Starting phenix.real_space_refine on Tue Aug 26 08:10:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fcn_28987/08_2025/8fcn_28987.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fcn_28987/08_2025/8fcn_28987.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fcn_28987/08_2025/8fcn_28987.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fcn_28987/08_2025/8fcn_28987.map" model { file = "/net/cci-nas-00/data/ceres_data/8fcn_28987/08_2025/8fcn_28987.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fcn_28987/08_2025/8fcn_28987.cif" } resolution = 2.95 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 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= -0.002 sd= 0.036 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 24 5.49 5 S 186 5.16 5 C 21942 2.51 5 N 6168 2.21 5 O 6714 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 112 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35034 Number of models: 1 Model: "" Number of chains: 18 Chain: "L" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 145 Classifications: {'peptide': 20} Link IDs: {'TRANS': 19} Chain: "F" Number of atoms: 5640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 721, 5640 Classifications: {'peptide': 721} Link IDs: {'PCIS': 3, 'PTRANS': 35, 'TRANS': 682} Chain breaks: 1 Chain: "K" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 145 Classifications: {'peptide': 20} Link IDs: {'TRANS': 19} Chain: "E" Number of atoms: 5640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 721, 5640 Classifications: {'peptide': 721} Link IDs: {'PCIS': 3, 'PTRANS': 35, 'TRANS': 682} Chain breaks: 1 Chain: "J" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 145 Classifications: {'peptide': 20} Link IDs: {'TRANS': 19} Chain: "D" Number of atoms: 5640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 721, 5640 Classifications: {'peptide': 721} Link IDs: {'PCIS': 3, 'PTRANS': 35, 'TRANS': 682} Chain breaks: 1 Chain: "I" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 145 Classifications: {'peptide': 20} Link IDs: {'TRANS': 19} Chain: "C" Number of atoms: 5640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 721, 5640 Classifications: {'peptide': 721} Link IDs: {'PCIS': 3, 'PTRANS': 35, 'TRANS': 682} Chain breaks: 1 Chain: "H" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 145 Classifications: {'peptide': 20} Link IDs: {'TRANS': 19} Chain: "B" Number of atoms: 5640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 721, 5640 Classifications: {'peptide': 721} Link IDs: {'PCIS': 3, 'PTRANS': 35, 'TRANS': 682} Chain breaks: 1 Chain: "G" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 145 Classifications: {'peptide': 20} Link IDs: {'TRANS': 19} Chain: "A" Number of atoms: 5640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 721, 5640 Classifications: {'peptide': 721} Link IDs: {'PCIS': 3, 'PTRANS': 35, 'TRANS': 682} Chain breaks: 1 Chain: "F" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.38, per 1000 atoms: 0.21 Number of scatterers: 35034 At special positions: 0 Unit cell: (182.646, 170.97, 97.578, 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 186 16.00 P 24 15.00 O 6714 8.00 N 6168 7.00 C 21942 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 - 3.00 Amino acid : True - 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=0, symmetry=0 Time building additional restraints: 2.77 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 715.3 nanoseconds 8820 Ramachandran restraints generated. 4410 Oldfield, 0 Emsley, 4410 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8316 Finding SS restraints... Secondary structure from input PDB file: 228 helices and 36 sheets defined 52.4% alpha, 13.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'L' and resid 49 through 68 Processing helix chain 'F' and resid 42 through 49 Processing helix chain 'F' and resid 85 through 93 Processing helix chain 'F' and resid 129 through 134 Processing helix chain 'F' and resid 134 through 140 Processing helix chain 'F' and resid 202 through 206 Processing helix chain 'F' and resid 209 through 226 removed outlier: 4.493A pdb=" N LEU F 222 " --> pdb=" O GLU F 218 " (cutoff:3.500A) Proline residue: F 223 - end of helix Processing helix chain 'F' and resid 226 through 231 removed outlier: 3.980A pdb=" N PHE F 230 " --> pdb=" O HIS F 226 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 263 Processing helix chain 'F' and resid 271 through 276 Processing helix chain 'F' and resid 281 through 296 removed outlier: 3.513A pdb=" N PHE F 290 " --> pdb=" O LEU F 286 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 309 Processing helix chain 'F' and resid 312 through 316 Processing helix chain 'F' and resid 318 through 334 Processing helix chain 'F' and resid 335 through 337 No H-bonds generated for 'chain 'F' and resid 335 through 337' Processing helix chain 'F' and resid 354 through 359 Processing helix chain 'F' and resid 373 through 384 Processing helix chain 'F' and resid 395 through 403 Processing helix chain 'F' and resid 407 through 431 removed outlier: 4.326A pdb=" N LEU F 429 " --> pdb=" O LYS F 425 " (cutoff:3.500A) Processing helix chain 'F' and resid 439 through 444 Processing helix chain 'F' and resid 448 through 459 Processing helix chain 'F' and resid 475 through 479 Processing helix chain 'F' and resid 482 through 494 Processing helix chain 'F' and resid 494 through 499 Processing helix chain 'F' and resid 499 through 506 removed outlier: 3.913A pdb=" N PHE F 503 " --> pdb=" O HIS F 499 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 535 Processing helix chain 'F' and resid 543 through 553 Processing helix chain 'F' and resid 557 through 569 removed outlier: 4.118A pdb=" N GLU F 561 " --> pdb=" O ALA F 557 " (cutoff:3.500A) Processing helix chain 'F' and resid 580 through 586 Processing helix chain 'F' and resid 598 through 610 Processing helix chain 'F' and resid 612 through 615 Processing helix chain 'F' and resid 625 through 629 Processing helix chain 'F' and resid 630 through 635 Processing helix chain 'F' and resid 649 through 661 Processing helix chain 'F' and resid 671 through 679 Processing helix chain 'F' and resid 683 through 706 removed outlier: 3.702A pdb=" N GLU F 706 " --> pdb=" O SER F 702 " (cutoff:3.500A) Processing helix chain 'F' and resid 732 through 740 Processing helix chain 'F' and resid 748 through 762 Processing helix chain 'K' and resid 50 through 68 Processing helix chain 'E' and resid 42 through 49 Processing helix chain 'E' and resid 85 through 93 Processing helix chain 'E' and resid 129 through 134 Processing helix chain 'E' and resid 134 through 140 Processing helix chain 'E' and resid 202 through 206 Processing helix chain 'E' and resid 209 through 226 removed outlier: 4.516A pdb=" N LEU E 222 " --> pdb=" O GLU E 218 " (cutoff:3.500A) Proline residue: E 223 - end of helix Processing helix chain 'E' and resid 226 through 231 removed outlier: 3.933A pdb=" N PHE E 230 " --> pdb=" O HIS E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 263 Processing helix chain 'E' and resid 271 through 276 Processing helix chain 'E' and resid 281 through 296 removed outlier: 3.518A pdb=" N PHE E 290 " --> pdb=" O LEU E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 309 Processing helix chain 'E' and resid 312 through 316 Processing helix chain 'E' and resid 318 through 334 Processing helix chain 'E' and resid 335 through 337 No H-bonds generated for 'chain 'E' and resid 335 through 337' Processing helix chain 'E' and resid 354 through 359 Processing helix chain 'E' and resid 373 through 384 Processing helix chain 'E' and resid 395 through 403 Processing helix chain 'E' and resid 407 through 431 removed outlier: 4.296A pdb=" N LEU E 429 " --> pdb=" O LYS E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 439 through 444 Processing helix chain 'E' and resid 448 through 459 Processing helix chain 'E' and resid 475 through 479 Processing helix chain 'E' and resid 482 through 494 Processing helix chain 'E' and resid 494 through 499 Processing helix chain 'E' and resid 499 through 506 removed outlier: 3.925A pdb=" N PHE E 503 " --> pdb=" O HIS E 499 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 535 Processing helix chain 'E' and resid 543 through 553 Processing helix chain 'E' and resid 557 through 569 removed outlier: 4.127A pdb=" N GLU E 561 " --> pdb=" O ALA E 557 " (cutoff:3.500A) Processing helix chain 'E' and resid 580 through 586 Processing helix chain 'E' and resid 598 through 610 Processing helix chain 'E' and resid 612 through 615 Processing helix chain 'E' and resid 625 through 629 Processing helix chain 'E' and resid 630 through 635 Processing helix chain 'E' and resid 649 through 661 Processing helix chain 'E' and resid 671 through 679 Processing helix chain 'E' and resid 683 through 706 removed outlier: 3.695A pdb=" N GLU E 706 " --> pdb=" O SER E 702 " (cutoff:3.500A) Processing helix chain 'E' and resid 732 through 740 removed outlier: 3.526A pdb=" N PHE E 736 " --> pdb=" O ARG E 732 " (cutoff:3.500A) Processing helix chain 'E' and resid 748 through 762 Processing helix chain 'J' and resid 50 through 68 Processing helix chain 'D' and resid 42 through 49 Processing helix chain 'D' and resid 85 through 93 Processing helix chain 'D' and resid 129 through 134 Processing helix chain 'D' and resid 134 through 140 Processing helix chain 'D' and resid 202 through 206 Processing helix chain 'D' and resid 209 through 226 removed outlier: 4.486A pdb=" N LEU D 222 " --> pdb=" O GLU D 218 " (cutoff:3.500A) Proline residue: D 223 - end of helix Processing helix chain 'D' and resid 226 through 231 removed outlier: 3.973A pdb=" N PHE D 230 " --> pdb=" O HIS D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 263 Processing helix chain 'D' and resid 271 through 276 Processing helix chain 'D' and resid 281 through 296 removed outlier: 3.514A pdb=" N PHE D 290 " --> pdb=" O LEU D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 309 Processing helix chain 'D' and resid 312 through 316 Processing helix chain 'D' and resid 318 through 334 Processing helix chain 'D' and resid 335 through 337 No H-bonds generated for 'chain 'D' and resid 335 through 337' Processing helix chain 'D' and resid 354 through 359 Processing helix chain 'D' and resid 373 through 384 Processing helix chain 'D' and resid 395 through 403 Processing helix chain 'D' and resid 407 through 431 removed outlier: 4.310A pdb=" N LEU D 429 " --> pdb=" O LYS D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 444 Processing helix chain 'D' and resid 448 through 459 Processing helix chain 'D' and resid 475 through 479 Processing helix chain 'D' and resid 482 through 494 Processing helix chain 'D' and resid 494 through 499 Processing helix chain 'D' and resid 499 through 506 removed outlier: 3.690A pdb=" N PHE D 503 " --> pdb=" O HIS D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 535 Processing helix chain 'D' and resid 543 through 553 Processing helix chain 'D' and resid 557 through 569 removed outlier: 4.129A pdb=" N GLU D 561 " --> pdb=" O ALA D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 580 through 586 Processing helix chain 'D' and resid 598 through 610 Processing helix chain 'D' and resid 612 through 615 Processing helix chain 'D' and resid 625 through 629 Processing helix chain 'D' and resid 630 through 635 Processing helix chain 'D' and resid 649 through 661 Processing helix chain 'D' and resid 671 through 679 Processing helix chain 'D' and resid 683 through 706 removed outlier: 3.690A pdb=" N GLU D 706 " --> pdb=" O SER D 702 " (cutoff:3.500A) Processing helix chain 'D' and resid 732 through 740 Processing helix chain 'D' and resid 748 through 762 Processing helix chain 'I' and resid 50 through 68 Processing helix chain 'C' and resid 42 through 49 Processing helix chain 'C' and resid 85 through 93 Processing helix chain 'C' and resid 129 through 134 Processing helix chain 'C' and resid 134 through 140 Processing helix chain 'C' and resid 202 through 206 Processing helix chain 'C' and resid 209 through 226 removed outlier: 4.529A pdb=" N LEU C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) Proline residue: C 223 - end of helix Processing helix chain 'C' and resid 226 through 231 removed outlier: 3.929A pdb=" N PHE C 230 " --> pdb=" O HIS C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 263 Processing helix chain 'C' and resid 271 through 276 Processing helix chain 'C' and resid 281 through 296 Processing helix chain 'C' and resid 305 through 309 Processing helix chain 'C' and resid 312 through 316 Processing helix chain 'C' and resid 318 through 334 Processing helix chain 'C' and resid 335 through 337 No H-bonds generated for 'chain 'C' and resid 335 through 337' Processing helix chain 'C' and resid 354 through 359 Processing helix chain 'C' and resid 373 through 384 Processing helix chain 'C' and resid 395 through 403 Processing helix chain 'C' and resid 407 through 431 removed outlier: 4.336A pdb=" N LEU C 429 " --> pdb=" O LYS C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 444 Processing helix chain 'C' and resid 448 through 459 Processing helix chain 'C' and resid 475 through 479 Processing helix chain 'C' and resid 482 through 494 Processing helix chain 'C' and resid 494 through 499 Processing helix chain 'C' and resid 499 through 506 removed outlier: 3.850A pdb=" N PHE C 503 " --> pdb=" O HIS C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 535 Processing helix chain 'C' and resid 543 through 553 Processing helix chain 'C' and resid 557 through 569 removed outlier: 4.130A pdb=" N GLU C 561 " --> pdb=" O ALA C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 586 Processing helix chain 'C' and resid 598 through 610 Processing helix chain 'C' and resid 612 through 615 Processing helix chain 'C' and resid 625 through 629 Processing helix chain 'C' and resid 630 through 635 Processing helix chain 'C' and resid 649 through 661 Processing helix chain 'C' and resid 671 through 679 Processing helix chain 'C' and resid 683 through 706 removed outlier: 3.698A pdb=" N GLU C 706 " --> pdb=" O SER C 702 " (cutoff:3.500A) Processing helix chain 'C' and resid 732 through 740 Processing helix chain 'C' and resid 748 through 762 Processing helix chain 'H' and resid 50 through 68 Processing helix chain 'B' and resid 42 through 49 Processing helix chain 'B' and resid 85 through 93 Processing helix chain 'B' and resid 129 through 134 Processing helix chain 'B' and resid 134 through 140 Processing helix chain 'B' and resid 202 through 206 Processing helix chain 'B' and resid 209 through 226 removed outlier: 4.497A pdb=" N LEU B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Proline residue: B 223 - end of helix Processing helix chain 'B' and resid 226 through 231 removed outlier: 3.951A pdb=" N PHE B 230 " --> pdb=" O HIS B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 263 Processing helix chain 'B' and resid 271 through 276 Processing helix chain 'B' and resid 281 through 296 removed outlier: 3.517A pdb=" N PHE B 290 " --> pdb=" O LEU B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 309 Processing helix chain 'B' and resid 312 through 316 Processing helix chain 'B' and resid 318 through 334 Processing helix chain 'B' and resid 335 through 337 No H-bonds generated for 'chain 'B' and resid 335 through 337' Processing helix chain 'B' and resid 354 through 359 Processing helix chain 'B' and resid 373 through 384 Processing helix chain 'B' and resid 395 through 403 Processing helix chain 'B' and resid 407 through 431 removed outlier: 4.299A pdb=" N LEU B 429 " --> pdb=" O LYS B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 444 Processing helix chain 'B' and resid 448 through 459 Processing helix chain 'B' and resid 475 through 479 Processing helix chain 'B' and resid 482 through 494 Processing helix chain 'B' and resid 494 through 499 Processing helix chain 'B' and resid 499 through 506 removed outlier: 3.897A pdb=" N PHE B 503 " --> pdb=" O HIS B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 535 Processing helix chain 'B' and resid 543 through 553 Processing helix chain 'B' and resid 557 through 569 removed outlier: 4.128A pdb=" N GLU B 561 " --> pdb=" O ALA B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 586 Processing helix chain 'B' and resid 598 through 610 Processing helix chain 'B' and resid 612 through 615 Processing helix chain 'B' and resid 625 through 629 Processing helix chain 'B' and resid 630 through 635 Processing helix chain 'B' and resid 649 through 661 Processing helix chain 'B' and resid 671 through 679 Processing helix chain 'B' and resid 683 through 706 removed outlier: 3.692A pdb=" N GLU B 706 " --> pdb=" O SER B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 740 Processing helix chain 'B' and resid 748 through 762 Processing helix chain 'G' and resid 50 through 68 Processing helix chain 'A' and resid 42 through 49 Processing helix chain 'A' and resid 85 through 93 Processing helix chain 'A' and resid 129 through 134 Processing helix chain 'A' and resid 134 through 140 Processing helix chain 'A' and resid 202 through 206 Processing helix chain 'A' and resid 209 through 226 removed outlier: 4.486A pdb=" N LEU A 222 " --> pdb=" O GLU A 218 " (cutoff:3.500A) Proline residue: A 223 - end of helix Processing helix chain 'A' and resid 226 through 231 removed outlier: 3.924A pdb=" N PHE A 230 " --> pdb=" O HIS A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 263 Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 281 through 296 removed outlier: 3.506A pdb=" N PHE A 290 " --> pdb=" O LEU A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 309 Processing helix chain 'A' and resid 312 through 316 Processing helix chain 'A' and resid 318 through 334 Processing helix chain 'A' and resid 335 through 337 No H-bonds generated for 'chain 'A' and resid 335 through 337' Processing helix chain 'A' and resid 354 through 359 Processing helix chain 'A' and resid 373 through 384 Processing helix chain 'A' and resid 395 through 403 Processing helix chain 'A' and resid 407 through 431 removed outlier: 4.319A pdb=" N LEU A 429 " --> pdb=" O LYS A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 444 Processing helix chain 'A' and resid 448 through 459 Processing helix chain 'A' and resid 475 through 479 Processing helix chain 'A' and resid 482 through 494 Processing helix chain 'A' and resid 494 through 499 Processing helix chain 'A' and resid 499 through 506 removed outlier: 3.854A pdb=" N PHE A 503 " --> pdb=" O HIS A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 535 Processing helix chain 'A' and resid 543 through 553 Processing helix chain 'A' and resid 557 through 569 removed outlier: 4.121A pdb=" N GLU A 561 " --> pdb=" O ALA A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 586 Processing helix chain 'A' and resid 598 through 610 Processing helix chain 'A' and resid 612 through 615 Processing helix chain 'A' and resid 625 through 629 Processing helix chain 'A' and resid 630 through 635 Processing helix chain 'A' and resid 649 through 661 Processing helix chain 'A' and resid 671 through 679 Processing helix chain 'A' and resid 683 through 706 removed outlier: 3.698A pdb=" N GLU A 706 " --> pdb=" O SER A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 740 removed outlier: 3.525A pdb=" N PHE A 736 " --> pdb=" O ARG A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 762 Processing sheet with id=AA1, first strand: chain 'F' and resid 25 through 30 Processing sheet with id=AA2, first strand: chain 'F' and resid 151 through 156 removed outlier: 5.391A pdb=" N VAL F 165 " --> pdb=" O LEU F 117 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LEU F 117 " --> pdb=" O VAL F 165 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU F 167 " --> pdb=" O HIS F 115 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ILE F 114 " --> pdb=" O HIS F 183 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 126 through 127 Processing sheet with id=AA4, first strand: chain 'F' and resid 145 through 147 Processing sheet with id=AA5, first strand: chain 'F' and resid 265 through 270 removed outlier: 6.205A pdb=" N PHE F 265 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N PHE F 302 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N PHE F 267 " --> pdb=" O PHE F 302 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N ASP F 304 " --> pdb=" O PHE F 267 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE F 269 " --> pdb=" O ASP F 304 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ALA F 299 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N MET F 344 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ILE F 303 " --> pdb=" O ALA F 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 469 through 470 removed outlier: 3.611A pdb=" N GLU F 470 " --> pdb=" O PHE F 539 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL F 514 " --> pdb=" O GLY F 621 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N THR F 623 " --> pdb=" O VAL F 514 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N PHE F 516 " --> pdb=" O THR F 623 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN F 641 " --> pdb=" O GLY F 513 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 25 through 29 Processing sheet with id=AA8, first strand: chain 'E' and resid 151 through 156 removed outlier: 5.374A pdb=" N VAL E 165 " --> pdb=" O LEU E 117 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LEU E 117 " --> pdb=" O VAL E 165 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ILE E 114 " --> pdb=" O HIS E 183 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 126 through 127 Processing sheet with id=AB1, first strand: chain 'E' and resid 145 through 147 Processing sheet with id=AB2, first strand: chain 'E' and resid 265 through 270 removed outlier: 6.202A pdb=" N PHE E 265 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N PHE E 302 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N PHE E 267 " --> pdb=" O PHE E 302 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N ASP E 304 " --> pdb=" O PHE E 267 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE E 269 " --> pdb=" O ASP E 304 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 469 through 470 removed outlier: 3.618A pdb=" N GLU E 470 " --> pdb=" O PHE E 539 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL E 514 " --> pdb=" O GLY E 621 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N THR E 623 " --> pdb=" O VAL E 514 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N PHE E 516 " --> pdb=" O THR E 623 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN E 641 " --> pdb=" O GLY E 513 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 25 through 29 Processing sheet with id=AB5, first strand: chain 'D' and resid 151 through 156 removed outlier: 5.353A pdb=" N VAL D 165 " --> pdb=" O LEU D 117 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N LEU D 117 " --> pdb=" O VAL D 165 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU D 167 " --> pdb=" O HIS D 115 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE D 114 " --> pdb=" O HIS D 183 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 126 through 127 Processing sheet with id=AB7, first strand: chain 'D' and resid 145 through 147 Processing sheet with id=AB8, first strand: chain 'D' and resid 265 through 270 removed outlier: 6.195A pdb=" N PHE D 265 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N PHE D 302 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N PHE D 267 " --> pdb=" O PHE D 302 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N ASP D 304 " --> pdb=" O PHE D 267 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE D 269 " --> pdb=" O ASP D 304 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 469 through 470 removed outlier: 3.616A pdb=" N GLU D 470 " --> pdb=" O PHE D 539 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL D 514 " --> pdb=" O GLY D 621 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N THR D 623 " --> pdb=" O VAL D 514 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N PHE D 516 " --> pdb=" O THR D 623 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN D 641 " --> pdb=" O GLY D 513 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 25 through 29 Processing sheet with id=AC2, first strand: chain 'C' and resid 151 through 156 removed outlier: 5.343A pdb=" N VAL C 165 " --> pdb=" O LEU C 117 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N LEU C 117 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE C 114 " --> pdb=" O HIS C 183 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 126 through 127 Processing sheet with id=AC4, first strand: chain 'C' and resid 144 through 147 removed outlier: 3.783A pdb=" N ARG C 144 " --> pdb=" O VAL C 176 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 265 through 270 removed outlier: 6.195A pdb=" N PHE C 265 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N PHE C 302 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N PHE C 267 " --> pdb=" O PHE C 302 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N ASP C 304 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE C 269 " --> pdb=" O ASP C 304 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 469 through 470 removed outlier: 3.613A pdb=" N GLU C 470 " --> pdb=" O PHE C 539 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN C 641 " --> pdb=" O GLY C 513 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 25 through 29 Processing sheet with id=AC8, first strand: chain 'B' and resid 151 through 156 removed outlier: 5.347A pdb=" N VAL B 165 " --> pdb=" O LEU B 117 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LEU B 117 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE B 114 " --> pdb=" O HIS B 183 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 126 through 127 Processing sheet with id=AD1, first strand: chain 'B' and resid 145 through 147 Processing sheet with id=AD2, first strand: chain 'B' and resid 265 through 270 removed outlier: 6.188A pdb=" N PHE B 265 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N PHE B 302 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N PHE B 267 " --> pdb=" O PHE B 302 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N ASP B 304 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ILE B 269 " --> pdb=" O ASP B 304 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 469 through 470 removed outlier: 3.615A pdb=" N GLU B 470 " --> pdb=" O PHE B 539 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N VAL B 514 " --> pdb=" O GLY B 621 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N THR B 623 " --> pdb=" O VAL B 514 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N PHE B 516 " --> pdb=" O THR B 623 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN B 641 " --> pdb=" O GLY B 513 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 25 through 29 Processing sheet with id=AD5, first strand: chain 'A' and resid 151 through 156 removed outlier: 5.427A pdb=" N VAL A 165 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N LEU A 117 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU A 167 " --> pdb=" O HIS A 115 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE A 114 " --> pdb=" O HIS A 183 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 126 through 127 Processing sheet with id=AD7, first strand: chain 'A' and resid 145 through 147 Processing sheet with id=AD8, first strand: chain 'A' and resid 265 through 270 removed outlier: 6.201A pdb=" N PHE A 265 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N PHE A 302 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N PHE A 267 " --> pdb=" O PHE A 302 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N ASP A 304 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE A 269 " --> pdb=" O ASP A 304 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 469 through 470 removed outlier: 3.614A pdb=" N GLU A 470 " --> pdb=" O PHE A 539 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL A 514 " --> pdb=" O GLY A 621 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N THR A 623 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N PHE A 516 " --> pdb=" O THR A 623 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLN A 641 " --> pdb=" O GLY A 513 " (cutoff:3.500A) 1678 hydrogen bonds defined for protein. 4692 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: 7.97 Time building geometry restraints manager: 3.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7205 1.33 - 1.45: 7383 1.45 - 1.57: 20680 1.57 - 1.69: 36 1.69 - 1.81: 300 Bond restraints: 35604 Sorted by residual: bond pdb=" C4 ADP F 901 " pdb=" C5 ADP F 901 " ideal model delta sigma weight residual 1.490 1.378 0.112 2.00e-02 2.50e+03 3.13e+01 bond pdb=" C4 ADP D 901 " pdb=" C5 ADP D 901 " ideal model delta sigma weight residual 1.490 1.378 0.112 2.00e-02 2.50e+03 3.11e+01 bond pdb=" C4 ADP A 901 " pdb=" C5 ADP A 901 " ideal model delta sigma weight residual 1.490 1.379 0.111 2.00e-02 2.50e+03 3.10e+01 bond pdb=" C4 ADP C 901 " pdb=" C5 ADP C 901 " ideal model delta sigma weight residual 1.490 1.379 0.111 2.00e-02 2.50e+03 3.09e+01 bond pdb=" C4 ADP B 901 " pdb=" C5 ADP B 901 " ideal model delta sigma weight residual 1.490 1.379 0.111 2.00e-02 2.50e+03 3.08e+01 ... (remaining 35599 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.47: 47298 2.47 - 4.94: 732 4.94 - 7.41: 72 7.41 - 9.88: 30 9.88 - 12.35: 6 Bond angle restraints: 48138 Sorted by residual: angle pdb=" N ILE C 590 " pdb=" CA ILE C 590 " pdb=" C ILE C 590 " ideal model delta sigma weight residual 111.56 106.66 4.90 8.60e-01 1.35e+00 3.25e+01 angle pdb=" N ILE E 590 " pdb=" CA ILE E 590 " pdb=" C ILE E 590 " ideal model delta sigma weight residual 111.56 106.68 4.88 8.60e-01 1.35e+00 3.22e+01 angle pdb=" N ILE B 590 " pdb=" CA ILE B 590 " pdb=" C ILE B 590 " ideal model delta sigma weight residual 111.56 106.69 4.87 8.60e-01 1.35e+00 3.21e+01 angle pdb=" N ILE D 590 " pdb=" CA ILE D 590 " pdb=" C ILE D 590 " ideal model delta sigma weight residual 111.56 106.70 4.86 8.60e-01 1.35e+00 3.19e+01 angle pdb=" N ILE A 590 " pdb=" CA ILE A 590 " pdb=" C ILE A 590 " ideal model delta sigma weight residual 111.56 106.71 4.85 8.60e-01 1.35e+00 3.18e+01 ... (remaining 48133 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 21767 35.98 - 71.97: 235 71.97 - 107.95: 42 107.95 - 143.93: 18 143.93 - 179.92: 6 Dihedral angle restraints: 22068 sinusoidal: 9258 harmonic: 12810 Sorted by residual: dihedral pdb=" O2A ADP D 901 " pdb=" O3A ADP D 901 " pdb=" PA ADP D 901 " pdb=" PB ADP D 901 " ideal model delta sinusoidal sigma weight residual 300.00 120.09 179.92 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O2A ADP E 901 " pdb=" O3A ADP E 901 " pdb=" PA ADP E 901 " pdb=" PB ADP E 901 " ideal model delta sinusoidal sigma weight residual 300.00 120.09 179.91 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O2A ADP B 901 " pdb=" O3A ADP B 901 " pdb=" PA ADP B 901 " pdb=" PB ADP B 901 " ideal model delta sinusoidal sigma weight residual -60.00 119.74 -179.74 1 2.00e+01 2.50e-03 4.80e+01 ... (remaining 22065 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 3941 0.048 - 0.096: 875 0.096 - 0.144: 468 0.144 - 0.191: 146 0.191 - 0.239: 12 Chirality restraints: 5442 Sorted by residual: chirality pdb=" CA ILE C 590 " pdb=" N ILE C 590 " pdb=" C ILE C 590 " pdb=" CB ILE C 590 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CA ILE E 590 " pdb=" N ILE E 590 " pdb=" C ILE E 590 " pdb=" CB ILE E 590 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA ILE D 590 " pdb=" N ILE D 590 " pdb=" C ILE D 590 " pdb=" CB ILE D 590 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 5439 not shown) Planarity restraints: 6312 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE C 360 " 0.010 2.00e-02 2.50e+03 2.08e-02 4.33e+00 pdb=" C PHE C 360 " -0.036 2.00e-02 2.50e+03 pdb=" O PHE C 360 " 0.013 2.00e-02 2.50e+03 pdb=" N GLY C 361 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE F 360 " -0.010 2.00e-02 2.50e+03 2.07e-02 4.27e+00 pdb=" C PHE F 360 " 0.036 2.00e-02 2.50e+03 pdb=" O PHE F 360 " -0.013 2.00e-02 2.50e+03 pdb=" N GLY F 361 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 360 " 0.010 2.00e-02 2.50e+03 2.06e-02 4.26e+00 pdb=" C PHE B 360 " -0.036 2.00e-02 2.50e+03 pdb=" O PHE B 360 " 0.013 2.00e-02 2.50e+03 pdb=" N GLY B 361 " 0.012 2.00e-02 2.50e+03 ... (remaining 6309 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 13327 2.90 - 3.40: 33996 3.40 - 3.90: 60355 3.90 - 4.40: 67758 4.40 - 4.90: 111683 Nonbonded interactions: 287119 Sorted by model distance: nonbonded pdb=" OE2 GLU C 30 " pdb=" NZ LYS C 217 " model vdw 2.403 3.120 nonbonded pdb=" OE2 GLU B 30 " pdb=" NZ LYS B 217 " model vdw 2.412 3.120 nonbonded pdb=" OE2 GLU D 30 " pdb=" NZ LYS D 217 " model vdw 2.432 3.120 nonbonded pdb=" OE2 GLU A 30 " pdb=" NZ LYS A 217 " model vdw 2.435 3.120 nonbonded pdb=" OE2 GLU E 30 " pdb=" NZ LYS E 217 " model vdw 2.437 3.120 ... (remaining 287114 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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 individual isotropic 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: 4.290 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: 0.030 Extract box with map and model: 0.530 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 29.870 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.070 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:6.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6233 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 0.112 35604 Z= 0.588 Angle : 0.816 12.350 48138 Z= 0.498 Chirality : 0.057 0.239 5442 Planarity : 0.003 0.042 6312 Dihedral : 12.732 179.915 13752 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 0.65 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.20 % Favored : 98.66 % Rotamer: Outliers : 0.11 % Allowed : 0.40 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.12), residues: 4410 helix: -0.26 (0.10), residues: 2052 sheet: 0.28 (0.16), residues: 828 loop : 0.95 (0.16), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 83 TYR 0.013 0.001 TYR D 244 PHE 0.007 0.001 PHE D 575 TRP 0.002 0.000 TRP D 454 HIS 0.001 0.000 HIS B 735 Details of bonding type rmsd covalent geometry : bond 0.01049 (35604) covalent geometry : angle 0.81601 (48138) hydrogen bonds : bond 0.21256 ( 1678) hydrogen bonds : angle 6.45545 ( 4692) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8820 Ramachandran restraints generated. 4410 Oldfield, 0 Emsley, 4410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8820 Ramachandran restraints generated. 4410 Oldfield, 0 Emsley, 4410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 838 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 834 time to evaluate : 1.365 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 outliers start: 4 outliers final: 6 residues processed: 838 average time/residue: 0.8892 time to fit residues: 850.5985 Evaluate side-chains 405 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 399 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 30 GLU Chi-restraints excluded: chain E residue 30 GLU Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain A residue 30 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 432 optimal weight: 0.9980 chunk 197 optimal weight: 0.7980 chunk 388 optimal weight: 10.0000 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 chunk 401 optimal weight: 2.9990 chunk 424 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 406 HIS F 602 ASN ** E 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 406 HIS E 602 ASN ** D 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 340 HIS ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 406 HIS C 602 ASN B 90 ASN ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 HIS ** A 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 602 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.089265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.060944 restraints weight = 100359.717| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 4.26 r_work: 0.2898 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 35604 Z= 0.155 Angle : 0.743 9.763 48138 Z= 0.356 Chirality : 0.046 0.206 5442 Planarity : 0.005 0.052 6312 Dihedral : 11.877 172.134 4956 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 2.61 % Allowed : 11.40 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.60 (0.12), residues: 4410 helix: 1.24 (0.11), residues: 2034 sheet: 0.68 (0.18), residues: 732 loop : 1.30 (0.16), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 322 TYR 0.022 0.002 TYR D 244 PHE 0.009 0.001 PHE E 516 TRP 0.007 0.001 TRP C 551 HIS 0.002 0.001 HIS A 317 Details of bonding type rmsd covalent geometry : bond 0.00346 (35604) covalent geometry : angle 0.74274 (48138) hydrogen bonds : bond 0.05428 ( 1678) hydrogen bonds : angle 4.66528 ( 4692) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8820 Ramachandran restraints generated. 4410 Oldfield, 0 Emsley, 4410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8820 Ramachandran restraints generated. 4410 Oldfield, 0 Emsley, 4410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 459 time to evaluate : 1.063 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: F 239 ARG cc_start: 0.8002 (mtt90) cc_final: 0.7009 (mtt-85) REVERT: F 304 ASP cc_start: 0.8659 (p0) cc_final: 0.7587 (p0) REVERT: F 335 LEU cc_start: 0.9317 (mt) cc_final: 0.9016 (mm) REVERT: F 354 ASP cc_start: 0.9408 (t0) cc_final: 0.9191 (t0) REVERT: F 489 LEU cc_start: 0.9692 (mt) cc_final: 0.9465 (mp) REVERT: F 560 ARG cc_start: 0.9198 (OUTLIER) cc_final: 0.8980 (ttm-80) REVERT: F 561 GLU cc_start: 0.8659 (mp0) cc_final: 0.8415 (mp0) REVERT: F 565 LYS cc_start: 0.9558 (OUTLIER) cc_final: 0.9282 (ttpp) REVERT: E 84 MET cc_start: 0.8876 (ptt) cc_final: 0.8551 (ptt) REVERT: E 427 MET cc_start: 0.8748 (tpp) cc_final: 0.8529 (tpp) REVERT: E 450 ASP cc_start: 0.9538 (m-30) cc_final: 0.9282 (p0) REVERT: E 470 GLU cc_start: 0.9037 (pt0) cc_final: 0.8833 (pm20) REVERT: E 616 ASN cc_start: 0.8671 (t0) cc_final: 0.8090 (p0) REVERT: E 754 LYS cc_start: 0.9570 (mmpt) cc_final: 0.9349 (mmtm) REVERT: D 84 MET cc_start: 0.8863 (ptt) cc_final: 0.8546 (tmm) REVERT: D 124 GLU cc_start: 0.9383 (tt0) cc_final: 0.9115 (mp0) REVERT: D 134 TYR cc_start: 0.9122 (m-80) cc_final: 0.8781 (m-80) REVERT: D 244 TYR cc_start: 0.8883 (p90) cc_final: 0.8518 (p90) REVERT: D 561 GLU cc_start: 0.8852 (mp0) cc_final: 0.8644 (mp0) REVERT: C 64 ARG cc_start: 0.8625 (tpm170) cc_final: 0.8377 (tpm170) REVERT: C 84 MET cc_start: 0.8838 (ptt) cc_final: 0.8622 (ppp) REVERT: C 124 GLU cc_start: 0.9453 (tt0) cc_final: 0.9185 (mp0) REVERT: C 244 TYR cc_start: 0.8899 (p90) cc_final: 0.8635 (p90) REVERT: C 304 ASP cc_start: 0.8702 (p0) cc_final: 0.7615 (p0) REVERT: C 315 LYS cc_start: 0.9408 (mmmt) cc_final: 0.9207 (pttt) REVERT: C 349 ARG cc_start: 0.8773 (mpp80) cc_final: 0.8544 (mpp80) REVERT: C 354 ASP cc_start: 0.9418 (t0) cc_final: 0.9137 (t0) REVERT: C 561 GLU cc_start: 0.8780 (mp0) cc_final: 0.8527 (mp0) REVERT: C 565 LYS cc_start: 0.9562 (OUTLIER) cc_final: 0.9320 (ttpp) REVERT: C 616 ASN cc_start: 0.8549 (t0) cc_final: 0.8083 (p0) REVERT: C 754 LYS cc_start: 0.9581 (mmpt) cc_final: 0.9367 (mmtm) REVERT: B 64 ARG cc_start: 0.8647 (tpm170) cc_final: 0.8434 (tpm170) REVERT: B 84 MET cc_start: 0.8929 (ptt) cc_final: 0.8699 (ppp) REVERT: B 275 MET cc_start: 0.9460 (mmp) cc_final: 0.9243 (mmp) REVERT: B 305 GLU cc_start: 0.9140 (mp0) cc_final: 0.8863 (mp0) REVERT: B 616 ASN cc_start: 0.8636 (t0) cc_final: 0.8062 (p0) REVERT: A 134 TYR cc_start: 0.9116 (m-80) cc_final: 0.8883 (m-80) REVERT: A 305 GLU cc_start: 0.9173 (mp0) cc_final: 0.8645 (mp0) REVERT: A 315 LYS cc_start: 0.9550 (mmmt) cc_final: 0.9154 (ptmt) REVERT: A 349 ARG cc_start: 0.8849 (mpp80) cc_final: 0.8619 (mpp80) REVERT: A 560 ARG cc_start: 0.9216 (OUTLIER) cc_final: 0.8964 (ptm160) REVERT: A 565 LYS cc_start: 0.9578 (OUTLIER) cc_final: 0.9318 (ttpp) REVERT: A 754 LYS cc_start: 0.9514 (mmpt) cc_final: 0.9284 (mmtt) outliers start: 98 outliers final: 16 residues processed: 508 average time/residue: 0.7220 time to fit residues: 429.0094 Evaluate side-chains 380 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 359 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 560 ARG Chi-restraints excluded: chain F residue 565 LYS Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 110 TYR Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 432 LEU Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 110 TYR Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain C residue 565 LYS Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 560 ARG Chi-restraints excluded: chain A residue 565 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 438 optimal weight: 4.9990 chunk 222 optimal weight: 40.0000 chunk 236 optimal weight: 20.0000 chunk 164 optimal weight: 20.0000 chunk 289 optimal weight: 0.9990 chunk 256 optimal weight: 6.9990 chunk 402 optimal weight: 3.9990 chunk 286 optimal weight: 0.7980 chunk 335 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 366 optimal weight: 3.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 421 GLN ** A 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.085606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.056568 restraints weight = 102633.666| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 4.30 r_work: 0.2783 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.3946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 35604 Z= 0.231 Angle : 0.740 10.136 48138 Z= 0.351 Chirality : 0.046 0.218 5442 Planarity : 0.005 0.074 6312 Dihedral : 10.512 169.280 4938 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.93 % Allowed : 12.19 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.71 (0.13), residues: 4410 helix: 1.52 (0.11), residues: 2046 sheet: 0.70 (0.18), residues: 732 loop : 1.07 (0.16), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 322 TYR 0.032 0.002 TYR C 203 PHE 0.015 0.002 PHE C 230 TRP 0.005 0.001 TRP A 476 HIS 0.005 0.001 HIS E 317 Details of bonding type rmsd covalent geometry : bond 0.00518 (35604) covalent geometry : angle 0.74041 (48138) hydrogen bonds : bond 0.04435 ( 1678) hydrogen bonds : angle 4.61667 ( 4692) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8820 Ramachandran restraints generated. 4410 Oldfield, 0 Emsley, 4410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8820 Ramachandran restraints generated. 4410 Oldfield, 0 Emsley, 4410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 361 time to evaluate : 1.608 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: F 84 MET cc_start: 0.8787 (OUTLIER) cc_final: 0.8507 (ppp) REVERT: F 303 ILE cc_start: 0.9108 (mt) cc_final: 0.8899 (mp) REVERT: F 305 GLU cc_start: 0.9127 (mp0) cc_final: 0.8878 (mp0) REVERT: F 354 ASP cc_start: 0.9468 (t0) cc_final: 0.9263 (t0) REVERT: F 488 GLU cc_start: 0.8868 (OUTLIER) cc_final: 0.8590 (mp0) REVERT: F 561 GLU cc_start: 0.8892 (mp0) cc_final: 0.8559 (mp0) REVERT: F 564 ASP cc_start: 0.9537 (t0) cc_final: 0.9290 (t0) REVERT: F 616 ASN cc_start: 0.8822 (t0) cc_final: 0.8520 (t0) REVERT: E 84 MET cc_start: 0.8660 (ptt) cc_final: 0.8398 (ppp) REVERT: E 134 TYR cc_start: 0.9272 (m-80) cc_final: 0.9011 (m-80) REVERT: E 305 GLU cc_start: 0.9207 (mt-10) cc_final: 0.8501 (mp0) REVERT: E 354 ASP cc_start: 0.9530 (t0) cc_final: 0.9235 (t0) REVERT: E 427 MET cc_start: 0.8887 (tpp) cc_final: 0.8650 (tpp) REVERT: E 450 ASP cc_start: 0.9570 (m-30) cc_final: 0.9265 (p0) REVERT: E 546 GLU cc_start: 0.9242 (tt0) cc_final: 0.8760 (tp30) REVERT: E 561 GLU cc_start: 0.8908 (mp0) cc_final: 0.8632 (mp0) REVERT: E 616 ASN cc_start: 0.8879 (t0) cc_final: 0.8515 (t0) REVERT: D 134 TYR cc_start: 0.9317 (m-80) cc_final: 0.8997 (m-80) REVERT: D 244 TYR cc_start: 0.8878 (p90) cc_final: 0.8614 (p90) REVERT: D 354 ASP cc_start: 0.9559 (t0) cc_final: 0.9240 (t0) REVERT: D 560 ARG cc_start: 0.9322 (ptp-110) cc_final: 0.8896 (ptm160) REVERT: D 561 GLU cc_start: 0.8966 (mp0) cc_final: 0.8639 (mp0) REVERT: D 564 ASP cc_start: 0.9521 (t0) cc_final: 0.9319 (t0) REVERT: D 616 ASN cc_start: 0.8909 (t0) cc_final: 0.8585 (t0) REVERT: C 64 ARG cc_start: 0.8625 (tpm170) cc_final: 0.8310 (tpm170) REVERT: C 84 MET cc_start: 0.8828 (ptt) cc_final: 0.8243 (ptt) REVERT: C 124 GLU cc_start: 0.9524 (tt0) cc_final: 0.9227 (mp0) REVERT: C 304 ASP cc_start: 0.9040 (p0) cc_final: 0.8823 (p0) REVERT: C 305 GLU cc_start: 0.9132 (mp0) cc_final: 0.8829 (mp0) REVERT: C 561 GLU cc_start: 0.8934 (mp0) cc_final: 0.8547 (mp0) REVERT: C 565 LYS cc_start: 0.9600 (OUTLIER) cc_final: 0.9329 (ttpp) REVERT: C 616 ASN cc_start: 0.8879 (t0) cc_final: 0.8596 (t0) REVERT: B 64 ARG cc_start: 0.8677 (tpm170) cc_final: 0.8383 (tpm170) REVERT: B 84 MET cc_start: 0.8872 (ptt) cc_final: 0.8579 (ppp) REVERT: B 134 TYR cc_start: 0.9239 (m-80) cc_final: 0.9035 (m-80) REVERT: B 305 GLU cc_start: 0.9062 (mp0) cc_final: 0.8526 (mp0) REVERT: B 354 ASP cc_start: 0.9458 (t0) cc_final: 0.9200 (t0) REVERT: B 450 ASP cc_start: 0.9187 (OUTLIER) cc_final: 0.8785 (p0) REVERT: B 546 GLU cc_start: 0.9251 (tt0) cc_final: 0.8747 (tp30) REVERT: B 561 GLU cc_start: 0.8919 (mp0) cc_final: 0.8646 (mp0) REVERT: B 616 ASN cc_start: 0.8841 (t0) cc_final: 0.8478 (t0) REVERT: A 84 MET cc_start: 0.8845 (OUTLIER) cc_final: 0.8620 (ppp) REVERT: A 134 TYR cc_start: 0.9314 (m-80) cc_final: 0.8963 (m-80) REVERT: A 354 ASP cc_start: 0.9512 (t0) cc_final: 0.9273 (t0) REVERT: A 368 ASP cc_start: 0.9202 (t70) cc_final: 0.9002 (t0) REVERT: A 561 GLU cc_start: 0.8990 (mp0) cc_final: 0.8756 (mp0) REVERT: A 565 LYS cc_start: 0.9597 (OUTLIER) cc_final: 0.9390 (ttpp) REVERT: A 616 ASN cc_start: 0.8911 (t0) cc_final: 0.8686 (t0) outliers start: 110 outliers final: 23 residues processed: 431 average time/residue: 0.6827 time to fit residues: 346.9197 Evaluate side-chains 348 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 319 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 488 GLU Chi-restraints excluded: chain F residue 560 ARG Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 110 TYR Chi-restraints excluded: chain E residue 432 LEU Chi-restraints excluded: chain E residue 560 ARG Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 670 VAL Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 110 TYR Chi-restraints excluded: chain C residue 565 LYS Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 560 ARG Chi-restraints excluded: chain A residue 565 LYS Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 757 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 93 optimal weight: 0.0060 chunk 35 optimal weight: 0.5980 chunk 371 optimal weight: 10.0000 chunk 205 optimal weight: 0.6980 chunk 89 optimal weight: 6.9990 chunk 321 optimal weight: 0.9980 chunk 200 optimal weight: 0.9990 chunk 245 optimal weight: 5.9990 chunk 80 optimal weight: 20.0000 chunk 134 optimal weight: 1.9990 chunk 77 optimal weight: 8.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.086600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.056950 restraints weight = 101840.578| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 4.35 r_work: 0.2817 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.4220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 35604 Z= 0.122 Angle : 0.666 8.840 48138 Z= 0.311 Chirality : 0.045 0.205 5442 Planarity : 0.004 0.048 6312 Dihedral : 9.931 153.705 4938 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.37 % Allowed : 13.29 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.88 (0.13), residues: 4410 helix: 1.75 (0.11), residues: 2022 sheet: 0.78 (0.18), residues: 732 loop : 1.05 (0.16), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 322 TYR 0.020 0.002 TYR E 203 PHE 0.008 0.001 PHE B 516 TRP 0.004 0.000 TRP B 454 HIS 0.003 0.000 HIS D 340 Details of bonding type rmsd covalent geometry : bond 0.00273 (35604) covalent geometry : angle 0.66606 (48138) hydrogen bonds : bond 0.03794 ( 1678) hydrogen bonds : angle 4.30393 ( 4692) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8820 Ramachandran restraints generated. 4410 Oldfield, 0 Emsley, 4410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8820 Ramachandran restraints generated. 4410 Oldfield, 0 Emsley, 4410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 358 time to evaluate : 1.504 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: F 305 GLU cc_start: 0.9038 (mp0) cc_final: 0.8473 (mp0) REVERT: F 354 ASP cc_start: 0.9465 (t0) cc_final: 0.9205 (t0) REVERT: F 488 GLU cc_start: 0.8886 (OUTLIER) cc_final: 0.8593 (mp0) REVERT: F 560 ARG cc_start: 0.9311 (OUTLIER) cc_final: 0.8820 (mtp-110) REVERT: F 561 GLU cc_start: 0.8890 (mp0) cc_final: 0.8545 (mp0) REVERT: F 565 LYS cc_start: 0.9616 (OUTLIER) cc_final: 0.9378 (ttpp) REVERT: F 616 ASN cc_start: 0.8855 (t0) cc_final: 0.8489 (t0) REVERT: E 84 MET cc_start: 0.8755 (ptt) cc_final: 0.8468 (ppp) REVERT: E 134 TYR cc_start: 0.9291 (m-80) cc_final: 0.8999 (m-80) REVERT: E 305 GLU cc_start: 0.9194 (mt-10) cc_final: 0.8564 (mp0) REVERT: E 354 ASP cc_start: 0.9482 (t0) cc_final: 0.9245 (t0) REVERT: E 379 GLU cc_start: 0.9448 (mt-10) cc_final: 0.8867 (mt-10) REVERT: E 432 LEU cc_start: 0.7326 (OUTLIER) cc_final: 0.7016 (pt) REVERT: E 442 MET cc_start: 0.9393 (mpp) cc_final: 0.8920 (pmm) REVERT: E 450 ASP cc_start: 0.9542 (m-30) cc_final: 0.9236 (p0) REVERT: E 546 GLU cc_start: 0.9211 (tt0) cc_final: 0.8732 (tp30) REVERT: E 561 GLU cc_start: 0.8891 (mp0) cc_final: 0.8599 (mp0) REVERT: E 616 ASN cc_start: 0.8900 (t0) cc_final: 0.8561 (t0) REVERT: D 134 TYR cc_start: 0.9316 (m-80) cc_final: 0.9045 (m-80) REVERT: D 305 GLU cc_start: 0.9154 (mt-10) cc_final: 0.8844 (mp0) REVERT: D 354 ASP cc_start: 0.9503 (t0) cc_final: 0.9238 (t0) REVERT: D 442 MET cc_start: 0.9381 (mpp) cc_final: 0.8845 (pmm) REVERT: D 561 GLU cc_start: 0.9015 (mp0) cc_final: 0.8639 (mp0) REVERT: C 64 ARG cc_start: 0.8589 (tpm170) cc_final: 0.8289 (tpm170) REVERT: C 124 GLU cc_start: 0.9512 (tt0) cc_final: 0.9216 (mp0) REVERT: C 305 GLU cc_start: 0.9014 (mp0) cc_final: 0.8479 (mp0) REVERT: C 349 ARG cc_start: 0.8873 (mpp80) cc_final: 0.8635 (mpp80) REVERT: C 354 ASP cc_start: 0.9428 (t0) cc_final: 0.9097 (t0) REVERT: C 379 GLU cc_start: 0.9404 (mt-10) cc_final: 0.8798 (mt-10) REVERT: C 561 GLU cc_start: 0.8976 (mp0) cc_final: 0.8536 (mp0) REVERT: C 565 LYS cc_start: 0.9615 (OUTLIER) cc_final: 0.9375 (ttpp) REVERT: C 616 ASN cc_start: 0.8912 (t0) cc_final: 0.8568 (t0) REVERT: B 64 ARG cc_start: 0.8675 (tpm170) cc_final: 0.8326 (tpm170) REVERT: B 84 MET cc_start: 0.8882 (ptt) cc_final: 0.8596 (ppp) REVERT: B 305 GLU cc_start: 0.9091 (mp0) cc_final: 0.8534 (mp0) REVERT: B 354 ASP cc_start: 0.9519 (t0) cc_final: 0.9273 (t0) REVERT: B 366 GLU cc_start: 0.8580 (mp0) cc_final: 0.8367 (mp0) REVERT: B 450 ASP cc_start: 0.9215 (OUTLIER) cc_final: 0.8833 (p0) REVERT: B 560 ARG cc_start: 0.9306 (ptp-110) cc_final: 0.9075 (ptm160) REVERT: B 561 GLU cc_start: 0.8875 (mp0) cc_final: 0.8571 (mp0) REVERT: B 616 ASN cc_start: 0.8846 (t0) cc_final: 0.8487 (t0) REVERT: A 84 MET cc_start: 0.8578 (OUTLIER) cc_final: 0.8316 (ppp) REVERT: A 134 TYR cc_start: 0.9309 (m-80) cc_final: 0.8992 (m-80) REVERT: A 173 TYR cc_start: 0.7708 (p90) cc_final: 0.7099 (p90) REVERT: A 315 LYS cc_start: 0.9577 (mmpt) cc_final: 0.9162 (mtmt) REVERT: A 354 ASP cc_start: 0.9485 (t0) cc_final: 0.9217 (t0) REVERT: A 442 MET cc_start: 0.9388 (mpp) cc_final: 0.8887 (pmm) REVERT: A 560 ARG cc_start: 0.9243 (OUTLIER) cc_final: 0.8896 (ptm160) REVERT: A 561 GLU cc_start: 0.8976 (mp0) cc_final: 0.8714 (mp0) REVERT: A 565 LYS cc_start: 0.9600 (OUTLIER) cc_final: 0.9395 (ttpp) REVERT: A 616 ASN cc_start: 0.8958 (t0) cc_final: 0.8644 (t0) outliers start: 89 outliers final: 17 residues processed: 413 average time/residue: 0.6882 time to fit residues: 337.0489 Evaluate side-chains 340 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 314 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 462 SER Chi-restraints excluded: chain F residue 488 GLU Chi-restraints excluded: chain F residue 560 ARG Chi-restraints excluded: chain F residue 565 LYS Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 110 TYR Chi-restraints excluded: chain E residue 432 LEU Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 110 TYR Chi-restraints excluded: chain C residue 462 SER Chi-restraints excluded: chain C residue 565 LYS Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 560 ARG Chi-restraints excluded: chain A residue 565 LYS Chi-restraints excluded: chain A residue 757 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 189 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 234 optimal weight: 0.0050 chunk 425 optimal weight: 0.7980 chunk 352 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 381 optimal weight: 0.7980 chunk 7 optimal weight: 7.9990 chunk 90 optimal weight: 9.9990 chunk 414 optimal weight: 5.9990 chunk 235 optimal weight: 0.4980 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 499 HIS ** E 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.086933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.057229 restraints weight = 102247.095| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 4.37 r_work: 0.2827 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.4400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 35604 Z= 0.117 Angle : 0.663 10.020 48138 Z= 0.307 Chirality : 0.044 0.219 5442 Planarity : 0.004 0.048 6312 Dihedral : 9.434 141.985 4938 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.18 % Allowed : 14.27 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.90 (0.13), residues: 4410 helix: 1.78 (0.11), residues: 2034 sheet: 0.83 (0.19), residues: 732 loop : 1.01 (0.16), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG B 349 TYR 0.027 0.002 TYR B 203 PHE 0.008 0.001 PHE F 152 TRP 0.002 0.000 TRP B 454 HIS 0.003 0.000 HIS D 340 Details of bonding type rmsd covalent geometry : bond 0.00264 (35604) covalent geometry : angle 0.66308 (48138) hydrogen bonds : bond 0.03550 ( 1678) hydrogen bonds : angle 4.19117 ( 4692) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8820 Ramachandran restraints generated. 4410 Oldfield, 0 Emsley, 4410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8820 Ramachandran restraints generated. 4410 Oldfield, 0 Emsley, 4410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 342 time to evaluate : 1.452 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: F 305 GLU cc_start: 0.9046 (mp0) cc_final: 0.8450 (mp0) REVERT: F 349 ARG cc_start: 0.8836 (mpp80) cc_final: 0.8553 (mpp80) REVERT: F 354 ASP cc_start: 0.9450 (t0) cc_final: 0.9088 (t70) REVERT: F 488 GLU cc_start: 0.8923 (OUTLIER) cc_final: 0.8644 (mp0) REVERT: F 560 ARG cc_start: 0.9196 (OUTLIER) cc_final: 0.8972 (ttp-110) REVERT: F 561 GLU cc_start: 0.8872 (mp0) cc_final: 0.8546 (mp0) REVERT: F 616 ASN cc_start: 0.8910 (t0) cc_final: 0.8560 (t0) REVERT: E 84 MET cc_start: 0.8766 (ptt) cc_final: 0.8501 (ppp) REVERT: E 134 TYR cc_start: 0.9293 (m-80) cc_final: 0.8999 (m-80) REVERT: E 305 GLU cc_start: 0.9161 (mt-10) cc_final: 0.8582 (mp0) REVERT: E 349 ARG cc_start: 0.8797 (mpp80) cc_final: 0.8512 (mpp80) REVERT: E 354 ASP cc_start: 0.9476 (t0) cc_final: 0.9258 (t0) REVERT: E 432 LEU cc_start: 0.7250 (OUTLIER) cc_final: 0.7040 (pt) REVERT: E 442 MET cc_start: 0.9413 (mpp) cc_final: 0.8846 (pmm) REVERT: E 450 ASP cc_start: 0.9532 (m-30) cc_final: 0.9220 (p0) REVERT: E 546 GLU cc_start: 0.9192 (tt0) cc_final: 0.8757 (tp30) REVERT: E 561 GLU cc_start: 0.8948 (mp0) cc_final: 0.8635 (mp0) REVERT: E 616 ASN cc_start: 0.8904 (t0) cc_final: 0.8580 (t0) REVERT: D 134 TYR cc_start: 0.9333 (m-80) cc_final: 0.9032 (m-80) REVERT: D 305 GLU cc_start: 0.9178 (mt-10) cc_final: 0.8502 (mp0) REVERT: D 354 ASP cc_start: 0.9453 (t0) cc_final: 0.9139 (t70) REVERT: D 442 MET cc_start: 0.9415 (mpp) cc_final: 0.8677 (pmm) REVERT: D 561 GLU cc_start: 0.9012 (mp0) cc_final: 0.8636 (mp0) REVERT: C 64 ARG cc_start: 0.8588 (tpm170) cc_final: 0.8238 (tpm170) REVERT: C 124 GLU cc_start: 0.9507 (tt0) cc_final: 0.9211 (mp0) REVERT: C 305 GLU cc_start: 0.9050 (mp0) cc_final: 0.8463 (mp0) REVERT: C 379 GLU cc_start: 0.9448 (mt-10) cc_final: 0.8832 (mt-10) REVERT: C 561 GLU cc_start: 0.9020 (mp0) cc_final: 0.8596 (mp0) REVERT: C 564 ASP cc_start: 0.9438 (OUTLIER) cc_final: 0.9218 (m-30) REVERT: C 565 LYS cc_start: 0.9619 (OUTLIER) cc_final: 0.9377 (ttpp) REVERT: B 64 ARG cc_start: 0.8670 (tpm170) cc_final: 0.8307 (tpm170) REVERT: B 84 MET cc_start: 0.8862 (ptt) cc_final: 0.8658 (ppp) REVERT: B 305 GLU cc_start: 0.9097 (mp0) cc_final: 0.8575 (mp0) REVERT: B 354 ASP cc_start: 0.9499 (t0) cc_final: 0.9254 (t0) REVERT: B 366 GLU cc_start: 0.8552 (mp0) cc_final: 0.8331 (mp0) REVERT: B 432 LEU cc_start: 0.7356 (OUTLIER) cc_final: 0.7081 (pt) REVERT: B 450 ASP cc_start: 0.9181 (OUTLIER) cc_final: 0.8787 (p0) REVERT: B 488 GLU cc_start: 0.9050 (OUTLIER) cc_final: 0.8820 (mp0) REVERT: B 546 GLU cc_start: 0.9219 (tt0) cc_final: 0.8769 (tp30) REVERT: B 560 ARG cc_start: 0.9308 (ptp-110) cc_final: 0.9034 (ptm160) REVERT: B 561 GLU cc_start: 0.8937 (mp0) cc_final: 0.8588 (mp0) REVERT: B 616 ASN cc_start: 0.8861 (t0) cc_final: 0.8520 (t0) REVERT: A 84 MET cc_start: 0.8656 (OUTLIER) cc_final: 0.8392 (ppp) REVERT: A 134 TYR cc_start: 0.9326 (m-80) cc_final: 0.9018 (m-80) REVERT: A 143 TYR cc_start: 0.8695 (m-80) cc_final: 0.8402 (m-80) REVERT: A 173 TYR cc_start: 0.7702 (p90) cc_final: 0.7153 (p90) REVERT: A 354 ASP cc_start: 0.9465 (t0) cc_final: 0.9173 (t0) REVERT: A 442 MET cc_start: 0.9411 (mpp) cc_final: 0.8709 (pmm) REVERT: A 560 ARG cc_start: 0.9195 (OUTLIER) cc_final: 0.8885 (ptm160) REVERT: A 561 GLU cc_start: 0.8976 (mp0) cc_final: 0.8707 (mp0) outliers start: 82 outliers final: 23 residues processed: 385 average time/residue: 0.6769 time to fit residues: 309.6349 Evaluate side-chains 348 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 315 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 244 TYR Chi-restraints excluded: chain F residue 462 SER Chi-restraints excluded: chain F residue 488 GLU Chi-restraints excluded: chain F residue 560 ARG Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 110 TYR Chi-restraints excluded: chain E residue 244 TYR Chi-restraints excluded: chain E residue 432 LEU Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 110 TYR Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 110 TYR Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 462 SER Chi-restraints excluded: chain C residue 488 GLU Chi-restraints excluded: chain C residue 564 ASP Chi-restraints excluded: chain C residue 565 LYS Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 560 ARG Chi-restraints excluded: chain A residue 757 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 404 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 205 optimal weight: 0.9990 chunk 83 optimal weight: 7.9990 chunk 193 optimal weight: 5.9990 chunk 170 optimal weight: 0.3980 chunk 419 optimal weight: 6.9990 chunk 408 optimal weight: 6.9990 chunk 157 optimal weight: 8.9990 chunk 38 optimal weight: 0.1980 chunk 410 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 421 GLN ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 421 GLN ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 ASN ** 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 = 0.3674 r_free = 0.3674 target = 0.086285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.056339 restraints weight = 102647.014| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 4.43 r_work: 0.2808 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.4559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 35604 Z= 0.135 Angle : 0.673 10.499 48138 Z= 0.311 Chirality : 0.044 0.216 5442 Planarity : 0.004 0.049 6312 Dihedral : 9.008 127.896 4938 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.16 % Allowed : 15.15 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.97 (0.13), residues: 4410 helix: 1.87 (0.11), residues: 2034 sheet: 0.88 (0.19), residues: 732 loop : 0.97 (0.16), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 349 TYR 0.014 0.002 TYR E 143 PHE 0.008 0.001 PHE E 152 TRP 0.003 0.001 TRP D 476 HIS 0.002 0.000 HIS D 340 Details of bonding type rmsd covalent geometry : bond 0.00309 (35604) covalent geometry : angle 0.67298 (48138) hydrogen bonds : bond 0.03489 ( 1678) hydrogen bonds : angle 4.14424 ( 4692) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8820 Ramachandran restraints generated. 4410 Oldfield, 0 Emsley, 4410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8820 Ramachandran restraints generated. 4410 Oldfield, 0 Emsley, 4410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 323 time to evaluate : 1.069 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: F 84 MET cc_start: 0.8325 (OUTLIER) cc_final: 0.8028 (ppp) REVERT: F 305 GLU cc_start: 0.9067 (mp0) cc_final: 0.8622 (mp0) REVERT: F 349 ARG cc_start: 0.8900 (mpp80) cc_final: 0.8631 (mpp80) REVERT: F 354 ASP cc_start: 0.9453 (t0) cc_final: 0.9077 (t70) REVERT: F 432 LEU cc_start: 0.7053 (OUTLIER) cc_final: 0.6799 (pt) REVERT: F 488 GLU cc_start: 0.8941 (OUTLIER) cc_final: 0.8636 (mp0) REVERT: F 561 GLU cc_start: 0.8977 (mp0) cc_final: 0.8561 (mp0) REVERT: F 565 LYS cc_start: 0.9611 (OUTLIER) cc_final: 0.9398 (ttpp) REVERT: F 616 ASN cc_start: 0.8954 (t0) cc_final: 0.8653 (t0) REVERT: E 84 MET cc_start: 0.8785 (ptt) cc_final: 0.8527 (ppp) REVERT: E 134 TYR cc_start: 0.9281 (m-80) cc_final: 0.8994 (m-80) REVERT: E 305 GLU cc_start: 0.9158 (mt-10) cc_final: 0.8591 (mp0) REVERT: E 349 ARG cc_start: 0.8838 (mpp80) cc_final: 0.8534 (mpp80) REVERT: E 354 ASP cc_start: 0.9477 (t0) cc_final: 0.9259 (t0) REVERT: E 379 GLU cc_start: 0.9483 (mt-10) cc_final: 0.8903 (mt-10) REVERT: E 442 MET cc_start: 0.9443 (mpp) cc_final: 0.8824 (pmm) REVERT: E 450 ASP cc_start: 0.9534 (m-30) cc_final: 0.9206 (p0) REVERT: E 546 GLU cc_start: 0.9196 (tt0) cc_final: 0.8750 (tp30) REVERT: E 561 GLU cc_start: 0.8941 (mp0) cc_final: 0.8579 (mp0) REVERT: E 616 ASN cc_start: 0.8924 (t0) cc_final: 0.8608 (t0) REVERT: D 46 MET cc_start: 0.9267 (OUTLIER) cc_final: 0.9023 (tmt) REVERT: D 134 TYR cc_start: 0.9334 (m-80) cc_final: 0.9030 (m-80) REVERT: D 305 GLU cc_start: 0.9198 (mt-10) cc_final: 0.8590 (mp0) REVERT: D 315 LYS cc_start: 0.9156 (pttt) cc_final: 0.8905 (mmpt) REVERT: D 354 ASP cc_start: 0.9451 (t0) cc_final: 0.9104 (t70) REVERT: D 442 MET cc_start: 0.9426 (mpp) cc_final: 0.8793 (pmm) REVERT: D 561 GLU cc_start: 0.9025 (mp0) cc_final: 0.8623 (mp0) REVERT: C 64 ARG cc_start: 0.8626 (tpm170) cc_final: 0.8133 (tpm170) REVERT: C 84 MET cc_start: 0.8771 (OUTLIER) cc_final: 0.8427 (ppp) REVERT: C 124 GLU cc_start: 0.9508 (tt0) cc_final: 0.9156 (mp0) REVERT: C 305 GLU cc_start: 0.9056 (mp0) cc_final: 0.8434 (mp0) REVERT: C 379 GLU cc_start: 0.9458 (mt-10) cc_final: 0.8888 (mt-10) REVERT: C 432 LEU cc_start: 0.7243 (OUTLIER) cc_final: 0.7016 (pt) REVERT: C 561 GLU cc_start: 0.9022 (mp0) cc_final: 0.8582 (mp0) REVERT: C 564 ASP cc_start: 0.9437 (OUTLIER) cc_final: 0.9209 (m-30) REVERT: C 565 LYS cc_start: 0.9628 (OUTLIER) cc_final: 0.9402 (ttpp) REVERT: C 616 ASN cc_start: 0.8998 (t0) cc_final: 0.8685 (t0) REVERT: B 64 ARG cc_start: 0.8695 (tpm170) cc_final: 0.8331 (tpm170) REVERT: B 84 MET cc_start: 0.8853 (ptt) cc_final: 0.8323 (ptt) REVERT: B 305 GLU cc_start: 0.9080 (mp0) cc_final: 0.8504 (mp0) REVERT: B 354 ASP cc_start: 0.9518 (t0) cc_final: 0.9308 (t0) REVERT: B 365 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7412 (mtt90) REVERT: B 366 GLU cc_start: 0.8561 (mp0) cc_final: 0.8270 (mp0) REVERT: B 450 ASP cc_start: 0.9159 (OUTLIER) cc_final: 0.8719 (p0) REVERT: B 546 GLU cc_start: 0.9221 (tt0) cc_final: 0.8782 (tp30) REVERT: B 561 GLU cc_start: 0.8944 (mp0) cc_final: 0.8571 (mp0) REVERT: B 616 ASN cc_start: 0.8908 (t0) cc_final: 0.8566 (t0) REVERT: A 84 MET cc_start: 0.8683 (OUTLIER) cc_final: 0.8429 (ppp) REVERT: A 134 TYR cc_start: 0.9334 (m-80) cc_final: 0.9077 (m-80) REVERT: A 143 TYR cc_start: 0.8659 (m-80) cc_final: 0.8392 (m-80) REVERT: A 173 TYR cc_start: 0.7764 (p90) cc_final: 0.7171 (p90) REVERT: A 315 LYS cc_start: 0.9409 (mmpt) cc_final: 0.9143 (mtmt) REVERT: A 354 ASP cc_start: 0.9485 (t0) cc_final: 0.9164 (t70) REVERT: A 560 ARG cc_start: 0.9206 (OUTLIER) cc_final: 0.8797 (ptm160) REVERT: A 561 GLU cc_start: 0.9003 (mp0) cc_final: 0.8685 (mp0) REVERT: A 564 ASP cc_start: 0.9452 (m-30) cc_final: 0.9219 (m-30) REVERT: A 616 ASN cc_start: 0.9021 (t0) cc_final: 0.8725 (t0) outliers start: 81 outliers final: 23 residues processed: 371 average time/residue: 0.6927 time to fit residues: 303.5463 Evaluate side-chains 337 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 301 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 244 TYR Chi-restraints excluded: chain F residue 432 LEU Chi-restraints excluded: chain F residue 488 GLU Chi-restraints excluded: chain F residue 565 LYS Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 244 TYR Chi-restraints excluded: chain E residue 459 SER Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 488 GLU Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 110 TYR Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 110 TYR Chi-restraints excluded: chain C residue 244 TYR Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain C residue 488 GLU Chi-restraints excluded: chain C residue 564 ASP Chi-restraints excluded: chain C residue 565 LYS Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 365 ARG Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 560 ARG Chi-restraints excluded: chain A residue 757 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 247 optimal weight: 4.9990 chunk 330 optimal weight: 1.9990 chunk 305 optimal weight: 5.9990 chunk 99 optimal weight: 0.9980 chunk 126 optimal weight: 1.9990 chunk 443 optimal weight: 0.9980 chunk 139 optimal weight: 0.1980 chunk 219 optimal weight: 5.9990 chunk 12 optimal weight: 9.9990 chunk 356 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 421 GLN ** E 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.086131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.056509 restraints weight = 102754.801| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 4.35 r_work: 0.2809 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.4705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 35604 Z= 0.132 Angle : 0.683 11.050 48138 Z= 0.314 Chirality : 0.045 0.225 5442 Planarity : 0.004 0.050 6312 Dihedral : 8.525 114.219 4938 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.78 % Allowed : 16.00 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.98 (0.13), residues: 4410 helix: 1.88 (0.11), residues: 2034 sheet: 0.93 (0.19), residues: 732 loop : 0.95 (0.16), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 560 TYR 0.026 0.002 TYR B 203 PHE 0.012 0.001 PHE A 52 TRP 0.005 0.001 TRP C 454 HIS 0.003 0.000 HIS D 340 Details of bonding type rmsd covalent geometry : bond 0.00301 (35604) covalent geometry : angle 0.68275 (48138) hydrogen bonds : bond 0.03431 ( 1678) hydrogen bonds : angle 4.11455 ( 4692) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8820 Ramachandran restraints generated. 4410 Oldfield, 0 Emsley, 4410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8820 Ramachandran restraints generated. 4410 Oldfield, 0 Emsley, 4410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 325 time to evaluate : 1.047 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: F 64 ARG cc_start: 0.8840 (ptp90) cc_final: 0.8616 (mtm-85) REVERT: F 84 MET cc_start: 0.8372 (OUTLIER) cc_final: 0.8102 (ppp) REVERT: F 305 GLU cc_start: 0.9065 (mp0) cc_final: 0.8609 (mp0) REVERT: F 349 ARG cc_start: 0.8859 (mpp80) cc_final: 0.8654 (mpp80) REVERT: F 354 ASP cc_start: 0.9449 (t0) cc_final: 0.9069 (t70) REVERT: F 432 LEU cc_start: 0.6999 (OUTLIER) cc_final: 0.6707 (pt) REVERT: F 488 GLU cc_start: 0.8936 (OUTLIER) cc_final: 0.8623 (mp0) REVERT: F 561 GLU cc_start: 0.9059 (mp0) cc_final: 0.8649 (mp0) REVERT: F 565 LYS cc_start: 0.9609 (OUTLIER) cc_final: 0.9395 (ttpp) REVERT: F 616 ASN cc_start: 0.8952 (t0) cc_final: 0.8651 (t0) REVERT: E 84 MET cc_start: 0.8782 (ptt) cc_final: 0.8531 (ppp) REVERT: E 134 TYR cc_start: 0.9284 (m-80) cc_final: 0.8983 (m-80) REVERT: E 305 GLU cc_start: 0.9213 (mt-10) cc_final: 0.8564 (mp0) REVERT: E 349 ARG cc_start: 0.8882 (mpp80) cc_final: 0.8553 (mpp80) REVERT: E 354 ASP cc_start: 0.9479 (t0) cc_final: 0.9264 (t0) REVERT: E 379 GLU cc_start: 0.9495 (mt-10) cc_final: 0.8910 (mt-10) REVERT: E 442 MET cc_start: 0.9472 (mpp) cc_final: 0.8862 (pmm) REVERT: E 546 GLU cc_start: 0.9172 (tt0) cc_final: 0.8745 (tp30) REVERT: E 561 GLU cc_start: 0.8976 (mp0) cc_final: 0.8599 (mp0) REVERT: E 616 ASN cc_start: 0.8958 (t0) cc_final: 0.8642 (t0) REVERT: D 46 MET cc_start: 0.9261 (OUTLIER) cc_final: 0.9044 (tmt) REVERT: D 134 TYR cc_start: 0.9337 (m-80) cc_final: 0.9025 (m-80) REVERT: D 305 GLU cc_start: 0.9214 (mt-10) cc_final: 0.8528 (mp0) REVERT: D 354 ASP cc_start: 0.9416 (t0) cc_final: 0.8979 (t70) REVERT: D 546 GLU cc_start: 0.9206 (tt0) cc_final: 0.8736 (tp30) REVERT: D 561 GLU cc_start: 0.9041 (mp0) cc_final: 0.8622 (mp0) REVERT: C 64 ARG cc_start: 0.8634 (tpm170) cc_final: 0.8121 (tpm170) REVERT: C 84 MET cc_start: 0.8831 (tmm) cc_final: 0.8574 (ppp) REVERT: C 124 GLU cc_start: 0.9510 (tt0) cc_final: 0.9182 (mp0) REVERT: C 217 LYS cc_start: 0.9664 (mtmt) cc_final: 0.9357 (mtmm) REVERT: C 305 GLU cc_start: 0.9098 (mp0) cc_final: 0.8422 (mp0) REVERT: C 379 GLU cc_start: 0.9471 (mt-10) cc_final: 0.8894 (mt-10) REVERT: C 432 LEU cc_start: 0.7211 (OUTLIER) cc_final: 0.6978 (pt) REVERT: C 560 ARG cc_start: 0.9322 (ptp-110) cc_final: 0.8787 (ttm110) REVERT: C 561 GLU cc_start: 0.9036 (mp0) cc_final: 0.8688 (mp0) REVERT: C 564 ASP cc_start: 0.9427 (OUTLIER) cc_final: 0.9203 (m-30) REVERT: C 565 LYS cc_start: 0.9639 (OUTLIER) cc_final: 0.9400 (ttpp) REVERT: C 616 ASN cc_start: 0.8996 (t0) cc_final: 0.8694 (t0) REVERT: B 46 MET cc_start: 0.8926 (ppp) cc_final: 0.8282 (ppp) REVERT: B 64 ARG cc_start: 0.8699 (tpm170) cc_final: 0.8297 (tpm170) REVERT: B 84 MET cc_start: 0.8838 (ptt) cc_final: 0.8339 (ptt) REVERT: B 253 LEU cc_start: 0.9495 (tp) cc_final: 0.9275 (tp) REVERT: B 305 GLU cc_start: 0.9084 (mp0) cc_final: 0.8516 (mp0) REVERT: B 354 ASP cc_start: 0.9515 (t0) cc_final: 0.9301 (t0) REVERT: B 365 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.7487 (mmm-85) REVERT: B 366 GLU cc_start: 0.8555 (mp0) cc_final: 0.8312 (mp0) REVERT: B 450 ASP cc_start: 0.9166 (OUTLIER) cc_final: 0.8727 (p0) REVERT: B 546 GLU cc_start: 0.9211 (tt0) cc_final: 0.8788 (tp30) REVERT: B 561 GLU cc_start: 0.8972 (mp0) cc_final: 0.8610 (mp0) REVERT: B 616 ASN cc_start: 0.8924 (t0) cc_final: 0.8574 (t0) REVERT: A 46 MET cc_start: 0.9274 (tpp) cc_final: 0.9065 (tmm) REVERT: A 84 MET cc_start: 0.8658 (OUTLIER) cc_final: 0.8429 (ppp) REVERT: A 134 TYR cc_start: 0.9319 (m-80) cc_final: 0.8982 (m-80) REVERT: A 173 TYR cc_start: 0.7777 (p90) cc_final: 0.7155 (p90) REVERT: A 354 ASP cc_start: 0.9450 (t0) cc_final: 0.9122 (t70) REVERT: A 365 ARG cc_start: 0.8263 (OUTLIER) cc_final: 0.7361 (mmm-85) REVERT: A 442 MET cc_start: 0.9440 (mpp) cc_final: 0.8819 (pmm) REVERT: A 546 GLU cc_start: 0.9201 (tt0) cc_final: 0.8741 (tp30) REVERT: A 560 ARG cc_start: 0.9189 (OUTLIER) cc_final: 0.8774 (ptm160) REVERT: A 561 GLU cc_start: 0.9013 (mp0) cc_final: 0.8703 (mp0) REVERT: A 564 ASP cc_start: 0.9454 (m-30) cc_final: 0.9200 (m-30) REVERT: A 616 ASN cc_start: 0.9026 (t0) cc_final: 0.8724 (t0) outliers start: 67 outliers final: 27 residues processed: 368 average time/residue: 0.6917 time to fit residues: 301.0456 Evaluate side-chains 338 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 298 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 30 GLU Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 244 TYR Chi-restraints excluded: chain F residue 432 LEU Chi-restraints excluded: chain F residue 488 GLU Chi-restraints excluded: chain F residue 565 LYS Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 244 TYR Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 488 GLU Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 110 TYR Chi-restraints excluded: chain D residue 359 ARG Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 244 TYR Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 488 GLU Chi-restraints excluded: chain C residue 564 ASP Chi-restraints excluded: chain C residue 565 LYS Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 244 TYR Chi-restraints excluded: chain B residue 365 ARG Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 244 TYR Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 560 ARG Chi-restraints excluded: chain A residue 757 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 351 optimal weight: 4.9990 chunk 126 optimal weight: 0.8980 chunk 309 optimal weight: 7.9990 chunk 189 optimal weight: 0.9990 chunk 315 optimal weight: 1.9990 chunk 441 optimal weight: 0.9990 chunk 182 optimal weight: 10.0000 chunk 96 optimal weight: 0.7980 chunk 331 optimal weight: 3.9990 chunk 431 optimal weight: 0.8980 chunk 17 optimal weight: 0.0770 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 603 GLN ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.086509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.056822 restraints weight = 102161.576| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 4.42 r_work: 0.2825 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.4820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 35604 Z= 0.118 Angle : 0.694 12.334 48138 Z= 0.317 Chirality : 0.045 0.230 5442 Planarity : 0.004 0.069 6312 Dihedral : 8.128 111.854 4938 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.70 % Allowed : 16.37 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.01 (0.13), residues: 4410 helix: 1.89 (0.11), residues: 2034 sheet: 0.96 (0.19), residues: 732 loop : 0.99 (0.16), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG B 349 TYR 0.016 0.001 TYR C 143 PHE 0.008 0.001 PHE D 758 TRP 0.005 0.001 TRP F 454 HIS 0.003 0.000 HIS D 340 Details of bonding type rmsd covalent geometry : bond 0.00269 (35604) covalent geometry : angle 0.69412 (48138) hydrogen bonds : bond 0.03320 ( 1678) hydrogen bonds : angle 4.04594 ( 4692) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8820 Ramachandran restraints generated. 4410 Oldfield, 0 Emsley, 4410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8820 Ramachandran restraints generated. 4410 Oldfield, 0 Emsley, 4410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 330 time to evaluate : 1.540 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: F 173 TYR cc_start: 0.7577 (p90) cc_final: 0.7024 (p90) REVERT: F 217 LYS cc_start: 0.9649 (mtmt) cc_final: 0.9317 (mtmm) REVERT: F 305 GLU cc_start: 0.9069 (mp0) cc_final: 0.8603 (mp0) REVERT: F 349 ARG cc_start: 0.8895 (mpp80) cc_final: 0.8676 (mpp80) REVERT: F 354 ASP cc_start: 0.9439 (t0) cc_final: 0.9060 (t70) REVERT: F 432 LEU cc_start: 0.6955 (OUTLIER) cc_final: 0.6664 (pt) REVERT: F 488 GLU cc_start: 0.8943 (OUTLIER) cc_final: 0.8658 (mp0) REVERT: F 561 GLU cc_start: 0.9134 (mp0) cc_final: 0.8698 (mp0) REVERT: F 565 LYS cc_start: 0.9607 (OUTLIER) cc_final: 0.9401 (ttpp) REVERT: F 616 ASN cc_start: 0.8953 (t0) cc_final: 0.8660 (t0) REVERT: F 700 ARG cc_start: 0.9336 (OUTLIER) cc_final: 0.9009 (ttp80) REVERT: E 84 MET cc_start: 0.8778 (ptt) cc_final: 0.8527 (ppp) REVERT: E 134 TYR cc_start: 0.9306 (m-80) cc_final: 0.9009 (m-80) REVERT: E 305 GLU cc_start: 0.9218 (mt-10) cc_final: 0.8581 (mp0) REVERT: E 349 ARG cc_start: 0.8892 (mpp80) cc_final: 0.8538 (mpp80) REVERT: E 354 ASP cc_start: 0.9473 (t0) cc_final: 0.9241 (t0) REVERT: E 379 GLU cc_start: 0.9493 (mt-10) cc_final: 0.8931 (mt-10) REVERT: E 442 MET cc_start: 0.9468 (mpp) cc_final: 0.8836 (pmm) REVERT: E 546 GLU cc_start: 0.9163 (tt0) cc_final: 0.8752 (tp30) REVERT: E 560 ARG cc_start: 0.9283 (ptp-110) cc_final: 0.9081 (ptm160) REVERT: E 561 GLU cc_start: 0.8980 (mp0) cc_final: 0.8589 (mp0) REVERT: E 616 ASN cc_start: 0.8964 (t0) cc_final: 0.8650 (t0) REVERT: D 46 MET cc_start: 0.9276 (OUTLIER) cc_final: 0.9073 (tmt) REVERT: D 134 TYR cc_start: 0.9337 (m-80) cc_final: 0.8989 (m-80) REVERT: D 217 LYS cc_start: 0.9684 (mtmt) cc_final: 0.9421 (mtmp) REVERT: D 305 GLU cc_start: 0.9226 (mt-10) cc_final: 0.8539 (mp0) REVERT: D 354 ASP cc_start: 0.9432 (t0) cc_final: 0.9035 (t70) REVERT: D 442 MET cc_start: 0.9424 (mpp) cc_final: 0.8739 (pmm) REVERT: D 546 GLU cc_start: 0.9176 (tt0) cc_final: 0.8726 (tp30) REVERT: D 561 GLU cc_start: 0.9031 (mp0) cc_final: 0.8597 (mp0) REVERT: C 64 ARG cc_start: 0.8643 (tpm170) cc_final: 0.8115 (tpm170) REVERT: C 84 MET cc_start: 0.8885 (tmm) cc_final: 0.8544 (ppp) REVERT: C 124 GLU cc_start: 0.9514 (tt0) cc_final: 0.9191 (mp0) REVERT: C 217 LYS cc_start: 0.9664 (mtmt) cc_final: 0.9316 (mtmm) REVERT: C 221 GLU cc_start: 0.9281 (OUTLIER) cc_final: 0.8752 (pm20) REVERT: C 305 GLU cc_start: 0.9111 (mp0) cc_final: 0.8708 (mp0) REVERT: C 379 GLU cc_start: 0.9465 (mt-10) cc_final: 0.8872 (mt-10) REVERT: C 432 LEU cc_start: 0.7199 (OUTLIER) cc_final: 0.6908 (pt) REVERT: C 546 GLU cc_start: 0.9214 (tt0) cc_final: 0.8812 (tp30) REVERT: C 560 ARG cc_start: 0.9325 (ptp-110) cc_final: 0.8767 (ttm110) REVERT: C 561 GLU cc_start: 0.9054 (mp0) cc_final: 0.8720 (mp0) REVERT: C 564 ASP cc_start: 0.9445 (OUTLIER) cc_final: 0.9228 (m-30) REVERT: C 565 LYS cc_start: 0.9637 (OUTLIER) cc_final: 0.9403 (ttpp) REVERT: C 616 ASN cc_start: 0.8978 (t0) cc_final: 0.8672 (t0) REVERT: C 700 ARG cc_start: 0.9321 (OUTLIER) cc_final: 0.8980 (ttp80) REVERT: B 32 ILE cc_start: 0.8825 (OUTLIER) cc_final: 0.8522 (mp) REVERT: B 46 MET cc_start: 0.8962 (ppp) cc_final: 0.8344 (ppp) REVERT: B 64 ARG cc_start: 0.8663 (tpm170) cc_final: 0.8235 (tpm170) REVERT: B 84 MET cc_start: 0.8838 (ptt) cc_final: 0.8326 (ptt) REVERT: B 253 LEU cc_start: 0.9468 (tp) cc_final: 0.9268 (tp) REVERT: B 305 GLU cc_start: 0.9071 (mp0) cc_final: 0.8501 (mp0) REVERT: B 354 ASP cc_start: 0.9520 (t0) cc_final: 0.9306 (t0) REVERT: B 450 ASP cc_start: 0.9143 (OUTLIER) cc_final: 0.8707 (p0) REVERT: B 546 GLU cc_start: 0.9212 (tt0) cc_final: 0.8803 (tp30) REVERT: B 561 GLU cc_start: 0.9001 (mp0) cc_final: 0.8613 (mp0) REVERT: B 616 ASN cc_start: 0.8943 (t0) cc_final: 0.8601 (t0) REVERT: A 84 MET cc_start: 0.8650 (OUTLIER) cc_final: 0.8439 (ppp) REVERT: A 134 TYR cc_start: 0.9329 (m-80) cc_final: 0.9040 (m-80) REVERT: A 173 TYR cc_start: 0.7789 (p90) cc_final: 0.7234 (p90) REVERT: A 315 LYS cc_start: 0.9451 (mmpt) cc_final: 0.9121 (mtmm) REVERT: A 354 ASP cc_start: 0.9468 (t0) cc_final: 0.9126 (t70) REVERT: A 442 MET cc_start: 0.9428 (mpp) cc_final: 0.8820 (pmm) REVERT: A 488 GLU cc_start: 0.8906 (OUTLIER) cc_final: 0.8661 (mm-30) REVERT: A 546 GLU cc_start: 0.9185 (tt0) cc_final: 0.8744 (tp30) REVERT: A 560 ARG cc_start: 0.9202 (OUTLIER) cc_final: 0.8754 (ptm160) REVERT: A 561 GLU cc_start: 0.9023 (mp0) cc_final: 0.8683 (mp0) REVERT: A 564 ASP cc_start: 0.9448 (m-30) cc_final: 0.9163 (m-30) outliers start: 64 outliers final: 28 residues processed: 370 average time/residue: 0.6885 time to fit residues: 300.5217 Evaluate side-chains 353 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 310 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 244 TYR Chi-restraints excluded: chain F residue 432 LEU Chi-restraints excluded: chain F residue 488 GLU Chi-restraints excluded: chain F residue 565 LYS Chi-restraints excluded: chain F residue 700 ARG Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 244 TYR Chi-restraints excluded: chain E residue 459 SER Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 488 GLU Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 110 TYR Chi-restraints excluded: chain D residue 244 TYR Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain C residue 244 TYR Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain C residue 488 GLU Chi-restraints excluded: chain C residue 564 ASP Chi-restraints excluded: chain C residue 565 LYS Chi-restraints excluded: chain C residue 700 ARG Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 244 TYR Chi-restraints excluded: chain B residue 359 ARG Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 488 GLU Chi-restraints excluded: chain A residue 560 ARG Chi-restraints excluded: chain A residue 757 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 286 optimal weight: 0.7980 chunk 364 optimal weight: 5.9990 chunk 384 optimal weight: 5.9990 chunk 142 optimal weight: 0.9980 chunk 190 optimal weight: 5.9990 chunk 42 optimal weight: 7.9990 chunk 219 optimal weight: 1.9990 chunk 334 optimal weight: 0.5980 chunk 256 optimal weight: 0.0170 chunk 146 optimal weight: 3.9990 chunk 235 optimal weight: 0.9990 overall best weight: 0.6820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 603 GLN ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 43 GLN ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 ASN ** 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 = 0.3690 r_free = 0.3690 target = 0.087938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.058702 restraints weight = 101691.355| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 4.40 r_work: 0.2834 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.4928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 35604 Z= 0.118 Angle : 0.717 15.123 48138 Z= 0.325 Chirality : 0.045 0.233 5442 Planarity : 0.004 0.062 6312 Dihedral : 7.853 111.065 4938 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.52 % Allowed : 16.75 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.02 (0.13), residues: 4410 helix: 1.93 (0.11), residues: 2016 sheet: 0.93 (0.19), residues: 726 loop : 0.98 (0.16), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 349 TYR 0.019 0.001 TYR B 203 PHE 0.011 0.001 PHE D 758 TRP 0.004 0.001 TRP F 454 HIS 0.004 0.000 HIS D 226 Details of bonding type rmsd covalent geometry : bond 0.00272 (35604) covalent geometry : angle 0.71692 (48138) hydrogen bonds : bond 0.03280 ( 1678) hydrogen bonds : angle 4.02942 ( 4692) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8820 Ramachandran restraints generated. 4410 Oldfield, 0 Emsley, 4410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8820 Ramachandran restraints generated. 4410 Oldfield, 0 Emsley, 4410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 326 time to evaluate : 1.047 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: F 305 GLU cc_start: 0.9067 (mp0) cc_final: 0.8605 (mp0) REVERT: F 349 ARG cc_start: 0.8891 (mpp80) cc_final: 0.8666 (mpp80) REVERT: F 354 ASP cc_start: 0.9434 (t0) cc_final: 0.8991 (t70) REVERT: F 432 LEU cc_start: 0.6938 (OUTLIER) cc_final: 0.6620 (pt) REVERT: F 488 GLU cc_start: 0.8938 (OUTLIER) cc_final: 0.8632 (mp0) REVERT: F 561 GLU cc_start: 0.9171 (mp0) cc_final: 0.8735 (mp0) REVERT: F 565 LYS cc_start: 0.9608 (OUTLIER) cc_final: 0.9402 (ttpp) REVERT: F 616 ASN cc_start: 0.8956 (t0) cc_final: 0.8676 (t0) REVERT: F 700 ARG cc_start: 0.9343 (OUTLIER) cc_final: 0.9017 (ttp80) REVERT: E 82 ILE cc_start: 0.9247 (OUTLIER) cc_final: 0.9015 (pt) REVERT: E 84 MET cc_start: 0.8773 (ptt) cc_final: 0.8505 (ppp) REVERT: E 134 TYR cc_start: 0.9318 (m-80) cc_final: 0.9029 (m-80) REVERT: E 305 GLU cc_start: 0.9216 (mt-10) cc_final: 0.8591 (mp0) REVERT: E 354 ASP cc_start: 0.9463 (t0) cc_final: 0.9231 (t0) REVERT: E 379 GLU cc_start: 0.9499 (mt-10) cc_final: 0.8931 (mt-10) REVERT: E 442 MET cc_start: 0.9471 (mpp) cc_final: 0.8820 (pmm) REVERT: E 546 GLU cc_start: 0.9158 (tt0) cc_final: 0.8853 (tp30) REVERT: E 560 ARG cc_start: 0.9285 (ptp-110) cc_final: 0.8909 (ptm160) REVERT: E 561 GLU cc_start: 0.8984 (mp0) cc_final: 0.8600 (mp0) REVERT: E 616 ASN cc_start: 0.8977 (t0) cc_final: 0.8661 (t0) REVERT: D 134 TYR cc_start: 0.9342 (m-80) cc_final: 0.9016 (m-80) REVERT: D 217 LYS cc_start: 0.9681 (mtmt) cc_final: 0.9403 (mtmp) REVERT: D 305 GLU cc_start: 0.9232 (mt-10) cc_final: 0.8578 (mp0) REVERT: D 354 ASP cc_start: 0.9398 (t0) cc_final: 0.9003 (t70) REVERT: D 442 MET cc_start: 0.9423 (mpp) cc_final: 0.8751 (pmm) REVERT: D 546 GLU cc_start: 0.9167 (tt0) cc_final: 0.8724 (tp30) REVERT: D 561 GLU cc_start: 0.9031 (mp0) cc_final: 0.8585 (mp0) REVERT: C 64 ARG cc_start: 0.8656 (tpm170) cc_final: 0.8103 (tpm170) REVERT: C 84 MET cc_start: 0.8896 (tmm) cc_final: 0.8557 (ppp) REVERT: C 124 GLU cc_start: 0.9525 (tt0) cc_final: 0.9192 (mp0) REVERT: C 217 LYS cc_start: 0.9662 (mtmt) cc_final: 0.9385 (mtmp) REVERT: C 305 GLU cc_start: 0.9095 (mp0) cc_final: 0.8686 (mp0) REVERT: C 379 GLU cc_start: 0.9462 (mt-10) cc_final: 0.8865 (mt-10) REVERT: C 442 MET cc_start: 0.9444 (mpm) cc_final: 0.9178 (mpp) REVERT: C 546 GLU cc_start: 0.9211 (tt0) cc_final: 0.8815 (tp30) REVERT: C 560 ARG cc_start: 0.9330 (ptp-110) cc_final: 0.8766 (ttm110) REVERT: C 561 GLU cc_start: 0.9046 (mp0) cc_final: 0.8699 (mp0) REVERT: C 564 ASP cc_start: 0.9454 (OUTLIER) cc_final: 0.9244 (m-30) REVERT: C 565 LYS cc_start: 0.9641 (OUTLIER) cc_final: 0.9423 (ttpp) REVERT: C 616 ASN cc_start: 0.8972 (t0) cc_final: 0.8679 (t0) REVERT: C 700 ARG cc_start: 0.9328 (OUTLIER) cc_final: 0.8999 (ttp80) REVERT: B 46 MET cc_start: 0.8967 (ppp) cc_final: 0.8345 (ppp) REVERT: B 64 ARG cc_start: 0.8672 (tpm170) cc_final: 0.8217 (tpm170) REVERT: B 84 MET cc_start: 0.8875 (ptt) cc_final: 0.8360 (ptt) REVERT: B 305 GLU cc_start: 0.9063 (mp0) cc_final: 0.8446 (mp0) REVERT: B 354 ASP cc_start: 0.9519 (t0) cc_final: 0.9315 (t0) REVERT: B 365 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.7321 (mmm-85) REVERT: B 450 ASP cc_start: 0.9144 (OUTLIER) cc_final: 0.8674 (p0) REVERT: B 546 GLU cc_start: 0.9178 (tt0) cc_final: 0.8867 (tp30) REVERT: B 561 GLU cc_start: 0.8983 (mp0) cc_final: 0.8585 (mp0) REVERT: B 616 ASN cc_start: 0.8946 (t0) cc_final: 0.8618 (t0) REVERT: A 134 TYR cc_start: 0.9330 (m-80) cc_final: 0.9045 (m-80) REVERT: A 158 MET cc_start: 0.9245 (mmp) cc_final: 0.9029 (mmm) REVERT: A 173 TYR cc_start: 0.7814 (p90) cc_final: 0.7255 (p90) REVERT: A 217 LYS cc_start: 0.9677 (mtmt) cc_final: 0.9384 (mtmp) REVERT: A 305 GLU cc_start: 0.9138 (mp0) cc_final: 0.8631 (mp0) REVERT: A 349 ARG cc_start: 0.9086 (mmm160) cc_final: 0.8872 (mmm-85) REVERT: A 354 ASP cc_start: 0.9483 (t0) cc_final: 0.9086 (t70) REVERT: A 365 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.7323 (mmm-85) REVERT: A 442 MET cc_start: 0.9426 (mpp) cc_final: 0.8788 (pmm) REVERT: A 488 GLU cc_start: 0.8899 (OUTLIER) cc_final: 0.8653 (mm-30) REVERT: A 546 GLU cc_start: 0.9173 (tt0) cc_final: 0.8738 (tp30) REVERT: A 560 ARG cc_start: 0.9218 (OUTLIER) cc_final: 0.8781 (ptm160) REVERT: A 561 GLU cc_start: 0.9030 (mp0) cc_final: 0.8686 (mp0) REVERT: A 564 ASP cc_start: 0.9459 (m-30) cc_final: 0.9163 (m-30) outliers start: 57 outliers final: 28 residues processed: 363 average time/residue: 0.6854 time to fit residues: 292.2836 Evaluate side-chains 351 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 310 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 244 TYR Chi-restraints excluded: chain F residue 402 GLU Chi-restraints excluded: chain F residue 432 LEU Chi-restraints excluded: chain F residue 488 GLU Chi-restraints excluded: chain F residue 565 LYS Chi-restraints excluded: chain F residue 700 ARG Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 244 TYR Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 488 GLU Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 110 TYR Chi-restraints excluded: chain D residue 244 TYR Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 244 TYR Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 488 GLU Chi-restraints excluded: chain C residue 564 ASP Chi-restraints excluded: chain C residue 565 LYS Chi-restraints excluded: chain C residue 700 ARG Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 244 TYR Chi-restraints excluded: chain B residue 365 ARG Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 488 GLU Chi-restraints excluded: chain A residue 560 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 407 optimal weight: 0.9980 chunk 243 optimal weight: 2.9990 chunk 293 optimal weight: 2.9990 chunk 165 optimal weight: 3.9990 chunk 75 optimal weight: 6.9990 chunk 266 optimal weight: 1.9990 chunk 222 optimal weight: 50.0000 chunk 310 optimal weight: 5.9990 chunk 404 optimal weight: 8.9990 chunk 288 optimal weight: 4.9990 chunk 285 optimal weight: 0.5980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 327 GLN ** E 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 421 GLN ** E 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 568 GLN ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.085454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.056197 restraints weight = 102872.195| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 4.26 r_work: 0.2795 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.5046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 35604 Z= 0.166 Angle : 0.758 16.770 48138 Z= 0.346 Chirality : 0.046 0.233 5442 Planarity : 0.004 0.069 6312 Dihedral : 7.832 116.226 4938 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.30 % Allowed : 17.33 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.02 (0.13), residues: 4410 helix: 1.95 (0.12), residues: 2010 sheet: 0.94 (0.19), residues: 732 loop : 0.95 (0.16), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG D 349 TYR 0.019 0.002 TYR B 203 PHE 0.010 0.001 PHE D 758 TRP 0.005 0.001 TRP D 476 HIS 0.003 0.001 HIS D 340 Details of bonding type rmsd covalent geometry : bond 0.00386 (35604) covalent geometry : angle 0.75827 (48138) hydrogen bonds : bond 0.03478 ( 1678) hydrogen bonds : angle 4.15554 ( 4692) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8820 Ramachandran restraints generated. 4410 Oldfield, 0 Emsley, 4410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8820 Ramachandran restraints generated. 4410 Oldfield, 0 Emsley, 4410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 301 time to evaluate : 1.111 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: F 217 LYS cc_start: 0.9656 (mtmt) cc_final: 0.9320 (mtmm) REVERT: F 305 GLU cc_start: 0.9067 (mp0) cc_final: 0.8579 (mp0) REVERT: F 354 ASP cc_start: 0.9424 (t0) cc_final: 0.9000 (t70) REVERT: F 432 LEU cc_start: 0.6844 (OUTLIER) cc_final: 0.6594 (pt) REVERT: F 488 GLU cc_start: 0.8950 (OUTLIER) cc_final: 0.8619 (mp0) REVERT: F 561 GLU cc_start: 0.9214 (mp0) cc_final: 0.8775 (mp0) REVERT: F 565 LYS cc_start: 0.9600 (OUTLIER) cc_final: 0.9383 (ttpp) REVERT: F 616 ASN cc_start: 0.8964 (t0) cc_final: 0.8686 (t0) REVERT: F 700 ARG cc_start: 0.9349 (OUTLIER) cc_final: 0.9032 (ttp80) REVERT: E 84 MET cc_start: 0.8749 (ptt) cc_final: 0.8510 (ppp) REVERT: E 134 TYR cc_start: 0.9327 (m-80) cc_final: 0.9052 (m-80) REVERT: E 305 GLU cc_start: 0.9207 (mt-10) cc_final: 0.8583 (mp0) REVERT: E 354 ASP cc_start: 0.9494 (t0) cc_final: 0.9282 (t0) REVERT: E 379 GLU cc_start: 0.9508 (mt-10) cc_final: 0.8922 (mt-10) REVERT: E 442 MET cc_start: 0.9511 (mpp) cc_final: 0.8880 (pmm) REVERT: E 546 GLU cc_start: 0.9150 (tt0) cc_final: 0.8841 (tp30) REVERT: E 561 GLU cc_start: 0.8992 (mp0) cc_final: 0.8617 (mp0) REVERT: E 616 ASN cc_start: 0.9034 (t0) cc_final: 0.8726 (t0) REVERT: D 134 TYR cc_start: 0.9343 (m-80) cc_final: 0.9024 (m-80) REVERT: D 217 LYS cc_start: 0.9681 (mtmt) cc_final: 0.9394 (mtmp) REVERT: D 305 GLU cc_start: 0.9229 (mt-10) cc_final: 0.8532 (mp0) REVERT: D 354 ASP cc_start: 0.9450 (t0) cc_final: 0.9029 (t70) REVERT: D 442 MET cc_start: 0.9474 (mpp) cc_final: 0.8974 (pmm) REVERT: D 546 GLU cc_start: 0.9181 (tt0) cc_final: 0.8734 (tp30) REVERT: D 561 GLU cc_start: 0.9067 (mp0) cc_final: 0.8613 (mp0) REVERT: D 564 ASP cc_start: 0.9474 (m-30) cc_final: 0.9228 (m-30) REVERT: D 616 ASN cc_start: 0.9034 (t0) cc_final: 0.8723 (t0) REVERT: C 64 ARG cc_start: 0.8707 (tpm170) cc_final: 0.8136 (tpm170) REVERT: C 84 MET cc_start: 0.8904 (tmm) cc_final: 0.8665 (ppp) REVERT: C 124 GLU cc_start: 0.9539 (tt0) cc_final: 0.9201 (mp0) REVERT: C 217 LYS cc_start: 0.9661 (mtmt) cc_final: 0.9396 (mtmm) REVERT: C 305 GLU cc_start: 0.9091 (mp0) cc_final: 0.8670 (mp0) REVERT: C 379 GLU cc_start: 0.9486 (mt-10) cc_final: 0.8881 (mt-10) REVERT: C 442 MET cc_start: 0.9461 (mpm) cc_final: 0.9194 (mpp) REVERT: C 546 GLU cc_start: 0.9189 (tt0) cc_final: 0.8797 (tp30) REVERT: C 561 GLU cc_start: 0.9059 (mp0) cc_final: 0.8591 (mp0) REVERT: C 565 LYS cc_start: 0.9637 (OUTLIER) cc_final: 0.9411 (ttpp) REVERT: C 616 ASN cc_start: 0.9015 (t0) cc_final: 0.8715 (t0) REVERT: C 700 ARG cc_start: 0.9330 (OUTLIER) cc_final: 0.8997 (ttp80) REVERT: B 46 MET cc_start: 0.8970 (ppp) cc_final: 0.8347 (ppp) REVERT: B 64 ARG cc_start: 0.8696 (tpm170) cc_final: 0.8243 (tpm170) REVERT: B 84 MET cc_start: 0.8858 (ptt) cc_final: 0.8315 (ptt) REVERT: B 305 GLU cc_start: 0.9092 (mp0) cc_final: 0.8450 (mp0) REVERT: B 365 ARG cc_start: 0.8121 (OUTLIER) cc_final: 0.7243 (mtt90) REVERT: B 450 ASP cc_start: 0.9138 (OUTLIER) cc_final: 0.8665 (p0) REVERT: B 546 GLU cc_start: 0.9153 (tt0) cc_final: 0.8852 (tp30) REVERT: B 561 GLU cc_start: 0.8987 (mp0) cc_final: 0.8610 (mp0) REVERT: B 616 ASN cc_start: 0.8994 (t0) cc_final: 0.8663 (t0) REVERT: A 134 TYR cc_start: 0.9327 (m-80) cc_final: 0.9038 (m-80) REVERT: A 158 MET cc_start: 0.9287 (mmp) cc_final: 0.9042 (mmm) REVERT: A 173 TYR cc_start: 0.7907 (p90) cc_final: 0.7403 (p90) REVERT: A 217 LYS cc_start: 0.9670 (mtmt) cc_final: 0.9363 (mtmp) REVERT: A 305 GLU cc_start: 0.9126 (mp0) cc_final: 0.8617 (mp0) REVERT: A 365 ARG cc_start: 0.8316 (OUTLIER) cc_final: 0.7613 (mmm-85) REVERT: A 442 MET cc_start: 0.9455 (mpp) cc_final: 0.8829 (pmm) REVERT: A 488 GLU cc_start: 0.8916 (OUTLIER) cc_final: 0.8678 (mm-30) REVERT: A 546 GLU cc_start: 0.9181 (tt0) cc_final: 0.8741 (tp30) REVERT: A 561 GLU cc_start: 0.9016 (mp0) cc_final: 0.8621 (mp0) REVERT: A 564 ASP cc_start: 0.9473 (m-30) cc_final: 0.9192 (m-30) REVERT: A 616 ASN cc_start: 0.9073 (t0) cc_final: 0.8751 (t0) outliers start: 49 outliers final: 30 residues processed: 335 average time/residue: 0.7833 time to fit residues: 305.8700 Evaluate side-chains 329 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 289 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 244 TYR Chi-restraints excluded: chain F residue 402 GLU Chi-restraints excluded: chain F residue 432 LEU Chi-restraints excluded: chain F residue 488 GLU Chi-restraints excluded: chain F residue 565 LYS Chi-restraints excluded: chain F residue 700 ARG Chi-restraints excluded: chain E residue 30 GLU Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 244 TYR Chi-restraints excluded: chain E residue 459 SER Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 488 GLU Chi-restraints excluded: chain E residue 550 MET Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 110 TYR Chi-restraints excluded: chain D residue 359 ARG Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 244 TYR Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 488 GLU Chi-restraints excluded: chain C residue 565 LYS Chi-restraints excluded: chain C residue 700 ARG Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 244 TYR Chi-restraints excluded: chain B residue 365 ARG Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 488 GLU Chi-restraints excluded: chain A residue 560 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 136 optimal weight: 6.9990 chunk 310 optimal weight: 7.9990 chunk 258 optimal weight: 6.9990 chunk 167 optimal weight: 7.9990 chunk 443 optimal weight: 1.9990 chunk 118 optimal weight: 0.0870 chunk 164 optimal weight: 5.9990 chunk 225 optimal weight: 7.9990 chunk 370 optimal weight: 60.0000 chunk 406 optimal weight: 0.4980 chunk 345 optimal weight: 6.9990 overall best weight: 3.1164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 348 ASN ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.084353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.054860 restraints weight = 103938.679| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 4.29 r_work: 0.2748 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.5164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 35604 Z= 0.240 Angle : 0.814 23.431 48138 Z= 0.376 Chirality : 0.047 0.231 5442 Planarity : 0.005 0.133 6312 Dihedral : 7.971 123.027 4938 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.49 % Allowed : 17.20 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.92 (0.13), residues: 4410 helix: 1.90 (0.12), residues: 2004 sheet: 0.87 (0.19), residues: 732 loop : 0.85 (0.16), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG B 349 TYR 0.017 0.002 TYR B 203 PHE 0.015 0.001 PHE D 758 TRP 0.007 0.001 TRP D 476 HIS 0.005 0.001 HIS D 317 Details of bonding type rmsd covalent geometry : bond 0.00543 (35604) covalent geometry : angle 0.81419 (48138) hydrogen bonds : bond 0.03699 ( 1678) hydrogen bonds : angle 4.32181 ( 4692) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11014.66 seconds wall clock time: 188 minutes 14.25 seconds (11294.25 seconds total)