 466 Processing helix chain 'E' and resid 532 through 544 removed outlier: 3.608A pdb=" N ILE E 536 " --> pdb=" O THR E 532 " (cutoff:3.500A) Processing helix chain 'E' and resid 552 through 570 Processing helix chain 'E' and resid 573 through 589 removed outlier: 3.822A pdb=" N VAL E 577 " --> pdb=" O GLN E 573 " (cutoff:3.500A) Processing helix chain 'E' and resid 610 through 623 removed outlier: 3.573A pdb=" N LEU E 614 " --> pdb=" O GLY E 610 " (cutoff:3.500A) Processing helix chain 'E' and resid 639 through 641 No H-bonds generated for 'chain 'E' and resid 639 through 641' Processing helix chain 'E' and resid 642 through 647 Processing helix chain 'E' and resid 655 through 659 removed outlier: 3.714A pdb=" N GLY E 659 " --> pdb=" O TYR E 656 " (cutoff:3.500A) Processing helix chain 'E' and resid 661 through 669 removed outlier: 3.815A pdb=" N ARG E 669 " --> pdb=" O ALA E 665 " (cutoff:3.500A) Processing helix chain 'E' and resid 678 through 682 removed outlier: 3.529A pdb=" N LYS E 681 " --> pdb=" O ALA E 678 " (cutoff:3.500A) Processing helix chain 'E' and resid 683 through 685 No H-bonds generated for 'chain 'E' and resid 683 through 685' Processing helix chain 'E' and resid 686 through 697 Processing helix chain 'E' and resid 721 through 729 Processing helix chain 'E' and resid 733 through 749 Processing helix chain 'E' and resid 750 through 757 removed outlier: 4.147A pdb=" N ASN E 755 " --> pdb=" O PRO E 751 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG E 756 " --> pdb=" O GLU E 752 " (cutoff:3.500A) Processing helix chain 'E' and resid 767 through 790 removed outlier: 3.564A pdb=" N ARG E 789 " --> pdb=" O ARG E 785 " (cutoff:3.500A) Processing helix chain 'E' and resid 798 through 807 Processing helix chain 'E' and resid 814 through 825 removed outlier: 3.558A pdb=" N LYS E 818 " --> pdb=" O ALA E 814 " (cutoff:3.500A) Processing helix chain 'E' and resid 825 through 835 Processing helix chain 'F' and resid 168 through 174 Processing helix chain 'F' and resid 183 through 195 removed outlier: 3.512A pdb=" N ILE F 187 " --> pdb=" O ARG F 183 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 225 Processing helix chain 'F' and resid 229 through 233 Processing helix chain 'F' and resid 241 through 248 removed outlier: 3.785A pdb=" N LEU F 245 " --> pdb=" O ASP F 241 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY F 248 " --> pdb=" O ALA F 244 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 269 Processing helix chain 'F' and resid 279 through 285 Processing helix chain 'F' and resid 294 through 304 Proline residue: F 301 - end of helix Processing helix chain 'F' and resid 316 through 322 Processing helix chain 'F' and resid 342 through 362 removed outlier: 4.971A pdb=" N GLU F 355 " --> pdb=" O ARG F 351 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N ARG F 356 " --> pdb=" O GLY F 352 " (cutoff:3.500A) Processing helix chain 'F' and resid 366 through 381 Processing helix chain 'F' and resid 387 through 406 Processing helix chain 'F' and resid 532 through 543 Processing helix chain 'F' and resid 558 through 560 No H-bonds generated for 'chain 'F' and resid 558 through 560' Processing helix chain 'F' and resid 561 through 570 removed outlier: 3.668A pdb=" N GLU F 565 " --> pdb=" O ARG F 561 " (cutoff:3.500A) Processing helix chain 'F' and resid 573 through 589 Processing helix chain 'F' and resid 610 through 622 Processing helix chain 'F' and resid 639 through 641 No H-bonds generated for 'chain 'F' and resid 639 through 641' Processing helix chain 'F' and resid 642 through 647 Processing helix chain 'F' and resid 660 through 669 removed outlier: 3.532A pdb=" N ALA F 665 " --> pdb=" O TYR F 661 " (cutoff:3.500A) Processing helix chain 'F' and resid 683 through 697 Processing helix chain 'F' and resid 721 through 729 Processing helix chain 'F' and resid 734 through 749 Processing helix chain 'F' and resid 767 through 790 removed outlier: 3.664A pdb=" N ILE F 771 " --> pdb=" O GLY F 767 " (cutoff:3.500A) Processing helix chain 'F' and resid 796 through 807 Processing helix chain 'F' and resid 814 through 834 removed outlier: 3.507A pdb=" N LYS F 818 " --> pdb=" O ALA F 814 " (cutoff:3.500A) Proline residue: F 828 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 236 through 239 removed outlier: 8.292A pdb=" N ALA A 313 " --> pdb=" O LEU A 275 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE A 277 " --> pdb=" O ALA A 313 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N THR A 314 " --> pdb=" O PRO A 202 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N LEU A 204 " --> pdb=" O THR A 314 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 629 through 633 removed outlier: 5.907A pdb=" N VAL A 630 " --> pdb=" O LEU A 675 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N ASP A 677 " --> pdb=" O VAL A 630 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ILE A 632 " --> pdb=" O ASP A 677 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N ILE A 674 " --> pdb=" O ILE A 715 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N THR A 717 " --> pdb=" O ILE A 674 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LEU A 676 " --> pdb=" O THR A 717 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL A 714 " --> pdb=" O GLY A 599 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N MET A 716 " --> pdb=" O PHE A 601 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU A 759 " --> pdb=" O SER A 600 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU A 602 " --> pdb=" O GLU A 759 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL A 761 " --> pdb=" O LEU A 602 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 698 through 700 Processing sheet with id=AA4, first strand: chain 'A' and resid 793 through 795 Processing sheet with id=AA5, first strand: chain 'B' and resid 165 through 167 removed outlier: 5.899A pdb=" N ARG B 236 " --> pdb=" O ILE B 274 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N PHE B 276 " --> pdb=" O ARG B 236 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N LEU B 238 " --> pdb=" O PHE B 276 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N ASP B 278 " --> pdb=" O LEU B 238 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N LEU B 240 " --> pdb=" O ASP B 278 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N ALA B 313 " --> pdb=" O LEU B 275 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N ILE B 277 " --> pdb=" O ALA B 313 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N THR B 314 " --> pdb=" O PRO B 202 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N LEU B 204 " --> pdb=" O THR B 314 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 630 through 633 removed outlier: 3.764A pdb=" N ASP B 677 " --> pdb=" O ILE B 632 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL B 713 " --> pdb=" O SER B 672 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLY B 599 " --> pdb=" O THR B 712 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N MET B 716 " --> pdb=" O PHE B 601 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU B 759 " --> pdb=" O SER B 600 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU B 602 " --> pdb=" O GLU B 759 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 793 through 795 Processing sheet with id=AA8, first strand: chain 'C' and resid 165 through 167 removed outlier: 6.445A pdb=" N ARG C 236 " --> pdb=" O ILE C 274 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N PHE C 276 " --> pdb=" O ARG C 236 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N LEU C 238 " --> pdb=" O PHE C 276 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ASP C 278 " --> pdb=" O LEU C 238 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LEU C 240 " --> pdb=" O ASP C 278 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N VAL C 311 " --> pdb=" O VAL C 273 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LEU C 275 " --> pdb=" O VAL C 311 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N ALA C 313 " --> pdb=" O LEU C 275 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N ILE C 277 " --> pdb=" O ALA C 313 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 202 through 205 Processing sheet with id=AB1, first strand: chain 'C' and resid 364 through 365 removed outlier: 6.726A pdb=" N GLN C 364 " --> pdb=" O VAL C 531 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 630 through 631 removed outlier: 6.636A pdb=" N VAL C 630 " --> pdb=" O LEU C 675 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N ASP C 677 " --> pdb=" O VAL C 630 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ILE C 674 " --> pdb=" O ILE C 715 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N THR C 717 " --> pdb=" O ILE C 674 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LEU C 676 " --> pdb=" O THR C 717 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU C 759 " --> pdb=" O SER C 600 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 698 through 700 Processing sheet with id=AB4, first strand: chain 'C' and resid 843 through 848 removed outlier: 3.512A pdb=" N ARG C 845 " --> pdb=" O VAL C 856 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 165 through 167 removed outlier: 6.400A pdb=" N ARG D 236 " --> pdb=" O ILE D 274 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N PHE D 276 " --> pdb=" O ARG D 236 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N LEU D 238 " --> pdb=" O PHE D 276 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ASP D 278 " --> pdb=" O LEU D 238 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N LEU D 240 " --> pdb=" O ASP D 278 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA D 313 " --> pdb=" O ILE D 277 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 630 through 631 removed outlier: 6.350A pdb=" N VAL D 630 " --> pdb=" O LEU D 675 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ILE D 674 " --> pdb=" O ILE D 715 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N THR D 717 " --> pdb=" O ILE D 674 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N LEU D 676 " --> pdb=" O THR D 717 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N PHE D 601 " --> pdb=" O MET D 716 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU D 759 " --> pdb=" O SER D 600 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU D 602 " --> pdb=" O GLU D 759 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 698 through 700 removed outlier: 3.869A pdb=" N LEU D 699 " --> pdb=" O VAL D 707 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 792 through 795 removed outlier: 3.801A pdb=" N ARG D 845 " --> pdb=" O VAL D 856 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 165 through 167 removed outlier: 5.223A pdb=" N ASP E 278 " --> pdb=" O LEU E 240 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA E 313 " --> pdb=" O ILE E 277 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 630 through 633 removed outlier: 6.046A pdb=" N PHE E 601 " --> pdb=" O MET E 716 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 698 through 700 removed outlier: 3.816A pdb=" N LEU E 699 " --> pdb=" O VAL E 707 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 792 through 795 removed outlier: 6.797A pdb=" N GLU E 792 " --> pdb=" O ILE E 844 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N LEU E 846 " --> pdb=" O GLU E 792 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N HIS E 794 " --> pdb=" O LEU E 846 " (cutoff:3.500A) removed outlier: 8.735A pdb=" N VAL E 848 " --> pdb=" O HIS E 794 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 165 through 167 Processing sheet with id=AC5, first strand: chain 'F' and resid 203 through 206 Processing sheet with id=AC6, first strand: chain 'F' and resid 364 through 365 removed outlier: 7.270A pdb=" N GLN F 364 " --> pdb=" O VAL F 531 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'F' and resid 629 through 631 removed outlier: 6.046A pdb=" N VAL F 630 " --> pdb=" O LEU F 675 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ILE F 674 " --> pdb=" O ILE F 715 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N THR F 717 " --> pdb=" O ILE F 674 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N LEU F 676 " --> pdb=" O THR F 717 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LEU F 602 " --> pdb=" O VAL F 761 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 698 through 700 Processing sheet with id=AC9, first strand: chain 'F' and resid 793 through 795 removed outlier: 7.670A pdb=" N HIS F 794 " --> pdb=" O LEU F 846 " (cutoff:3.500A) removed outlier: 8.746A pdb=" N VAL F 848 " --> pdb=" O HIS F 794 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ARG F 845 " --> pdb=" O VAL F 856 " (cutoff:3.500A) 1438 hydrogen bonds defined for protein. 4245 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: 11.98 Time building geometry restraints manager: 11.66 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: 10204 1.36 - 1.51: 8221 1.51 - 1.65: 10651 1.65 - 1.80: 156 1.80 - 1.95: 37 Bond restraints: 29269 Sorted by residual: bond pdb=" O1B AGS D1003 " pdb=" PB AGS D1003 " ideal model delta sigma weight residual 1.481 1.556 -0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" CB PHE C 687 " pdb=" CG PHE C 687 " ideal model delta sigma weight residual 1.502 1.443 0.059 2.30e-02 1.89e+03 6.65e+00 bond pdb=" CB GLN D 692 " pdb=" CG GLN D 692 " ideal model delta sigma weight residual 1.520 1.444 0.076 3.00e-02 1.11e+03 6.48e+00 bond pdb=" CG GLN C 385 " pdb=" CD GLN C 385 " ideal model delta sigma weight residual 1.516 1.453 0.063 2.50e-02 1.60e+03 6.35e+00 bond pdb=" CB GLU D 613 " pdb=" CG GLU D 613 " ideal model delta sigma weight residual 1.520 1.446 0.074 3.00e-02 1.11e+03 6.11e+00 ... (remaining 29264 not shown) Histogram of bond angle deviations from ideal: 95.33 - 103.60: 377 103.60 - 111.87: 13933 111.87 - 120.14: 13612 120.14 - 128.41: 11444 128.41 - 136.69: 189 Bond angle restraints: 39555 Sorted by residual: angle pdb=" C HIS C 641 " pdb=" N SER C 642 " pdb=" CA SER C 642 " ideal model delta sigma weight residual 121.54 131.23 -9.69 1.91e+00 2.74e-01 2.57e+01 angle pdb=" C GLY E 610 " pdb=" N LYS E 611 " pdb=" CA LYS E 611 " ideal model delta sigma weight residual 120.88 112.88 8.00 1.62e+00 3.81e-01 2.44e+01 angle pdb=" C ARG B 645 " pdb=" N LEU B 646 " pdb=" CA LEU B 646 " ideal model delta sigma weight residual 121.66 113.49 8.17 1.76e+00 3.23e-01 2.15e+01 angle pdb=" C PHE B 749 " pdb=" N ARG B 750 " pdb=" CA ARG B 750 " ideal model delta sigma weight residual 120.97 134.06 -13.09 2.84e+00 1.24e-01 2.13e+01 angle pdb=" C MET D 293 " pdb=" N ASP D 294 " pdb=" CA ASP D 294 " ideal model delta sigma weight residual 122.44 116.97 5.47 1.19e+00 7.06e-01 2.11e+01 ... (remaining 39550 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.80: 17588 24.80 - 49.61: 401 49.61 - 74.41: 41 74.41 - 99.21: 11 99.21 - 124.02: 2 Dihedral angle restraints: 18043 sinusoidal: 7634 harmonic: 10409 Sorted by residual: dihedral pdb=" O1B ADP F1001 " pdb=" O3A ADP F1001 " pdb=" PB ADP F1001 " pdb=" PA ADP F1001 " ideal model delta sinusoidal sigma weight residual 300.00 175.98 124.02 1 2.00e+01 2.50e-03 3.74e+01 dihedral pdb=" CA TYR C 653 " pdb=" C TYR C 653 " pdb=" N VAL C 654 " pdb=" CA VAL C 654 " ideal model delta harmonic sigma weight residual -180.00 -149.92 -30.08 0 5.00e+00 4.00e-02 3.62e+01 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 180.00 149.98 30.02 0 5.00e+00 4.00e-02 3.61e+01 ... (remaining 18040 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 3210 0.060 - 0.120: 1048 0.120 - 0.179: 189 0.179 - 0.239: 22 0.239 - 0.299: 4 Chirality restraints: 4473 Sorted by residual: chirality pdb=" PB AGS D1003 " pdb=" O2B AGS D1003 " pdb=" O3A AGS D1003 " pdb=" O3B AGS D1003 " both_signs ideal model delta sigma weight residual True 3.18 3.48 -0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" PB AGS D1001 " pdb=" O2B AGS D1001 " pdb=" O3A AGS D1001 " pdb=" O3B AGS D1001 " both_signs ideal model delta sigma weight residual True 3.18 2.91 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CB ILE E 571 " pdb=" CA ILE E 571 " pdb=" CG1 ILE E 571 " pdb=" CG2 ILE E 571 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.61e+00 ... (remaining 4470 not shown) Planarity restraints: 5164 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP E 543 " -0.037 2.00e-02 2.50e+03 3.14e-02 2.46e+01 pdb=" CG TRP E 543 " 0.080 2.00e-02 2.50e+03 pdb=" CD1 TRP E 543 " -0.042 2.00e-02 2.50e+03 pdb=" CD2 TRP E 543 " 0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP E 543 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP E 543 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP E 543 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 543 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 543 " -0.013 2.00e-02 2.50e+03 pdb=" CH2 TRP E 543 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 367 " 0.048 5.00e-02 4.00e+02 7.15e-02 8.19e+00 pdb=" N PRO C 368 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO C 368 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 368 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS D 683 " 0.045 5.00e-02 4.00e+02 6.73e-02 7.25e+00 pdb=" N PRO D 684 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO D 684 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO D 684 " 0.037 5.00e-02 4.00e+02 ... (remaining 5161 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 5675 2.77 - 3.30: 27398 3.30 - 3.83: 48520 3.83 - 4.37: 56355 4.37 - 4.90: 94771 Nonbonded interactions: 232719 Sorted by model distance: nonbonded pdb=" O GLN D 195 " pdb=" OG SER E 399 " model vdw 2.235 3.040 nonbonded pdb=" OH TYR B 656 " pdb=" OE1 GLU C 658 " model vdw 2.239 3.040 nonbonded pdb=" O1B AGS D1003 " pdb=" O2A AGS D1003 " model vdw 2.248 3.040 nonbonded pdb=" OH TYR A 656 " pdb=" OE1 GLU B 658 " model vdw 2.250 3.040 nonbonded pdb=" OD1 ASP B 677 " pdb=" OG1 THR B 717 " model vdw 2.252 3.040 ... (remaining 232714 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 159 through 858) selection = (chain 'B' and (resid 159 through 287 or resid 293 through 543 or resid 553 thro \ ugh 858)) selection = (chain 'C' and (resid 159 through 287 or resid 293 through 408 or resid 527 thro \ ugh 543 or resid 553 through 858)) selection = (chain 'D' and (resid 159 through 408 or resid 527 through 543 or resid 553 thro \ ugh 858)) selection = (chain 'E' and (resid 159 through 408 or resid 527 through 543 or resid 553 thro \ ugh 858)) selection = (chain 'F' and resid 159 through 858) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.980 Check model and map are aligned: 0.190 Set scattering table: 0.240 Process input model: 74.150 Find NCS groups from input model: 1.830 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6730 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 : 0.009 0.100 29269 Z= 0.591 Angle : 1.074 15.878 39555 Z= 0.572 Chirality : 0.058 0.299 4473 Planarity : 0.008 0.072 5164 Dihedral : 11.032 124.017 11327 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 0.10 % Allowed : 1.06 % Favored : 98.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.77 (0.11), residues: 3578 helix: -2.25 (0.09), residues: 1888 sheet: -2.85 (0.25), residues: 356 loop : -2.50 (0.15), residues: 1334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.080 0.006 TRP E 543 HIS 0.014 0.002 HIS F 747 PHE 0.037 0.004 PHE D 763 TYR 0.030 0.003 TYR B 322 ARG 0.019 0.001 ARG C 332 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7156 Ramachandran restraints generated. 3578 Oldfield, 0 Emsley, 3578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7156 Ramachandran restraints generated. 3578 Oldfield, 0 Emsley, 3578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 3024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 612 time to evaluate : 3.032 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 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: A 194 LEU cc_start: 0.8506 (mt) cc_final: 0.8232 (tp) REVERT: A 293 MET cc_start: 0.0194 (tpt) cc_final: -0.0891 (mmt) REVERT: A 723 ASP cc_start: 0.9453 (m-30) cc_final: 0.9215 (p0) REVERT: B 293 MET cc_start: 0.4802 (mmt) cc_final: 0.4521 (mmt) REVERT: B 602 LEU cc_start: 0.7729 (tp) cc_final: 0.6921 (tp) REVERT: E 350 LEU cc_start: 0.8124 (mt) cc_final: 0.7910 (tp) REVERT: F 403 MET cc_start: 0.9102 (mtp) cc_final: 0.8203 (tpt) REVERT: F 661 TYR cc_start: 0.7678 (t80) cc_final: 0.7448 (t80) outliers start: 3 outliers final: 0 residues processed: 615 average time/residue: 0.4842 time to fit residues: 443.0679 Evaluate side-chains 335 residues out of total 3024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 335 time to evaluate : 3.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 303 optimal weight: 4.9990 chunk 272 optimal weight: 5.9990 chunk 150 optimal weight: 20.0000 chunk 92 optimal weight: 4.9990 chunk 183 optimal weight: 0.9980 chunk 145 optimal weight: 2.9990 chunk 281 optimal weight: 0.9980 chunk 108 optimal weight: 5.9990 chunk 171 optimal weight: 10.0000 chunk 209 optimal weight: 1.9990 chunk 326 optimal weight: 9.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 GLN A 281 HIS A 641 HIS A 726 GLN ** A 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 823 GLN A 849 ASN A 858 HIS B 192 GLN B 195 GLN B 641 HIS ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 806 ASN ** B 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 824 GLN ** B 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 858 HIS C 221 GLN C 297 ASN C 421 GLN ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 849 ASN D 192 GLN D 195 GLN D 421 GLN D 567 HIS D 641 HIS D 711 ASN D 794 HIS D 822 GLN D 849 ASN D 858 HIS E 321 GLN E 361 HIS ** E 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 567 HIS E 692 GLN E 822 GLN E 858 HIS F 281 HIS F 297 ASN F 309 HIS F 321 GLN F 620 ASN F 688 ASN ** F 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 857 GLN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 29269 Z= 0.232 Angle : 0.735 11.841 39555 Z= 0.375 Chirality : 0.046 0.246 4473 Planarity : 0.006 0.069 5164 Dihedral : 9.773 117.088 4193 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 0.10 % Allowed : 2.39 % Favored : 97.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.13), residues: 3578 helix: -0.70 (0.11), residues: 1959 sheet: -2.52 (0.24), residues: 376 loop : -1.86 (0.17), residues: 1243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 543 HIS 0.006 0.001 HIS C 794 PHE 0.031 0.003 PHE C 333 TYR 0.026 0.002 TYR A 812 ARG 0.021 0.001 ARG C 669 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7156 Ramachandran restraints generated. 3578 Oldfield, 0 Emsley, 3578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7156 Ramachandran restraints generated. 3578 Oldfield, 0 Emsley, 3578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 3024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 397 time to evaluate : 3.454 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 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: A 194 LEU cc_start: 0.8684 (mt) cc_final: 0.8299 (tp) REVERT: A 293 MET cc_start: 0.0250 (tpt) cc_final: -0.1172 (mmt) REVERT: A 337 PHE cc_start: 0.8431 (m-80) cc_final: 0.8223 (m-10) REVERT: A 403 MET cc_start: 0.8118 (mtt) cc_final: 0.7667 (mtt) REVERT: B 280 LEU cc_start: 0.7997 (tt) cc_final: 0.7694 (tt) REVERT: B 544 THR cc_start: 0.8658 (OUTLIER) cc_final: 0.7668 (p) REVERT: B 629 MET cc_start: 0.6408 (ppp) cc_final: 0.5455 (ppp) REVERT: C 281 HIS cc_start: 0.5911 (p-80) cc_final: 0.3672 (p-80) REVERT: C 329 LEU cc_start: 0.7765 (mt) cc_final: 0.7520 (mt) REVERT: C 629 MET cc_start: 0.6319 (ppp) cc_final: 0.5062 (ppp) REVERT: E 321 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.7868 (pp30) REVERT: E 737 MET cc_start: 0.5762 (mmt) cc_final: 0.5094 (mmt) REVERT: F 403 MET cc_start: 0.9068 (mtp) cc_final: 0.8262 (tpt) REVERT: F 629 MET cc_start: 0.5656 (mmm) cc_final: 0.4655 (mmm) REVERT: F 737 MET cc_start: 0.7856 (mtt) cc_final: 0.6840 (mmm) outliers start: 3 outliers final: 0 residues processed: 400 average time/residue: 0.4329 time to fit residues: 265.8992 Evaluate side-chains 292 residues out of total 3024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 290 time to evaluate : 3.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 181 optimal weight: 5.9990 chunk 101 optimal weight: 0.6980 chunk 271 optimal weight: 8.9990 chunk 221 optimal weight: 6.9990 chunk 89 optimal weight: 2.9990 chunk 326 optimal weight: 5.9990 chunk 352 optimal weight: 9.9990 chunk 290 optimal weight: 9.9990 chunk 323 optimal weight: 7.9990 chunk 111 optimal weight: 20.0000 chunk 262 optimal weight: 8.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 567 HIS ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 770 HIS A 794 HIS ** A 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 192 GLN B 692 GLN ** B 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 824 GLN B 849 ASN ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 GLN C 221 GLN ** C 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 747 HIS E 297 ASN E 321 GLN E 421 GLN E 454 GLN E 564 GLN ** E 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 620 ASN F 726 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.3879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 29269 Z= 0.274 Angle : 0.705 9.527 39555 Z= 0.359 Chirality : 0.044 0.202 4473 Planarity : 0.005 0.057 5164 Dihedral : 9.405 119.134 4193 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 0.07 % Allowed : 2.66 % Favored : 97.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.14), residues: 3578 helix: -0.12 (0.11), residues: 1998 sheet: -2.27 (0.25), residues: 379 loop : -1.60 (0.18), residues: 1201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 543 HIS 0.007 0.001 HIS C 281 PHE 0.022 0.002 PHE F 729 TYR 0.021 0.002 TYR B 322 ARG 0.025 0.001 ARG C 379 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7156 Ramachandran restraints generated. 3578 Oldfield, 0 Emsley, 3578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7156 Ramachandran restraints generated. 3578 Oldfield, 0 Emsley, 3578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 3024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 340 time to evaluate : 3.257 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: A 194 LEU cc_start: 0.8845 (mt) cc_final: 0.8422 (tp) REVERT: A 293 MET cc_start: 0.0135 (tpt) cc_final: -0.0813 (tpp) REVERT: A 337 PHE cc_start: 0.8612 (m-80) cc_final: 0.8407 (m-10) REVERT: A 403 MET cc_start: 0.8183 (mtt) cc_final: 0.7698 (mtt) REVERT: A 595 ASN cc_start: 0.8719 (t0) cc_final: 0.8475 (t0) REVERT: B 629 MET cc_start: 0.6471 (ppp) cc_final: 0.5663 (ppp) REVERT: D 281 HIS cc_start: 0.7033 (p-80) cc_final: 0.6701 (p-80) REVERT: E 194 LEU cc_start: 0.9089 (tp) cc_final: 0.8889 (tt) REVERT: E 298 MET cc_start: 0.7241 (ttt) cc_final: 0.6953 (ttt) REVERT: E 321 GLN cc_start: 0.8726 (OUTLIER) cc_final: 0.8441 (pp30) REVERT: E 350 LEU cc_start: 0.8119 (tp) cc_final: 0.7866 (tp) REVERT: E 562 MET cc_start: 0.7658 (tmm) cc_final: 0.7411 (tmm) REVERT: E 737 MET cc_start: 0.5759 (mmt) cc_final: 0.5404 (mmp) REVERT: F 602 LEU cc_start: 0.8497 (pt) cc_final: 0.8257 (pt) REVERT: F 629 MET cc_start: 0.5963 (mmm) cc_final: 0.5380 (tpp) REVERT: F 737 MET cc_start: 0.8010 (mtt) cc_final: 0.6857 (mmm) outliers start: 2 outliers final: 1 residues processed: 341 average time/residue: 0.4220 time to fit residues: 225.7976 Evaluate side-chains 246 residues out of total 3024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 244 time to evaluate : 3.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 322 optimal weight: 6.9990 chunk 245 optimal weight: 0.9990 chunk 169 optimal weight: 1.9990 chunk 36 optimal weight: 7.9990 chunk 155 optimal weight: 1.9990 chunk 219 optimal weight: 9.9990 chunk 327 optimal weight: 7.9990 chunk 347 optimal weight: 2.9990 chunk 171 optimal weight: 7.9990 chunk 310 optimal weight: 5.9990 chunk 93 optimal weight: 8.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 574 ASN ** A 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 692 GLN ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 264 ASN ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 297 ASN ** E 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 620 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.4365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 29269 Z= 0.200 Angle : 0.645 9.600 39555 Z= 0.327 Chirality : 0.044 0.258 4473 Planarity : 0.005 0.071 5164 Dihedral : 9.189 119.558 4193 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 0.03 % Allowed : 2.16 % Favored : 97.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.14), residues: 3578 helix: 0.19 (0.11), residues: 1989 sheet: -2.17 (0.25), residues: 389 loop : -1.47 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 543 HIS 0.005 0.001 HIS F 360 PHE 0.027 0.002 PHE C 333 TYR 0.017 0.001 TYR A 322 ARG 0.009 0.000 ARG C 379 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7156 Ramachandran restraints generated. 3578 Oldfield, 0 Emsley, 3578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7156 Ramachandran restraints generated. 3578 Oldfield, 0 Emsley, 3578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 3024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 309 time to evaluate : 3.489 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: A 194 LEU cc_start: 0.8889 (mt) cc_final: 0.8525 (tp) REVERT: A 293 MET cc_start: 0.0185 (tpt) cc_final: -0.0540 (tpp) REVERT: A 595 ASN cc_start: 0.8644 (t0) cc_final: 0.8380 (t0) REVERT: B 629 MET cc_start: 0.6537 (ppp) cc_final: 0.6027 (ppp) REVERT: C 629 MET cc_start: 0.6889 (ppp) cc_final: 0.6387 (ppp) REVERT: D 737 MET cc_start: 0.7000 (mtt) cc_final: 0.6655 (mmt) REVERT: D 753 PHE cc_start: 0.6328 (t80) cc_final: 0.6128 (t80) REVERT: E 194 LEU cc_start: 0.9032 (tp) cc_final: 0.8817 (tt) REVERT: E 298 MET cc_start: 0.7049 (ttt) cc_final: 0.6756 (ttt) REVERT: E 350 LEU cc_start: 0.8109 (tp) cc_final: 0.7844 (tp) REVERT: F 403 MET cc_start: 0.8785 (mtm) cc_final: 0.8340 (tpt) REVERT: F 737 MET cc_start: 0.8018 (mtt) cc_final: 0.7020 (mmm) outliers start: 1 outliers final: 1 residues processed: 310 average time/residue: 0.4092 time to fit residues: 199.8155 Evaluate side-chains 241 residues out of total 3024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 240 time to evaluate : 3.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 289 optimal weight: 5.9990 chunk 196 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 chunk 258 optimal weight: 5.9990 chunk 143 optimal weight: 10.0000 chunk 296 optimal weight: 8.9990 chunk 239 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 177 optimal weight: 8.9990 chunk 311 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 747 HIS B 794 HIS ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 174 GLN D 427 GLN D 688 ASN ** E 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 321 GLN E 692 GLN ** E 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 620 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.5094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 29269 Z= 0.270 Angle : 0.678 10.019 39555 Z= 0.345 Chirality : 0.043 0.189 4473 Planarity : 0.005 0.054 5164 Dihedral : 9.118 121.194 4193 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 17.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 0.03 % Allowed : 2.36 % Favored : 97.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.14), residues: 3578 helix: 0.40 (0.12), residues: 1985 sheet: -2.03 (0.24), residues: 423 loop : -1.33 (0.19), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 543 HIS 0.012 0.001 HIS D 281 PHE 0.018 0.002 PHE C 333 TYR 0.025 0.002 TYR C 322 ARG 0.006 0.001 ARG A 331 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7156 Ramachandran restraints generated. 3578 Oldfield, 0 Emsley, 3578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7156 Ramachandran restraints generated. 3578 Oldfield, 0 Emsley, 3578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 3024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 278 time to evaluate : 3.053 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: A 194 LEU cc_start: 0.8979 (mt) cc_final: 0.8562 (tp) REVERT: A 293 MET cc_start: 0.0559 (tpt) cc_final: -0.0220 (tpp) REVERT: A 403 MET cc_start: 0.8059 (mtt) cc_final: 0.7847 (mtt) REVERT: A 595 ASN cc_start: 0.8816 (t0) cc_final: 0.8587 (t0) REVERT: A 716 MET cc_start: 0.9130 (pmm) cc_final: 0.8852 (pmm) REVERT: B 293 MET cc_start: 0.5409 (tpp) cc_final: 0.5049 (tpp) REVERT: B 629 MET cc_start: 0.7119 (ppp) cc_final: 0.6352 (ppp) REVERT: C 629 MET cc_start: 0.7092 (ppp) cc_final: 0.5892 (ppp) REVERT: C 825 ILE cc_start: 0.8811 (mp) cc_final: 0.8595 (mp) REVERT: D 242 MET cc_start: 0.6476 (mtp) cc_final: 0.5268 (mtp) REVERT: E 194 LEU cc_start: 0.9066 (tp) cc_final: 0.8856 (tt) REVERT: E 298 MET cc_start: 0.7543 (ttt) cc_final: 0.7255 (ttt) REVERT: E 321 GLN cc_start: 0.8597 (OUTLIER) cc_final: 0.7049 (pp30) REVERT: E 350 LEU cc_start: 0.8204 (tp) cc_final: 0.7846 (tp) REVERT: E 737 MET cc_start: 0.6365 (mmp) cc_final: 0.5944 (mmm) REVERT: F 403 MET cc_start: 0.8843 (mtm) cc_final: 0.8480 (tpt) REVERT: F 737 MET cc_start: 0.8196 (mtt) cc_final: 0.7292 (mmm) outliers start: 1 outliers final: 0 residues processed: 279 average time/residue: 0.4025 time to fit residues: 178.2833 Evaluate side-chains 209 residues out of total 3024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 208 time to evaluate : 3.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 116 optimal weight: 10.0000 chunk 312 optimal weight: 0.5980 chunk 68 optimal weight: 20.0000 chunk 203 optimal weight: 5.9990 chunk 85 optimal weight: 20.0000 chunk 347 optimal weight: 0.3980 chunk 288 optimal weight: 6.9990 chunk 160 optimal weight: 10.0000 chunk 28 optimal weight: 8.9990 chunk 114 optimal weight: 20.0000 chunk 182 optimal weight: 3.9990 overall best weight: 3.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 HIS ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 822 GLN ** D 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 769 GLN ** E 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 192 GLN F 620 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.5534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 29269 Z= 0.224 Angle : 0.644 10.526 39555 Z= 0.325 Chirality : 0.043 0.268 4473 Planarity : 0.005 0.056 5164 Dihedral : 8.994 119.596 4193 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.14), residues: 3578 helix: 0.55 (0.12), residues: 2004 sheet: -1.94 (0.25), residues: 388 loop : -1.14 (0.19), residues: 1186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP A 543 HIS 0.008 0.001 HIS D 281 PHE 0.016 0.002 PHE D 729 TYR 0.023 0.001 TYR C 322 ARG 0.010 0.000 ARG C 418 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7156 Ramachandran restraints generated. 3578 Oldfield, 0 Emsley, 3578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7156 Ramachandran restraints generated. 3578 Oldfield, 0 Emsley, 3578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 3024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 276 time to evaluate : 3.299 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: A 194 LEU cc_start: 0.8963 (mt) cc_final: 0.8666 (tp) REVERT: A 293 MET cc_start: 0.0803 (tpt) cc_final: -0.0182 (tpp) REVERT: A 320 ARG cc_start: 0.9166 (ptp-170) cc_final: 0.8936 (ptp-110) REVERT: A 403 MET cc_start: 0.8256 (mtt) cc_final: 0.7996 (mtt) REVERT: A 595 ASN cc_start: 0.8839 (t0) cc_final: 0.8593 (t0) REVERT: A 638 MET cc_start: 0.8263 (mmm) cc_final: 0.7921 (mmm) REVERT: B 293 MET cc_start: 0.5630 (tpp) cc_final: 0.4987 (tpp) REVERT: B 629 MET cc_start: 0.7191 (ppp) cc_final: 0.6583 (ppp) REVERT: C 629 MET cc_start: 0.7054 (ppp) cc_final: 0.5926 (ppp) REVERT: E 194 LEU cc_start: 0.9095 (tp) cc_final: 0.8880 (tt) REVERT: E 298 MET cc_start: 0.7647 (ttt) cc_final: 0.7368 (ttt) REVERT: E 350 LEU cc_start: 0.8196 (tp) cc_final: 0.7846 (tp) REVERT: E 691 LEU cc_start: 0.8738 (mt) cc_final: 0.8474 (mt) REVERT: E 737 MET cc_start: 0.6489 (mmp) cc_final: 0.6037 (mmm) REVERT: F 403 MET cc_start: 0.8874 (mtm) cc_final: 0.8508 (tpt) REVERT: F 629 MET cc_start: 0.5151 (mmp) cc_final: 0.2885 (tpp) outliers start: 0 outliers final: 0 residues processed: 276 average time/residue: 0.4223 time to fit residues: 184.6993 Evaluate side-chains 205 residues out of total 3024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 3.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 334 optimal weight: 20.0000 chunk 39 optimal weight: 5.9990 chunk 197 optimal weight: 5.9990 chunk 253 optimal weight: 0.0970 chunk 196 optimal weight: 0.8980 chunk 292 optimal weight: 10.0000 chunk 193 optimal weight: 9.9990 chunk 346 optimal weight: 5.9990 chunk 216 optimal weight: 10.0000 chunk 210 optimal weight: 5.9990 chunk 159 optimal weight: 0.0970 overall best weight: 2.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 ASN ** A 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 GLN ** E 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 620 ASN F 770 HIS F 849 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.5840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 29269 Z= 0.195 Angle : 0.623 15.808 39555 Z= 0.312 Chirality : 0.043 0.196 4473 Planarity : 0.004 0.051 5164 Dihedral : 8.844 118.065 4193 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.15), residues: 3578 helix: 0.70 (0.12), residues: 1995 sheet: -1.75 (0.26), residues: 392 loop : -1.00 (0.19), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 543 HIS 0.005 0.001 HIS F 747 PHE 0.018 0.002 PHE C 333 TYR 0.023 0.001 TYR D 656 ARG 0.008 0.000 ARG B 528 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7156 Ramachandran restraints generated. 3578 Oldfield, 0 Emsley, 3578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7156 Ramachandran restraints generated. 3578 Oldfield, 0 Emsley, 3578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 3024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 269 time to evaluate : 3.557 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: A 194 LEU cc_start: 0.8972 (mt) cc_final: 0.8690 (tp) REVERT: A 293 MET cc_start: 0.0446 (tpt) cc_final: -0.0379 (tpp) REVERT: A 320 ARG cc_start: 0.9154 (ptp-170) cc_final: 0.8914 (ptp-110) REVERT: A 403 MET cc_start: 0.8255 (mtt) cc_final: 0.7984 (mtt) REVERT: A 595 ASN cc_start: 0.8869 (t0) cc_final: 0.8609 (t0) REVERT: A 716 MET cc_start: 0.9100 (pmm) cc_final: 0.8776 (pmm) REVERT: B 293 MET cc_start: 0.5407 (tpp) cc_final: 0.4857 (tpp) REVERT: B 629 MET cc_start: 0.7183 (ppp) cc_final: 0.6635 (ppp) REVERT: C 629 MET cc_start: 0.7079 (ppp) cc_final: 0.5925 (ppp) REVERT: E 194 LEU cc_start: 0.9066 (tp) cc_final: 0.8851 (tt) REVERT: E 240 LEU cc_start: 0.8584 (tp) cc_final: 0.8303 (tp) REVERT: E 298 MET cc_start: 0.7706 (ttt) cc_final: 0.7445 (ttt) REVERT: E 350 LEU cc_start: 0.8147 (tp) cc_final: 0.7793 (tp) REVERT: E 691 LEU cc_start: 0.8728 (mt) cc_final: 0.8390 (mt) REVERT: E 737 MET cc_start: 0.6698 (mmp) cc_final: 0.6267 (mmm) REVERT: F 403 MET cc_start: 0.8879 (mtm) cc_final: 0.8568 (tpt) REVERT: F 629 MET cc_start: 0.5015 (mmp) cc_final: 0.2963 (tpp) REVERT: F 737 MET cc_start: 0.8183 (mtt) cc_final: 0.7450 (mmm) outliers start: 0 outliers final: 0 residues processed: 269 average time/residue: 0.4216 time to fit residues: 180.9674 Evaluate side-chains 203 residues out of total 3024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 3.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 214 optimal weight: 20.0000 chunk 138 optimal weight: 7.9990 chunk 206 optimal weight: 0.5980 chunk 104 optimal weight: 5.9990 chunk 67 optimal weight: 0.5980 chunk 219 optimal weight: 1.9990 chunk 235 optimal weight: 10.0000 chunk 171 optimal weight: 0.1980 chunk 32 optimal weight: 9.9990 chunk 271 optimal weight: 3.9990 chunk 314 optimal weight: 6.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 HIS ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 GLN ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 174 GLN ** D 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 620 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.6026 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: