Starting phenix.real_space_refine on Thu Sep 18 12:37:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jo5_61644/09_2025/9jo5_61644.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jo5_61644/09_2025/9jo5_61644.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jo5_61644/09_2025/9jo5_61644.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jo5_61644/09_2025/9jo5_61644.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jo5_61644/09_2025/9jo5_61644.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jo5_61644/09_2025/9jo5_61644.map" } resolution = 2.8 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= 0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 294 5.49 5 Mg 1 5.21 5 S 26 5.16 5 C 9822 2.51 5 N 3120 2.21 5 O 3770 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17033 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 801 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 707 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "C" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 811 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "D" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 718 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 716 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 88} Chain: "G" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2975 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3011 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "K" Number of atoms: 4946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 608, 4946 Classifications: {'peptide': 608} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 588} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.54, per 1000 atoms: 0.21 Number of scatterers: 17033 At special positions: 0 Unit cell: (105.002, 119.075, 155.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 26 16.00 P 294 15.00 Mg 1 11.99 O 3770 8.00 N 3120 7.00 C 9822 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: 1.41 Conformation dependent library (CDL) restraints added in 476.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2604 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 13 sheets defined 62.9% alpha, 3.0% beta 135 base pairs and 262 stacking pairs defined. Time for finding SS restraints: 2.65 Creating SS restraints... Processing helix chain 'A' and resid 45 through 55 removed outlier: 3.551A pdb=" N ILE A 51 " --> pdb=" O ALA A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 76 Processing helix chain 'A' and resid 86 through 114 removed outlier: 3.675A pdb=" N LEU A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.661A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.131A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS B 59 " --> pdb=" O ARG B 55 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL B 60 " --> pdb=" O GLY B 56 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 46 through 72 Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 92 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 removed outlier: 3.563A pdb=" N VAL D 38 " --> pdb=" O TYR D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 120 Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 64 through 76 removed outlier: 3.686A pdb=" N LEU E 70 " --> pdb=" O PRO E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.640A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.690A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 27 through 36 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 92 through 97 removed outlier: 3.963A pdb=" N LEU G 96 " --> pdb=" O GLU G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 removed outlier: 3.539A pdb=" N ILE H 91 " --> pdb=" O THR H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 121 removed outlier: 3.546A pdb=" N ALA H 104 " --> pdb=" O PRO H 100 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 91 removed outlier: 3.706A pdb=" N LEU K 91 " --> pdb=" O LYS K 87 " (cutoff:3.500A) Processing helix chain 'K' and resid 102 through 115 Processing helix chain 'K' and resid 119 through 130 removed outlier: 3.809A pdb=" N ILE K 123 " --> pdb=" O PHE K 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 130 through 141 removed outlier: 3.914A pdb=" N VAL K 139 " --> pdb=" O GLN K 135 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU K 140 " --> pdb=" O VAL K 136 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU K 141 " --> pdb=" O LEU K 137 " (cutoff:3.500A) Processing helix chain 'K' and resid 197 through 213 Processing helix chain 'K' and resid 226 through 241 Processing helix chain 'K' and resid 253 through 255 No H-bonds generated for 'chain 'K' and resid 253 through 255' Processing helix chain 'K' and resid 256 through 267 Processing helix chain 'K' and resid 279 through 290 Processing helix chain 'K' and resid 302 through 309 Processing helix chain 'K' and resid 309 through 315 removed outlier: 3.802A pdb=" N LEU K 313 " --> pdb=" O GLU K 309 " (cutoff:3.500A) Processing helix chain 'K' and resid 325 through 330 removed outlier: 3.691A pdb=" N ARG K 328 " --> pdb=" O GLU K 325 " (cutoff:3.500A) Processing helix chain 'K' and resid 334 through 342 removed outlier: 4.121A pdb=" N GLU K 342 " --> pdb=" O GLN K 338 " (cutoff:3.500A) Processing helix chain 'K' and resid 360 through 371 Processing helix chain 'K' and resid 378 through 386 Processing helix chain 'K' and resid 390 through 406 removed outlier: 4.103A pdb=" N GLN K 394 " --> pdb=" O THR K 390 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LYS K 399 " --> pdb=" O ASP K 395 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLN K 400 " --> pdb=" O LYS K 396 " (cutoff:3.500A) Processing helix chain 'K' and resid 407 through 409 No H-bonds generated for 'chain 'K' and resid 407 through 409' Processing helix chain 'K' and resid 434 through 448 Processing helix chain 'K' and resid 461 through 478 Processing helix chain 'K' and resid 501 through 518 removed outlier: 4.667A pdb=" N GLU K 516 " --> pdb=" O LYS K 512 " (cutoff:3.500A) Processing helix chain 'K' and resid 527 through 542 removed outlier: 3.625A pdb=" N LEU K 531 " --> pdb=" O MET K 527 " (cutoff:3.500A) Processing helix chain 'K' and resid 556 through 565 Processing helix chain 'K' and resid 601 through 610 removed outlier: 3.799A pdb=" N ASP K 605 " --> pdb=" O ASN K 601 " (cutoff:3.500A) Processing helix chain 'K' and resid 631 through 654 removed outlier: 4.038A pdb=" N LYS K 635 " --> pdb=" O SER K 631 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE K 636 " --> pdb=" O VAL K 632 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LEU K 637 " --> pdb=" O GLU K 633 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N GLU K 638 " --> pdb=" O GLU K 634 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASP K 647 " --> pdb=" O LYS K 643 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLN K 648 " --> pdb=" O LEU K 644 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU K 649 " --> pdb=" O ARG K 645 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL K 650 " --> pdb=" O LEU K 646 " (cutoff:3.500A) Processing helix chain 'K' and resid 669 through 676 Processing helix chain 'K' and resid 678 through 685 removed outlier: 3.744A pdb=" N VAL K 682 " --> pdb=" O GLY K 678 " (cutoff:3.500A) Processing helix chain 'K' and resid 707 through 728 removed outlier: 3.839A pdb=" N LEU K 711 " --> pdb=" O ASP K 707 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR K 728 " --> pdb=" O ALA K 724 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.316A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.013A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.731A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.825A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.165A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'K' and resid 273 through 275 removed outlier: 6.637A pdb=" N PHE K 248 " --> pdb=" O VAL K 299 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N ALA K 301 " --> pdb=" O PHE K 248 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N VAL K 250 " --> pdb=" O ALA K 301 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N LEU K 249 " --> pdb=" O ILE K 322 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N ILE K 321 " --> pdb=" O LEU K 349 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 425 through 426 removed outlier: 6.199A pdb=" N LYS K 425 " --> pdb=" O VAL K 623 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'K' and resid 429 through 431 removed outlier: 6.235A pdb=" N LEU K 429 " --> pdb=" O VAL K 627 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'K' and resid 524 through 525 588 hydrogen bonds defined for protein. 1728 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 344 hydrogen bonds 676 hydrogen bond angles 0 basepair planarities 135 basepair parallelities 262 stacking parallelities Total time for adding SS restraints: 4.28 Time building geometry restraints manager: 1.85 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: 3094 1.33 - 1.45: 5512 1.45 - 1.57: 8696 1.57 - 1.69: 585 1.69 - 1.81: 45 Bond restraints: 17932 Sorted by residual: bond pdb=" CA GLU K 418 " pdb=" C GLU K 418 " ideal model delta sigma weight residual 1.521 1.452 0.069 1.19e-02 7.06e+03 3.35e+01 bond pdb=" N THR K 419 " pdb=" CA THR K 419 " ideal model delta sigma weight residual 1.458 1.412 0.046 1.14e-02 7.69e+03 1.66e+01 bond pdb=" CA THR K 419 " pdb=" C THR K 419 " ideal model delta sigma weight residual 1.524 1.474 0.051 1.29e-02 6.01e+03 1.54e+01 bond pdb=" CA SER K 420 " pdb=" C SER K 420 " ideal model delta sigma weight residual 1.523 1.481 0.042 1.34e-02 5.57e+03 9.93e+00 bond pdb=" N SER K 420 " pdb=" CA SER K 420 " ideal model delta sigma weight residual 1.457 1.425 0.033 1.29e-02 6.01e+03 6.49e+00 ... (remaining 17927 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 25012 2.38 - 4.77: 418 4.77 - 7.15: 34 7.15 - 9.54: 5 9.54 - 11.92: 1 Bond angle restraints: 25470 Sorted by residual: angle pdb=" N THR K 419 " pdb=" CA THR K 419 " pdb=" C THR K 419 " ideal model delta sigma weight residual 112.41 100.49 11.92 1.30e+00 5.92e-01 8.41e+01 angle pdb=" CA VAL K 417 " pdb=" C VAL K 417 " pdb=" N GLU K 418 " ideal model delta sigma weight residual 116.60 109.80 6.80 1.45e+00 4.76e-01 2.20e+01 angle pdb=" N GLU K 418 " pdb=" CA GLU K 418 " pdb=" C GLU K 418 " ideal model delta sigma weight residual 108.90 116.04 -7.14 1.63e+00 3.76e-01 1.92e+01 angle pdb=" O VAL K 417 " pdb=" C VAL K 417 " pdb=" N GLU K 418 " ideal model delta sigma weight residual 122.57 128.04 -5.47 1.25e+00 6.40e-01 1.91e+01 angle pdb=" N ILE K 397 " pdb=" CA ILE K 397 " pdb=" C ILE K 397 " ideal model delta sigma weight residual 112.98 107.79 5.19 1.25e+00 6.40e-01 1.73e+01 ... (remaining 25465 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.81: 8570 35.81 - 71.62: 1469 71.62 - 107.43: 37 107.43 - 143.24: 0 143.24 - 179.05: 4 Dihedral angle restraints: 10080 sinusoidal: 6058 harmonic: 4022 Sorted by residual: dihedral pdb=" O2A ADP K1202 " pdb=" O3A ADP K1202 " pdb=" PA ADP K1202 " pdb=" PB ADP K1202 " ideal model delta sinusoidal sigma weight residual -60.00 42.08 -102.08 1 2.00e+01 2.50e-03 2.90e+01 dihedral pdb=" CA PRO K 479 " pdb=" C PRO K 479 " pdb=" N TYR K 480 " pdb=" CA TYR K 480 " ideal model delta harmonic sigma weight residual 180.00 159.17 20.83 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" C4' DT I 38 " pdb=" C3' DT I 38 " pdb=" O3' DT I 38 " pdb=" P DA I 39 " ideal model delta sinusoidal sigma weight residual -140.00 39.05 -179.05 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 10077 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1913 0.045 - 0.090: 795 0.090 - 0.136: 151 0.136 - 0.181: 19 0.181 - 0.226: 5 Chirality restraints: 2883 Sorted by residual: chirality pdb=" C3' DT I 38 " pdb=" C4' DT I 38 " pdb=" O3' DT I 38 " pdb=" C2' DT I 38 " both_signs ideal model delta sigma weight residual False -2.66 -2.43 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CB ILE H 36 " pdb=" CA ILE H 36 " pdb=" CG1 ILE H 36 " pdb=" CG2 ILE H 36 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CB THR K 352 " pdb=" CA THR K 352 " pdb=" OG1 THR K 352 " pdb=" CG2 THR K 352 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 8.98e-01 ... (remaining 2880 not shown) Planarity restraints: 2222 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL K 417 " 0.027 2.00e-02 2.50e+03 5.88e-02 3.46e+01 pdb=" C VAL K 417 " -0.102 2.00e-02 2.50e+03 pdb=" O VAL K 417 " 0.040 2.00e-02 2.50e+03 pdb=" N GLU K 418 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE G 25 " -0.019 2.00e-02 2.50e+03 1.77e-02 5.46e+00 pdb=" CG PHE G 25 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 PHE G 25 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE G 25 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE G 25 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE G 25 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE G 25 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 20 " -0.031 2.00e-02 2.50e+03 1.32e-02 4.81e+00 pdb=" N9 DA I 20 " 0.028 2.00e-02 2.50e+03 pdb=" C8 DA I 20 " 0.004 2.00e-02 2.50e+03 pdb=" N7 DA I 20 " 0.000 2.00e-02 2.50e+03 pdb=" C5 DA I 20 " 0.003 2.00e-02 2.50e+03 pdb=" C6 DA I 20 " -0.006 2.00e-02 2.50e+03 pdb=" N6 DA I 20 " -0.009 2.00e-02 2.50e+03 pdb=" N1 DA I 20 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DA I 20 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DA I 20 " 0.006 2.00e-02 2.50e+03 pdb=" C4 DA I 20 " 0.003 2.00e-02 2.50e+03 ... (remaining 2219 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 143 2.53 - 3.13: 13213 3.13 - 3.72: 29476 3.72 - 4.31: 41909 4.31 - 4.90: 62129 Nonbonded interactions: 146870 Sorted by model distance: nonbonded pdb="MG MG K1201 " pdb=" O3B ADP K1202 " model vdw 1.943 2.170 nonbonded pdb=" N2 DG I 44 " pdb=" O2 DC J 104 " model vdw 1.954 2.496 nonbonded pdb=" O2 DC I 45 " pdb=" N2 DG J 103 " model vdw 1.973 2.496 nonbonded pdb=" OH TYR K 199 " pdb=" O LEU K 225 " model vdw 2.073 3.040 nonbonded pdb=" OH TYR E 99 " pdb=" OE1 GLU E 133 " model vdw 2.139 3.040 ... (remaining 146865 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 40 through 134) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 14 through 101) } ncs_group { reference = (chain 'C' and (resid 12 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB )) or resid 75 through 118)) selection = (chain 'G' and ((resid 12 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 118)) } ncs_group { reference = chain 'D' selection = (chain 'H' and (resid 29 through 30 or (resid 31 and (name N or name CA or name \ C or name O or name CB )) or resid 32 through 53 or (resid 54 through 55 and (na \ me N or name CA or name C or name O or name CB )) or resid 56 through 121)) } 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: 2.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 18.440 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.076 17932 Z= 0.468 Angle : 0.803 11.919 25470 Z= 0.468 Chirality : 0.048 0.226 2883 Planarity : 0.004 0.059 2222 Dihedral : 26.063 179.048 7476 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.30 % Favored : 92.63 % Rotamer: Outliers : 0.09 % Allowed : 0.17 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -0.42 (0.23), residues: 1357 helix: 0.79 (0.18), residues: 816 sheet: -2.80 (0.61), residues: 61 loop : -1.79 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 99 TYR 0.033 0.002 TYR K 320 PHE 0.041 0.002 PHE G 25 TRP 0.034 0.003 TRP K 600 HIS 0.004 0.001 HIS F 18 Details of bonding type rmsd covalent geometry : bond 0.01051 (17932) covalent geometry : angle 0.80265 (25470) hydrogen bonds : bond 0.13350 ( 932) hydrogen bonds : angle 4.81266 ( 2404) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 167 time to evaluate : 0.589 Fit side-chains REVERT: C 90 ASP cc_start: 0.8584 (t0) cc_final: 0.8372 (t0) REVERT: D 65 ASP cc_start: 0.8533 (t70) cc_final: 0.8152 (t0) REVERT: D 73 GLU cc_start: 0.8323 (tp30) cc_final: 0.8101 (tp30) REVERT: D 76 ARG cc_start: 0.8395 (mtm-85) cc_final: 0.8153 (mtm-85) REVERT: H 73 GLU cc_start: 0.8505 (tp30) cc_final: 0.8193 (tp30) REVERT: K 211 HIS cc_start: 0.8391 (t70) cc_final: 0.8178 (t-90) REVERT: K 223 MET cc_start: 0.8601 (ttt) cc_final: 0.8372 (tpp) REVERT: K 294 CYS cc_start: 0.8294 (m) cc_final: 0.8024 (m) REVERT: K 418 GLU cc_start: 0.7297 (OUTLIER) cc_final: 0.6707 (tm-30) REVERT: K 527 MET cc_start: 0.8822 (tmm) cc_final: 0.8389 (tmt) REVERT: K 606 LEU cc_start: 0.9532 (tt) cc_final: 0.9031 (tt) REVERT: K 609 MET cc_start: 0.9477 (ptm) cc_final: 0.8727 (ppp) outliers start: 1 outliers final: 1 residues processed: 168 average time/residue: 0.9773 time to fit residues: 176.2258 Evaluate side-chains 136 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 134 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 418 GLU Chi-restraints excluded: chain K residue 524 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.0470 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.5682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 361 HIS K 526 GLN ** K 565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 586 ASN K 603 GLN K 677 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.096744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.064676 restraints weight = 47013.683| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.19 r_work: 0.3034 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 17932 Z= 0.214 Angle : 0.644 8.575 25470 Z= 0.366 Chirality : 0.039 0.173 2883 Planarity : 0.004 0.040 2222 Dihedral : 29.434 179.719 4721 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 1.28 % Allowed : 9.35 % Favored : 89.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 0.25 (0.23), residues: 1357 helix: 1.33 (0.18), residues: 834 sheet: -2.81 (0.66), residues: 50 loop : -1.62 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 96 TYR 0.018 0.002 TYR K 499 PHE 0.016 0.002 PHE G 25 TRP 0.018 0.002 TRP K 364 HIS 0.005 0.001 HIS K 111 Details of bonding type rmsd covalent geometry : bond 0.00479 (17932) covalent geometry : angle 0.64432 (25470) hydrogen bonds : bond 0.05822 ( 932) hydrogen bonds : angle 3.65906 ( 2404) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 150 time to evaluate : 0.473 Fit side-chains REVERT: D 65 ASP cc_start: 0.8837 (t70) cc_final: 0.8317 (t0) REVERT: D 90 GLU cc_start: 0.9000 (mp0) cc_final: 0.8720 (mp0) REVERT: D 102 GLU cc_start: 0.8712 (mm-30) cc_final: 0.8504 (mm-30) REVERT: F 95 ARG cc_start: 0.8732 (OUTLIER) cc_final: 0.7576 (mtp85) REVERT: H 39 TYR cc_start: 0.8082 (t80) cc_final: 0.7851 (t80) REVERT: H 83 ARG cc_start: 0.8962 (mmt-90) cc_final: 0.8483 (mmt90) REVERT: H 90 GLU cc_start: 0.8952 (mm-30) cc_final: 0.7888 (mp0) REVERT: K 433 MET cc_start: 0.7408 (tmm) cc_final: 0.7125 (tmm) REVERT: K 470 MET cc_start: 0.9484 (tpp) cc_final: 0.9250 (tpp) REVERT: K 473 ARG cc_start: 0.8978 (mtm-85) cc_final: 0.8722 (mmm160) REVERT: K 524 PHE cc_start: 0.8252 (m-80) cc_final: 0.7532 (t80) REVERT: K 570 LYS cc_start: 0.9278 (mppt) cc_final: 0.8838 (pptt) REVERT: K 674 MET cc_start: 0.7901 (tpt) cc_final: 0.7586 (tpt) outliers start: 15 outliers final: 4 residues processed: 160 average time/residue: 0.8991 time to fit residues: 155.2440 Evaluate side-chains 143 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 138 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain K residue 546 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 97 optimal weight: 4.9990 chunk 141 optimal weight: 5.9990 chunk 38 optimal weight: 0.0370 chunk 55 optimal weight: 0.8980 chunk 136 optimal weight: 0.9990 chunk 102 optimal weight: 6.9990 chunk 48 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 chunk 27 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 496 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 526 GLN ** K 565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 607 GLN ** 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 = 0.3875 r_free = 0.3875 target = 0.099312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.067674 restraints weight = 47671.747| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.23 r_work: 0.3118 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17932 Z= 0.153 Angle : 0.586 7.373 25470 Z= 0.335 Chirality : 0.036 0.187 2883 Planarity : 0.004 0.041 2222 Dihedral : 28.901 179.648 4716 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 1.70 % Allowed : 12.93 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 0.76 (0.23), residues: 1357 helix: 1.76 (0.18), residues: 836 sheet: -2.61 (0.63), residues: 55 loop : -1.46 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 99 TYR 0.014 0.001 TYR K 499 PHE 0.013 0.001 PHE K 109 TRP 0.022 0.002 TRP K 364 HIS 0.003 0.001 HIS K 111 Details of bonding type rmsd covalent geometry : bond 0.00332 (17932) covalent geometry : angle 0.58626 (25470) hydrogen bonds : bond 0.04580 ( 932) hydrogen bonds : angle 3.29063 ( 2404) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 163 time to evaluate : 0.419 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8664 (pm20) cc_final: 0.8454 (pm20) REVERT: C 92 GLU cc_start: 0.8802 (mm-30) cc_final: 0.8513 (mm-30) REVERT: D 65 ASP cc_start: 0.8821 (t70) cc_final: 0.8303 (t0) REVERT: D 90 GLU cc_start: 0.8917 (mp0) cc_final: 0.8653 (mp0) REVERT: D 102 GLU cc_start: 0.8629 (mm-30) cc_final: 0.8367 (mm-30) REVERT: D 105 LYS cc_start: 0.8758 (ttmm) cc_final: 0.8351 (tttp) REVERT: E 87 SER cc_start: 0.8801 (OUTLIER) cc_final: 0.8512 (t) REVERT: F 93 GLN cc_start: 0.8911 (OUTLIER) cc_final: 0.7932 (mp10) REVERT: F 95 ARG cc_start: 0.8747 (OUTLIER) cc_final: 0.7601 (mtp85) REVERT: G 64 GLU cc_start: 0.8647 (tm-30) cc_final: 0.8016 (tp30) REVERT: G 90 ASP cc_start: 0.8941 (t0) cc_final: 0.8706 (t0) REVERT: H 31 LYS cc_start: 0.8931 (ttmm) cc_final: 0.8481 (mtmm) REVERT: H 39 TYR cc_start: 0.8095 (t80) cc_final: 0.7783 (t80) REVERT: H 83 ARG cc_start: 0.8916 (mmt-90) cc_final: 0.8471 (mmt90) REVERT: H 90 GLU cc_start: 0.8937 (mm-30) cc_final: 0.7889 (mp0) REVERT: H 102 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7606 (mm-30) REVERT: K 349 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7463 (tt) REVERT: K 433 MET cc_start: 0.7324 (tmm) cc_final: 0.6957 (tmt) REVERT: K 452 VAL cc_start: 0.7637 (OUTLIER) cc_final: 0.7349 (m) REVERT: K 470 MET cc_start: 0.9521 (tpp) cc_final: 0.9259 (tpp) REVERT: K 524 PHE cc_start: 0.8266 (m-80) cc_final: 0.7463 (t80) REVERT: K 570 LYS cc_start: 0.9261 (mppt) cc_final: 0.8976 (pmtt) REVERT: K 609 MET cc_start: 0.9043 (ptm) cc_final: 0.8572 (ppp) REVERT: K 674 MET cc_start: 0.7836 (tpt) cc_final: 0.7548 (tpt) outliers start: 20 outliers final: 6 residues processed: 176 average time/residue: 0.8316 time to fit residues: 157.8982 Evaluate side-chains 156 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 145 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain K residue 349 LEU Chi-restraints excluded: chain K residue 409 LEU Chi-restraints excluded: chain K residue 452 VAL Chi-restraints excluded: chain K residue 546 CYS Chi-restraints excluded: chain K residue 579 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 141 optimal weight: 6.9990 chunk 94 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 101 optimal weight: 0.8980 chunk 95 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 139 optimal weight: 7.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN E 76 GLN ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 496 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 607 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.096559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.064382 restraints weight = 47315.980| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 2.21 r_work: 0.3033 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 17932 Z= 0.250 Angle : 0.629 8.770 25470 Z= 0.358 Chirality : 0.039 0.213 2883 Planarity : 0.004 0.038 2222 Dihedral : 29.207 178.888 4716 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 1.79 % Allowed : 14.63 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 0.71 (0.23), residues: 1357 helix: 1.68 (0.18), residues: 837 sheet: -2.11 (0.65), residues: 62 loop : -1.48 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 96 TYR 0.013 0.001 TYR E 54 PHE 0.016 0.002 PHE G 25 TRP 0.019 0.002 TRP K 364 HIS 0.004 0.001 HIS D 46 Details of bonding type rmsd covalent geometry : bond 0.00566 (17932) covalent geometry : angle 0.62914 (25470) hydrogen bonds : bond 0.05819 ( 932) hydrogen bonds : angle 3.40285 ( 2404) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 146 time to evaluate : 0.441 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8612 (pm20) cc_final: 0.8399 (pm20) REVERT: C 92 GLU cc_start: 0.8808 (mm-30) cc_final: 0.8513 (mm-30) REVERT: D 65 ASP cc_start: 0.8807 (t70) cc_final: 0.8349 (t0) REVERT: D 90 GLU cc_start: 0.9048 (mp0) cc_final: 0.8510 (mp0) REVERT: D 102 GLU cc_start: 0.8732 (mm-30) cc_final: 0.8462 (mm-30) REVERT: D 105 LYS cc_start: 0.8794 (ttmm) cc_final: 0.8412 (tttp) REVERT: E 87 SER cc_start: 0.8941 (OUTLIER) cc_final: 0.8733 (t) REVERT: F 93 GLN cc_start: 0.8982 (OUTLIER) cc_final: 0.8003 (mp10) REVERT: F 95 ARG cc_start: 0.8779 (OUTLIER) cc_final: 0.7515 (mtp85) REVERT: G 61 GLU cc_start: 0.8447 (tp30) cc_final: 0.7946 (tp30) REVERT: G 64 GLU cc_start: 0.8661 (tm-30) cc_final: 0.8034 (tp30) REVERT: G 90 ASP cc_start: 0.8973 (t0) cc_final: 0.8666 (t0) REVERT: H 31 LYS cc_start: 0.9023 (ttmm) cc_final: 0.8546 (mtmm) REVERT: H 39 TYR cc_start: 0.8146 (t80) cc_final: 0.7874 (t80) REVERT: H 83 ARG cc_start: 0.8967 (mmt-90) cc_final: 0.8504 (mmt90) REVERT: H 90 GLU cc_start: 0.8951 (mm-30) cc_final: 0.7971 (mp0) REVERT: K 349 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.8102 (tp) REVERT: K 433 MET cc_start: 0.7376 (tmm) cc_final: 0.7096 (tmm) REVERT: K 452 VAL cc_start: 0.7678 (OUTLIER) cc_final: 0.7398 (m) REVERT: K 524 PHE cc_start: 0.8327 (m-80) cc_final: 0.7817 (t80) REVERT: K 570 LYS cc_start: 0.9261 (mppt) cc_final: 0.8996 (pmtt) REVERT: K 609 MET cc_start: 0.9113 (ptm) cc_final: 0.8626 (ppp) REVERT: K 674 MET cc_start: 0.7811 (tpt) cc_final: 0.7505 (tpt) outliers start: 21 outliers final: 6 residues processed: 161 average time/residue: 0.9101 time to fit residues: 157.4777 Evaluate side-chains 153 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 142 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain K residue 298 VAL Chi-restraints excluded: chain K residue 349 LEU Chi-restraints excluded: chain K residue 409 LEU Chi-restraints excluded: chain K residue 452 VAL Chi-restraints excluded: chain K residue 546 CYS Chi-restraints excluded: chain K residue 579 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 153 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 109 optimal weight: 7.9990 chunk 112 optimal weight: 8.9990 chunk 127 optimal weight: 7.9990 chunk 148 optimal weight: 7.9990 chunk 14 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 140 optimal weight: 6.9990 chunk 76 optimal weight: 3.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 496 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 565 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 = 0.3816 r_free = 0.3816 target = 0.095794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.063516 restraints weight = 47085.988| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 2.23 r_work: 0.3015 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 17932 Z= 0.288 Angle : 0.652 8.789 25470 Z= 0.368 Chirality : 0.040 0.204 2883 Planarity : 0.004 0.041 2222 Dihedral : 29.305 178.543 4716 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.55 % Allowed : 14.71 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 0.68 (0.23), residues: 1357 helix: 1.66 (0.18), residues: 829 sheet: -2.20 (0.66), residues: 62 loop : -1.43 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 99 TYR 0.013 0.002 TYR E 54 PHE 0.016 0.002 PHE K 574 TRP 0.019 0.002 TRP K 364 HIS 0.004 0.001 HIS D 46 Details of bonding type rmsd covalent geometry : bond 0.00653 (17932) covalent geometry : angle 0.65178 (25470) hydrogen bonds : bond 0.06177 ( 932) hydrogen bonds : angle 3.46122 ( 2404) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 145 time to evaluate : 0.525 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8590 (pm20) cc_final: 0.8338 (pm20) REVERT: C 92 GLU cc_start: 0.8793 (mm-30) cc_final: 0.8480 (mm-30) REVERT: D 43 LYS cc_start: 0.9143 (mmtp) cc_final: 0.8936 (mptp) REVERT: D 65 ASP cc_start: 0.8784 (t70) cc_final: 0.8293 (t0) REVERT: D 90 GLU cc_start: 0.9064 (mp0) cc_final: 0.8528 (mp0) REVERT: D 102 GLU cc_start: 0.8732 (mm-30) cc_final: 0.8508 (mm-30) REVERT: E 87 SER cc_start: 0.8969 (OUTLIER) cc_final: 0.8743 (t) REVERT: F 93 GLN cc_start: 0.8977 (OUTLIER) cc_final: 0.7858 (mp10) REVERT: F 95 ARG cc_start: 0.8798 (OUTLIER) cc_final: 0.7526 (mtp85) REVERT: G 61 GLU cc_start: 0.8523 (tp30) cc_final: 0.8006 (tp30) REVERT: G 64 GLU cc_start: 0.8664 (tm-30) cc_final: 0.8074 (tp30) REVERT: G 90 ASP cc_start: 0.8984 (t0) cc_final: 0.8646 (t0) REVERT: H 31 LYS cc_start: 0.9058 (ttmm) cc_final: 0.8498 (mtmm) REVERT: H 39 TYR cc_start: 0.8211 (t80) cc_final: 0.7916 (t80) REVERT: H 83 ARG cc_start: 0.8965 (mmt-90) cc_final: 0.8503 (mmt90) REVERT: H 90 GLU cc_start: 0.8998 (mm-30) cc_final: 0.7948 (mp0) REVERT: H 102 GLU cc_start: 0.8239 (mm-30) cc_final: 0.7960 (mm-30) REVERT: K 349 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8156 (tp) REVERT: K 433 MET cc_start: 0.7432 (tmm) cc_final: 0.7065 (tmt) REVERT: K 452 VAL cc_start: 0.7681 (OUTLIER) cc_final: 0.7404 (m) REVERT: K 524 PHE cc_start: 0.8516 (m-80) cc_final: 0.7893 (t80) REVERT: K 570 LYS cc_start: 0.9234 (mppt) cc_final: 0.9003 (pmtt) REVERT: K 674 MET cc_start: 0.7638 (tpt) cc_final: 0.7335 (tpt) outliers start: 30 outliers final: 12 residues processed: 163 average time/residue: 0.8719 time to fit residues: 152.8062 Evaluate side-chains 158 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 141 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 73 GLU Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 298 VAL Chi-restraints excluded: chain K residue 349 LEU Chi-restraints excluded: chain K residue 401 LEU Chi-restraints excluded: chain K residue 409 LEU Chi-restraints excluded: chain K residue 452 VAL Chi-restraints excluded: chain K residue 546 CYS Chi-restraints excluded: chain K residue 579 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 140 optimal weight: 0.9990 chunk 149 optimal weight: 1.9990 chunk 148 optimal weight: 7.9990 chunk 4 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 chunk 155 optimal weight: 0.0370 chunk 81 optimal weight: 2.9990 chunk 139 optimal weight: 8.9990 chunk 120 optimal weight: 0.9990 chunk 150 optimal weight: 20.0000 chunk 19 optimal weight: 0.0040 overall best weight: 0.6076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 496 HIS ** K 565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 653 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.098804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.067181 restraints weight = 46981.082| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.22 r_work: 0.3095 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17932 Z= 0.151 Angle : 0.600 9.901 25470 Z= 0.338 Chirality : 0.036 0.183 2883 Planarity : 0.004 0.040 2222 Dihedral : 28.906 179.888 4716 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.87 % Allowed : 16.33 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 1.06 (0.24), residues: 1357 helix: 2.00 (0.18), residues: 828 sheet: -2.39 (0.68), residues: 55 loop : -1.32 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 99 TYR 0.010 0.001 TYR G 57 PHE 0.018 0.001 PHE K 574 TRP 0.025 0.002 TRP K 364 HIS 0.003 0.001 HIS K 478 Details of bonding type rmsd covalent geometry : bond 0.00327 (17932) covalent geometry : angle 0.59987 (25470) hydrogen bonds : bond 0.04519 ( 932) hydrogen bonds : angle 3.19120 ( 2404) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 151 time to evaluate : 0.318 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8580 (pm20) cc_final: 0.8356 (pm20) REVERT: C 92 GLU cc_start: 0.8791 (mm-30) cc_final: 0.8521 (mm-30) REVERT: D 65 ASP cc_start: 0.8754 (t70) cc_final: 0.8285 (t0) REVERT: D 90 GLU cc_start: 0.9006 (mp0) cc_final: 0.8485 (mp0) REVERT: D 102 GLU cc_start: 0.8652 (mm-30) cc_final: 0.8373 (mm-30) REVERT: D 105 LYS cc_start: 0.8773 (ttmm) cc_final: 0.8354 (tttp) REVERT: E 87 SER cc_start: 0.8840 (OUTLIER) cc_final: 0.8556 (t) REVERT: F 84 MET cc_start: 0.9350 (mmm) cc_final: 0.9090 (mmp) REVERT: F 93 GLN cc_start: 0.8922 (OUTLIER) cc_final: 0.7943 (mp10) REVERT: F 95 ARG cc_start: 0.8766 (OUTLIER) cc_final: 0.7548 (mtp85) REVERT: G 61 GLU cc_start: 0.8447 (tp30) cc_final: 0.7916 (tp30) REVERT: G 64 GLU cc_start: 0.8627 (tm-30) cc_final: 0.8010 (tp30) REVERT: G 90 ASP cc_start: 0.9019 (t0) cc_final: 0.8659 (t0) REVERT: H 31 LYS cc_start: 0.9040 (ttmm) cc_final: 0.8565 (mtmm) REVERT: H 39 TYR cc_start: 0.8080 (t80) cc_final: 0.7724 (t80) REVERT: H 65 ASP cc_start: 0.8915 (t0) cc_final: 0.8682 (t0) REVERT: H 83 ARG cc_start: 0.8897 (mmt-90) cc_final: 0.8463 (mmt90) REVERT: H 90 GLU cc_start: 0.8971 (mm-30) cc_final: 0.7879 (mp0) REVERT: H 102 GLU cc_start: 0.7983 (mm-30) cc_final: 0.7781 (mm-30) REVERT: K 349 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7867 (tp) REVERT: K 433 MET cc_start: 0.7398 (OUTLIER) cc_final: 0.6972 (tmt) REVERT: K 524 PHE cc_start: 0.8476 (m-80) cc_final: 0.7891 (t80) REVERT: K 570 LYS cc_start: 0.9190 (mppt) cc_final: 0.8947 (pmtt) REVERT: K 609 MET cc_start: 0.8997 (ptm) cc_final: 0.8471 (ppp) REVERT: K 674 MET cc_start: 0.7633 (tpt) cc_final: 0.7348 (tpt) outliers start: 22 outliers final: 8 residues processed: 161 average time/residue: 0.8849 time to fit residues: 153.1319 Evaluate side-chains 158 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 145 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain K residue 298 VAL Chi-restraints excluded: chain K residue 344 THR Chi-restraints excluded: chain K residue 349 LEU Chi-restraints excluded: chain K residue 433 MET Chi-restraints excluded: chain K residue 546 CYS Chi-restraints excluded: chain K residue 576 LEU Chi-restraints excluded: chain K residue 579 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 145 optimal weight: 2.9990 chunk 111 optimal weight: 8.9990 chunk 101 optimal weight: 6.9990 chunk 7 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 86 optimal weight: 5.9990 chunk 137 optimal weight: 20.0000 chunk 117 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 9 optimal weight: 9.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 653 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.096101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.063747 restraints weight = 46779.072| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.24 r_work: 0.3015 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 17932 Z= 0.286 Angle : 0.658 11.805 25470 Z= 0.369 Chirality : 0.040 0.171 2883 Planarity : 0.004 0.047 2222 Dihedral : 29.213 178.296 4716 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.38 % Allowed : 17.09 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 0.87 (0.23), residues: 1357 helix: 1.82 (0.18), residues: 829 sheet: -2.16 (0.65), residues: 62 loop : -1.36 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 99 TYR 0.011 0.002 TYR K 743 PHE 0.014 0.002 PHE K 574 TRP 0.026 0.002 TRP K 384 HIS 0.004 0.001 HIS D 46 Details of bonding type rmsd covalent geometry : bond 0.00651 (17932) covalent geometry : angle 0.65825 (25470) hydrogen bonds : bond 0.06067 ( 932) hydrogen bonds : angle 3.39582 ( 2404) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 141 time to evaluate : 0.456 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8573 (pm20) cc_final: 0.8339 (pm20) REVERT: D 65 ASP cc_start: 0.8803 (t70) cc_final: 0.8352 (t0) REVERT: D 90 GLU cc_start: 0.9059 (mp0) cc_final: 0.8512 (mp0) REVERT: D 102 GLU cc_start: 0.8728 (mm-30) cc_final: 0.8518 (mm-30) REVERT: E 87 SER cc_start: 0.8968 (OUTLIER) cc_final: 0.8741 (t) REVERT: F 84 MET cc_start: 0.9406 (mmm) cc_final: 0.8901 (mmm) REVERT: F 93 GLN cc_start: 0.9020 (OUTLIER) cc_final: 0.7925 (mp10) REVERT: F 95 ARG cc_start: 0.8797 (OUTLIER) cc_final: 0.7542 (mtp85) REVERT: G 61 GLU cc_start: 0.8519 (tp30) cc_final: 0.8037 (tp30) REVERT: G 64 GLU cc_start: 0.8693 (tm-30) cc_final: 0.8095 (tp30) REVERT: G 90 ASP cc_start: 0.9022 (t0) cc_final: 0.8666 (t0) REVERT: H 39 TYR cc_start: 0.8219 (t80) cc_final: 0.7914 (t80) REVERT: H 83 ARG cc_start: 0.8963 (mmt-90) cc_final: 0.8512 (mmt90) REVERT: H 90 GLU cc_start: 0.8957 (mm-30) cc_final: 0.7926 (mp0) REVERT: H 102 GLU cc_start: 0.8278 (mm-30) cc_final: 0.7938 (mm-30) REVERT: K 349 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8174 (tp) REVERT: K 433 MET cc_start: 0.7393 (OUTLIER) cc_final: 0.6898 (tmt) REVERT: K 524 PHE cc_start: 0.8501 (m-80) cc_final: 0.7838 (t80) REVERT: K 570 LYS cc_start: 0.9193 (mppt) cc_final: 0.8963 (pmtt) REVERT: K 609 MET cc_start: 0.8996 (ptm) cc_final: 0.8460 (ppp) REVERT: K 674 MET cc_start: 0.7607 (tpt) cc_final: 0.7328 (tpt) outliers start: 28 outliers final: 14 residues processed: 157 average time/residue: 0.9320 time to fit residues: 157.1767 Evaluate side-chains 158 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 139 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 73 GLU Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 298 VAL Chi-restraints excluded: chain K residue 344 THR Chi-restraints excluded: chain K residue 349 LEU Chi-restraints excluded: chain K residue 433 MET Chi-restraints excluded: chain K residue 546 CYS Chi-restraints excluded: chain K residue 579 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 73 optimal weight: 5.9990 chunk 131 optimal weight: 10.0000 chunk 87 optimal weight: 5.9990 chunk 143 optimal weight: 9.9990 chunk 139 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 53 optimal weight: 0.0970 chunk 7 optimal weight: 0.7980 chunk 130 optimal weight: 10.0000 chunk 16 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 653 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.097820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.065961 restraints weight = 47134.567| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.24 r_work: 0.3064 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 17932 Z= 0.164 Angle : 0.620 12.273 25470 Z= 0.348 Chirality : 0.037 0.175 2883 Planarity : 0.004 0.046 2222 Dihedral : 29.099 179.746 4716 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.79 % Allowed : 18.11 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 1.01 (0.24), residues: 1357 helix: 1.94 (0.18), residues: 830 sheet: -2.33 (0.67), residues: 55 loop : -1.30 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 99 TYR 0.010 0.001 TYR G 57 PHE 0.016 0.001 PHE K 574 TRP 0.035 0.002 TRP K 384 HIS 0.003 0.001 HIS D 46 Details of bonding type rmsd covalent geometry : bond 0.00362 (17932) covalent geometry : angle 0.62024 (25470) hydrogen bonds : bond 0.04874 ( 932) hydrogen bonds : angle 3.27917 ( 2404) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 144 time to evaluate : 0.539 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8592 (pm20) cc_final: 0.8323 (pm20) REVERT: C 92 GLU cc_start: 0.8845 (mm-30) cc_final: 0.8540 (mm-30) REVERT: D 65 ASP cc_start: 0.8825 (t70) cc_final: 0.8363 (t0) REVERT: D 90 GLU cc_start: 0.9013 (mp0) cc_final: 0.8494 (mp0) REVERT: D 102 GLU cc_start: 0.8717 (mm-30) cc_final: 0.8491 (mm-30) REVERT: E 87 SER cc_start: 0.8928 (OUTLIER) cc_final: 0.8682 (t) REVERT: F 93 GLN cc_start: 0.8990 (OUTLIER) cc_final: 0.8017 (mp10) REVERT: F 95 ARG cc_start: 0.8821 (OUTLIER) cc_final: 0.7567 (mtp85) REVERT: G 61 GLU cc_start: 0.8473 (tp30) cc_final: 0.8043 (tp30) REVERT: G 64 GLU cc_start: 0.8653 (tm-30) cc_final: 0.8113 (tp30) REVERT: G 90 ASP cc_start: 0.8989 (t0) cc_final: 0.8625 (t0) REVERT: H 31 LYS cc_start: 0.9063 (ttmm) cc_final: 0.8442 (mtmm) REVERT: H 39 TYR cc_start: 0.8140 (t80) cc_final: 0.7833 (t80) REVERT: H 83 ARG cc_start: 0.8932 (mmt-90) cc_final: 0.8506 (mmt90) REVERT: H 90 GLU cc_start: 0.8983 (mm-30) cc_final: 0.7993 (mp0) REVERT: H 102 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7887 (mm-30) REVERT: K 349 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8121 (tp) REVERT: K 433 MET cc_start: 0.7431 (OUTLIER) cc_final: 0.6916 (tmt) REVERT: K 524 PHE cc_start: 0.8512 (m-80) cc_final: 0.7867 (t80) REVERT: K 570 LYS cc_start: 0.9166 (mppt) cc_final: 0.8944 (pmtt) REVERT: K 609 MET cc_start: 0.8974 (ptm) cc_final: 0.8414 (ppp) REVERT: K 674 MET cc_start: 0.7615 (tpt) cc_final: 0.7320 (tpt) outliers start: 21 outliers final: 9 residues processed: 157 average time/residue: 0.9919 time to fit residues: 167.1720 Evaluate side-chains 155 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 141 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain K residue 298 VAL Chi-restraints excluded: chain K residue 344 THR Chi-restraints excluded: chain K residue 349 LEU Chi-restraints excluded: chain K residue 409 LEU Chi-restraints excluded: chain K residue 433 MET Chi-restraints excluded: chain K residue 546 CYS Chi-restraints excluded: chain K residue 579 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 114 optimal weight: 0.0010 chunk 90 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 chunk 121 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 148 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 overall best weight: 1.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 565 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 = 0.3854 r_free = 0.3854 target = 0.098031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.066099 restraints weight = 47030.448| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.22 r_work: 0.3079 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17932 Z= 0.175 Angle : 0.618 12.371 25470 Z= 0.345 Chirality : 0.037 0.174 2883 Planarity : 0.004 0.046 2222 Dihedral : 28.938 179.373 4716 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 1.62 % Allowed : 18.88 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 1.03 (0.24), residues: 1357 helix: 1.96 (0.18), residues: 836 sheet: -2.26 (0.68), residues: 55 loop : -1.36 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 99 TYR 0.009 0.001 TYR G 57 PHE 0.016 0.001 PHE K 574 TRP 0.035 0.002 TRP K 384 HIS 0.003 0.001 HIS D 46 Details of bonding type rmsd covalent geometry : bond 0.00390 (17932) covalent geometry : angle 0.61835 (25470) hydrogen bonds : bond 0.04852 ( 932) hydrogen bonds : angle 3.22864 ( 2404) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 145 time to evaluate : 0.543 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8561 (pm20) cc_final: 0.8261 (pm20) REVERT: D 65 ASP cc_start: 0.8776 (t70) cc_final: 0.8318 (t0) REVERT: D 90 GLU cc_start: 0.9010 (mp0) cc_final: 0.8508 (mp0) REVERT: D 102 GLU cc_start: 0.8693 (mm-30) cc_final: 0.8486 (mm-30) REVERT: E 87 SER cc_start: 0.8873 (OUTLIER) cc_final: 0.8610 (t) REVERT: F 93 GLN cc_start: 0.8961 (OUTLIER) cc_final: 0.7987 (mp10) REVERT: F 95 ARG cc_start: 0.8786 (OUTLIER) cc_final: 0.7535 (mtp85) REVERT: G 61 GLU cc_start: 0.8466 (tp30) cc_final: 0.8012 (tp30) REVERT: G 64 GLU cc_start: 0.8624 (tm-30) cc_final: 0.8054 (tp30) REVERT: G 90 ASP cc_start: 0.8966 (t0) cc_final: 0.8594 (t0) REVERT: H 31 LYS cc_start: 0.9040 (ttmm) cc_final: 0.8378 (mtmm) REVERT: H 39 TYR cc_start: 0.8139 (t80) cc_final: 0.7830 (t80) REVERT: H 83 ARG cc_start: 0.8899 (mmt-90) cc_final: 0.8473 (mmt90) REVERT: H 90 GLU cc_start: 0.8987 (mm-30) cc_final: 0.7960 (mp0) REVERT: H 102 GLU cc_start: 0.8153 (mm-30) cc_final: 0.7873 (mm-30) REVERT: K 349 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.8012 (tp) REVERT: K 433 MET cc_start: 0.7382 (OUTLIER) cc_final: 0.6951 (tmt) REVERT: K 524 PHE cc_start: 0.8538 (m-80) cc_final: 0.7863 (t80) REVERT: K 570 LYS cc_start: 0.9189 (mppt) cc_final: 0.8963 (pmtt) REVERT: K 609 MET cc_start: 0.8958 (ptm) cc_final: 0.8406 (ppp) REVERT: K 674 MET cc_start: 0.7561 (tpt) cc_final: 0.7258 (tpt) outliers start: 19 outliers final: 8 residues processed: 157 average time/residue: 0.9854 time to fit residues: 165.8911 Evaluate side-chains 155 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 142 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain K residue 298 VAL Chi-restraints excluded: chain K residue 344 THR Chi-restraints excluded: chain K residue 349 LEU Chi-restraints excluded: chain K residue 433 MET Chi-restraints excluded: chain K residue 546 CYS Chi-restraints excluded: chain K residue 579 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 160 optimal weight: 0.4980 chunk 18 optimal weight: 0.6980 chunk 118 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 74 optimal weight: 4.9990 chunk 16 optimal weight: 0.5980 chunk 68 optimal weight: 0.8980 chunk 93 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 90 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 76 GLN ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 565 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 = 0.3861 r_free = 0.3861 target = 0.098411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.066573 restraints weight = 46704.738| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.22 r_work: 0.3084 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17932 Z= 0.158 Angle : 0.622 13.013 25470 Z= 0.346 Chirality : 0.036 0.268 2883 Planarity : 0.004 0.064 2222 Dihedral : 28.930 179.443 4716 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.53 % Allowed : 19.39 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 1.14 (0.24), residues: 1357 helix: 2.04 (0.18), residues: 830 sheet: -2.11 (0.69), residues: 55 loop : -1.26 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 96 TYR 0.010 0.001 TYR G 57 PHE 0.014 0.001 PHE K 574 TRP 0.037 0.002 TRP K 384 HIS 0.004 0.001 HIS D 46 Details of bonding type rmsd covalent geometry : bond 0.00348 (17932) covalent geometry : angle 0.62158 (25470) hydrogen bonds : bond 0.04715 ( 932) hydrogen bonds : angle 3.21215 ( 2404) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 145 time to evaluate : 0.560 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8566 (pm20) cc_final: 0.8287 (pm20) REVERT: C 74 LYS cc_start: 0.9426 (mppt) cc_final: 0.9217 (mmtm) REVERT: D 65 ASP cc_start: 0.8769 (t70) cc_final: 0.8303 (t0) REVERT: D 90 GLU cc_start: 0.9003 (mp0) cc_final: 0.8514 (mp0) REVERT: D 102 GLU cc_start: 0.8686 (mm-30) cc_final: 0.8485 (mm-30) REVERT: E 87 SER cc_start: 0.8863 (OUTLIER) cc_final: 0.8599 (t) REVERT: F 93 GLN cc_start: 0.8956 (OUTLIER) cc_final: 0.7978 (mp10) REVERT: F 95 ARG cc_start: 0.8791 (OUTLIER) cc_final: 0.7545 (mtp85) REVERT: G 61 GLU cc_start: 0.8461 (tp30) cc_final: 0.8009 (tp30) REVERT: G 64 GLU cc_start: 0.8619 (tm-30) cc_final: 0.8059 (tp30) REVERT: G 90 ASP cc_start: 0.8956 (t0) cc_final: 0.8551 (t0) REVERT: H 31 LYS cc_start: 0.9034 (ttmm) cc_final: 0.8381 (mtmm) REVERT: H 39 TYR cc_start: 0.8123 (t80) cc_final: 0.7807 (t80) REVERT: H 83 ARG cc_start: 0.8890 (mmt-90) cc_final: 0.8469 (mmt90) REVERT: H 90 GLU cc_start: 0.8985 (mm-30) cc_final: 0.7966 (mp0) REVERT: H 102 GLU cc_start: 0.8124 (mm-30) cc_final: 0.7843 (mm-30) REVERT: K 349 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7992 (tp) REVERT: K 433 MET cc_start: 0.7369 (OUTLIER) cc_final: 0.6845 (tmt) REVERT: K 524 PHE cc_start: 0.8533 (m-80) cc_final: 0.7877 (t80) REVERT: K 570 LYS cc_start: 0.9191 (mppt) cc_final: 0.8959 (pmtt) REVERT: K 609 MET cc_start: 0.8929 (ptm) cc_final: 0.8419 (ppp) REVERT: K 674 MET cc_start: 0.7566 (tpt) cc_final: 0.7256 (tpt) outliers start: 18 outliers final: 10 residues processed: 155 average time/residue: 0.9634 time to fit residues: 160.3951 Evaluate side-chains 159 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 144 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain K residue 298 VAL Chi-restraints excluded: chain K residue 344 THR Chi-restraints excluded: chain K residue 349 LEU Chi-restraints excluded: chain K residue 433 MET Chi-restraints excluded: chain K residue 546 CYS Chi-restraints excluded: chain K residue 579 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 79 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 158 optimal weight: 8.9990 chunk 151 optimal weight: 8.9990 chunk 86 optimal weight: 5.9990 chunk 113 optimal weight: 0.0020 chunk 115 optimal weight: 1.9990 chunk 146 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 overall best weight: 2.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 76 GLN ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 653 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.096990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.065044 restraints weight = 46982.856| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.19 r_work: 0.3052 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 17932 Z= 0.254 Angle : 0.656 13.168 25470 Z= 0.365 Chirality : 0.039 0.195 2883 Planarity : 0.004 0.051 2222 Dihedral : 29.123 178.485 4716 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 1.70 % Allowed : 18.96 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 0.94 (0.23), residues: 1357 helix: 1.87 (0.18), residues: 835 sheet: -1.89 (0.66), residues: 62 loop : -1.39 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 99 TYR 0.008 0.001 TYR G 57 PHE 0.014 0.001 PHE K 574 TRP 0.036 0.002 TRP K 384 HIS 0.004 0.001 HIS D 46 Details of bonding type rmsd covalent geometry : bond 0.00577 (17932) covalent geometry : angle 0.65642 (25470) hydrogen bonds : bond 0.05692 ( 932) hydrogen bonds : angle 3.34474 ( 2404) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6267.40 seconds wall clock time: 107 minutes 16.17 seconds (6436.17 seconds total)