Starting phenix.real_space_refine on Fri Jul 3 23:06:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jo5_61644/07_2026/9jo5_61644.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jo5_61644/07_2026/9jo5_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9jo5_61644/07_2026/9jo5_61644.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jo5_61644/07_2026/9jo5_61644.map" model { file = "/net/cci-nas-00/data/ceres_data/9jo5_61644/07_2026/9jo5_61644.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jo5_61644/07_2026/9jo5_61644.cif" } 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-dev-6108/lib/python3.11/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: 3.10, per 1000 atoms: 0.18 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: 1.14 Conformation dependent library (CDL) restraints added in 470.3 milliseconds 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: 1.81 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: 3.27 Time building geometry restraints manager: 1.59 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=" N1 DC I 82 " pdb=" C6 DC I 82 " ideal model delta sigma weight residual 1.367 1.337 0.030 6.00e-03 2.78e+04 2.54e+01 bond pdb=" N1 DC I 92 " pdb=" C6 DC I 92 " ideal model delta sigma weight residual 1.367 1.338 0.029 6.00e-03 2.78e+04 2.35e+01 bond pdb=" N1 DC J 65 " pdb=" C6 DC J 65 " ideal model delta sigma weight residual 1.367 1.341 0.026 6.00e-03 2.78e+04 1.93e+01 bond pdb=" C3' DA J 90 " pdb=" O3' DA J 90 " ideal model delta sigma weight residual 1.435 1.379 0.056 1.30e-02 5.92e+03 1.85e+01 ... (remaining 17927 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 24778 2.38 - 4.77: 650 4.77 - 7.15: 36 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=" O4' DC I 28 " pdb=" C4' DC I 28 " pdb=" C3' DC I 28 " ideal model delta sigma weight residual 106.00 101.59 4.41 6.00e-01 2.78e+00 5.41e+01 angle pdb=" O4' DG I 102 " pdb=" C4' DG I 102 " pdb=" C3' DG I 102 " ideal model delta sigma weight residual 106.00 101.90 4.10 6.00e-01 2.78e+00 4.67e+01 angle pdb=" O4' DA I 91 " pdb=" C4' DA I 91 " pdb=" C3' DA I 91 " ideal model delta sigma weight residual 106.00 102.00 4.00 6.00e-01 2.78e+00 4.44e+01 angle pdb=" O4' DA J 116 " pdb=" C4' DA J 116 " pdb=" C3' DA J 116 " ideal model delta sigma weight residual 106.00 102.19 3.81 6.00e-01 2.78e+00 4.04e+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 - 0.059: 2122 0.059 - 0.119: 658 0.119 - 0.178: 97 0.178 - 0.237: 5 0.237 - 0.296: 1 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 -2.73 -2.43 -0.30 2.00e-01 2.50e+01 2.19e+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: 2.400 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.860 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 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:6.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 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= 0.842 Angle : 0.904 11.919 25470 Z= 0.723 Chirality : 0.055 0.296 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 are 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/Z covalent geometry : bond 0.01090 / 0.84 (17932) covalent geometry : angle 0.90366 / 0.72 (25470) hydrogen bonds : bond 0.13350 / 8.81 ( 932) hydrogen bonds : angle 4.81266 / 3.54 ( 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 : 0.394 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: 0.8324 (tp30) cc_final: 0.8101 (tp30) REVERT: D 76 ARG cc_start: 0.8395 (mtm-85) cc_final: 0.8154 (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: 0.7874 time to fit residues: 142.4192 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 : 0.422 ------------------------------------------------------------------------------- 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: 10.0000 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: 10.0000 chunk 122 optimal weight: 0.0470 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 2.9990 overall best weight: 1.7682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.096217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.063953 restraints weight = 47073.812| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 2.20 r_work: 0.3007 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17932 Z= 0.206 Angle : 0.755 10.134 25470 Z= 0.415 Chirality : 0.051 0.418 2883 Planarity : 0.005 0.044 2222 Dihedral : 29.903 179.228 4721 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.45 % Allowed : 9.69 % Favored : 88.86 % 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 are not related in a simple way. whole: -0.00 (0.23), residues: 1357 helix: 1.08 (0.18), residues: 833 sheet: -2.84 (0.65), residues: 50 loop : -1.62 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 96 TYR 0.020 0.002 TYR K 499 PHE 0.017 0.002 PHE G 25 TRP 0.022 0.002 TRP K 384 HIS 0.005 0.001 HIS K 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.21 (17932) covalent geometry : angle 0.75497 / 0.42 (25470) hydrogen bonds : bond 0.06765 / 4.55 ( 932) hydrogen bonds : angle 3.91961 / 2.82 ( 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 167 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 150 time to evaluate : 0.528 Fit side-chains REVERT: A 56 LYS cc_start: 0.9404 (OUTLIER) cc_final: 0.9168 (ttpt) REVERT: A 79 LYS cc_start: 0.9373 (tttt) cc_final: 0.9115 (tttm) REVERT: D 65 ASP cc_start: 0.8876 (t70) cc_final: 0.8382 (t0) REVERT: D 73 GLU cc_start: 0.8969 (tp30) cc_final: 0.8749 (mm-30) REVERT: D 90 GLU cc_start: 0.8932 (mp0) cc_final: 0.8688 (mp0) REVERT: D 102 GLU cc_start: 0.8716 (mm-30) cc_final: 0.8489 (mm-30) REVERT: F 95 ARG cc_start: 0.8718 (OUTLIER) cc_final: 0.7545 (mtp85) REVERT: G 13 LYS cc_start: 0.9047 (tptt) cc_final: 0.8845 (tptt) REVERT: K 294 CYS cc_start: 0.8241 (m) cc_final: 0.8034 (m) REVERT: K 418 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7077 (tm-30) REVERT: K 433 MET cc_start: 0.7231 (tmm) cc_final: 0.6948 (tmm) REVERT: K 470 MET cc_start: 0.9455 (tpp) cc_final: 0.9246 (tpp) REVERT: K 524 PHE cc_start: 0.8121 (m-80) cc_final: 0.7293 (t80) REVERT: K 527 MET cc_start: 0.8902 (tmm) cc_final: 0.8623 (tmt) REVERT: K 674 MET cc_start: 0.7973 (tpt) cc_final: 0.7686 (tpt) outliers start: 17 outliers final: 2 residues processed: 159 average time/residue: 0.8633 time to fit residues: 147.7593 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 : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain K residue 418 GLU 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: 9.9990 chunk 141 optimal weight: 8.9990 chunk 38 optimal weight: 0.6980 chunk 55 optimal weight: 0.4980 chunk 136 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 3 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 86 ASN K 526 GLN ** K 565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 677 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.097981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.066101 restraints weight = 47267.257| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.21 r_work: 0.3073 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 17932 Z= 0.153 Angle : 0.667 8.331 25470 Z= 0.378 Chirality : 0.046 0.372 2883 Planarity : 0.004 0.039 2222 Dihedral : 29.565 178.904 4719 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.62 % Allowed : 11.48 % Favored : 86.90 % 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 are not related in a simple way. whole: 0.43 (0.23), residues: 1357 helix: 1.43 (0.18), residues: 834 sheet: -2.45 (0.60), residues: 61 loop : -1.45 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 96 TYR 0.016 0.001 TYR K 499 PHE 0.016 0.001 PHE K 737 TRP 0.021 0.002 TRP K 364 HIS 0.005 0.001 HIS H 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.15 (17932) covalent geometry : angle 0.66657 / 0.38 (25470) hydrogen bonds : bond 0.05593 / 3.76 ( 932) hydrogen bonds : angle 3.60041 / 2.59 ( 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 174 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 155 time to evaluate : 0.487 Fit side-chains REVERT: A 56 LYS cc_start: 0.9439 (OUTLIER) cc_final: 0.9174 (ttpt) REVERT: A 79 LYS cc_start: 0.9342 (tttt) cc_final: 0.9087 (tttm) REVERT: D 65 ASP cc_start: 0.8773 (t70) cc_final: 0.8277 (t0) REVERT: D 90 GLU cc_start: 0.8939 (mp0) cc_final: 0.8655 (mp0) REVERT: D 102 GLU cc_start: 0.8671 (mm-30) cc_final: 0.8452 (mm-30) REVERT: E 87 SER cc_start: 0.8874 (OUTLIER) cc_final: 0.8614 (t) REVERT: F 95 ARG cc_start: 0.8711 (OUTLIER) cc_final: 0.7545 (mtp85) REVERT: G 64 GLU cc_start: 0.8681 (tm-30) cc_final: 0.8014 (tp30) REVERT: H 39 TYR cc_start: 0.8143 (t80) cc_final: 0.7900 (t80) REVERT: H 83 ARG cc_start: 0.8869 (mmt-90) cc_final: 0.8418 (mmt90) REVERT: H 90 GLU cc_start: 0.8943 (mm-30) cc_final: 0.7952 (mp0) REVERT: H 102 GLU cc_start: 0.8020 (mm-30) cc_final: 0.7785 (mm-30) REVERT: K 294 CYS cc_start: 0.8192 (m) cc_final: 0.7985 (m) REVERT: K 349 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7947 (tp) REVERT: K 433 MET cc_start: 0.7456 (tmm) cc_final: 0.7119 (tmm) REVERT: K 524 PHE cc_start: 0.8182 (m-80) cc_final: 0.7351 (t80) REVERT: K 609 MET cc_start: 0.9072 (ptm) cc_final: 0.8614 (ppp) REVERT: K 674 MET cc_start: 0.7816 (tpt) cc_final: 0.7518 (tpt) outliers start: 19 outliers final: 2 residues processed: 168 average time/residue: 0.7809 time to fit residues: 142.3517 Evaluate side-chains 151 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 145 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain E residue 87 SER 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 546 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 141 optimal weight: 3.9990 chunk 94 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 chunk 101 optimal weight: 4.9990 chunk 95 optimal weight: 10.0000 chunk 64 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 18 optimal weight: 0.3980 chunk 85 optimal weight: 9.9990 chunk 139 optimal weight: 5.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN ** 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** K 607 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.096661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.064448 restraints weight = 47328.227| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.20 r_work: 0.3035 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17932 Z= 0.213 Angle : 0.688 8.838 25470 Z= 0.383 Chirality : 0.047 0.417 2883 Planarity : 0.004 0.038 2222 Dihedral : 29.596 179.796 4716 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 1.45 % Allowed : 14.29 % Favored : 84.27 % 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 are not related in a simple way. whole: 0.53 (0.23), residues: 1357 helix: 1.52 (0.18), residues: 834 sheet: -2.45 (0.65), residues: 50 loop : -1.48 (0.27), residues: 473 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 0.002 PHE G 25 TRP 0.025 0.002 TRP K 384 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.21 (17932) covalent geometry : angle 0.68785 / 0.38 (25470) hydrogen bonds : bond 0.06339 / 4.29 ( 932) hydrogen bonds : angle 3.61829 / 2.61 ( 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 161 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 144 time to evaluate : 0.406 Fit side-chains REVERT: A 79 LYS cc_start: 0.9354 (tttt) cc_final: 0.9102 (tttm) REVERT: D 65 ASP cc_start: 0.8796 (t70) cc_final: 0.8289 (t0) REVERT: D 90 GLU cc_start: 0.9016 (mp0) cc_final: 0.8726 (mp0) REVERT: D 102 GLU cc_start: 0.8738 (mm-30) cc_final: 0.8507 (mm-30) REVERT: E 87 SER cc_start: 0.8889 (OUTLIER) cc_final: 0.8649 (t) REVERT: F 92 ARG cc_start: 0.9257 (OUTLIER) cc_final: 0.8765 (mtp-110) REVERT: F 95 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.7553 (mtp85) REVERT: G 61 GLU cc_start: 0.8414 (tp30) cc_final: 0.7923 (tp30) REVERT: G 64 GLU cc_start: 0.8676 (tm-30) cc_final: 0.8012 (tp30) REVERT: H 39 TYR cc_start: 0.8171 (t80) cc_final: 0.7923 (t80) REVERT: H 73 GLU cc_start: 0.9138 (tp30) cc_final: 0.8935 (mm-30) REVERT: H 83 ARG cc_start: 0.8956 (mmt-90) cc_final: 0.8495 (mmt90) REVERT: H 90 GLU cc_start: 0.8939 (mm-30) cc_final: 0.7882 (mp0) REVERT: H 96 ARG cc_start: 0.8870 (mpt-90) cc_final: 0.8666 (mtt-85) REVERT: H 102 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7822 (mm-30) REVERT: K 294 CYS cc_start: 0.8252 (m) cc_final: 0.8049 (m) REVERT: K 349 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.8075 (tp) REVERT: K 433 MET cc_start: 0.7468 (tmm) cc_final: 0.7151 (tmm) REVERT: K 524 PHE cc_start: 0.8340 (m-80) cc_final: 0.7559 (t80) REVERT: K 674 MET cc_start: 0.7843 (tpt) cc_final: 0.7565 (tpt) outliers start: 17 outliers final: 4 residues processed: 157 average time/residue: 0.8088 time to fit residues: 136.7188 Evaluate side-chains 149 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 141 time to evaluate : 0.533 ------------------------------------------------------------------------------- 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 92 ARG 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 546 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 153 optimal weight: 6.9990 chunk 106 optimal weight: 10.0000 chunk 109 optimal weight: 5.9990 chunk 112 optimal weight: 0.9990 chunk 127 optimal weight: 0.0980 chunk 148 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 140 optimal weight: 3.9990 chunk 76 optimal weight: 9.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.098188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.066472 restraints weight = 47015.020| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.21 r_work: 0.3091 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17932 Z= 0.146 Angle : 0.645 9.343 25470 Z= 0.362 Chirality : 0.045 0.370 2883 Planarity : 0.004 0.039 2222 Dihedral : 29.447 179.577 4716 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.96 % Allowed : 15.22 % Favored : 82.82 % 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 are not related in a simple way. whole: 0.76 (0.23), residues: 1357 helix: 1.75 (0.18), residues: 828 sheet: -2.31 (0.67), residues: 50 loop : -1.45 (0.27), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG E 53 TYR 0.015 0.001 TYR K 499 PHE 0.011 0.001 PHE K 574 TRP 0.031 0.002 TRP K 384 HIS 0.003 0.001 HIS K 478 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.15 (17932) covalent geometry : angle 0.64535 / 0.36 (25470) hydrogen bonds : bond 0.05208 / 3.50 ( 932) hydrogen bonds : angle 3.43102 / 2.47 ( 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 170 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 147 time to evaluate : 0.423 Fit side-chains REVERT: A 79 LYS cc_start: 0.9330 (tttt) cc_final: 0.9019 (tttm) REVERT: C 92 GLU cc_start: 0.8800 (mm-30) cc_final: 0.8570 (mm-30) REVERT: C 111 ILE cc_start: 0.8855 (pt) cc_final: 0.8553 (mt) REVERT: D 65 ASP cc_start: 0.8822 (t70) cc_final: 0.8332 (t0) REVERT: D 90 GLU cc_start: 0.8939 (mp0) cc_final: 0.8639 (mp0) REVERT: D 102 GLU cc_start: 0.8662 (mm-30) cc_final: 0.8391 (mm-30) REVERT: D 105 LYS cc_start: 0.8777 (ttmm) cc_final: 0.8393 (tttp) REVERT: E 87 SER cc_start: 0.8864 (OUTLIER) cc_final: 0.8607 (t) REVERT: F 93 GLN cc_start: 0.9011 (OUTLIER) cc_final: 0.8074 (mp10) REVERT: F 95 ARG cc_start: 0.8717 (OUTLIER) cc_final: 0.7521 (mtp85) REVERT: G 61 GLU cc_start: 0.8375 (tp30) cc_final: 0.7852 (tp30) REVERT: G 64 GLU cc_start: 0.8627 (tm-30) cc_final: 0.8031 (tp30) REVERT: H 31 LYS cc_start: 0.8939 (ttmm) cc_final: 0.8288 (mtmm) REVERT: H 39 TYR cc_start: 0.8106 (t80) cc_final: 0.7804 (t80) REVERT: H 83 ARG cc_start: 0.8890 (mmt-90) cc_final: 0.8463 (mmt90) REVERT: H 90 GLU cc_start: 0.8941 (mm-30) cc_final: 0.7895 (mp0) REVERT: H 102 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7672 (mm-30) REVERT: K 294 CYS cc_start: 0.8242 (m) cc_final: 0.8027 (m) REVERT: K 349 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7985 (tp) REVERT: K 433 MET cc_start: 0.7469 (tmm) cc_final: 0.7105 (tmm) REVERT: K 524 PHE cc_start: 0.8304 (m-80) cc_final: 0.7799 (t80) REVERT: K 609 MET cc_start: 0.8948 (ptm) cc_final: 0.8516 (ppp) REVERT: K 674 MET cc_start: 0.7761 (tpt) cc_final: 0.7468 (tpt) outliers start: 23 outliers final: 6 residues processed: 162 average time/residue: 0.7538 time to fit residues: 132.1242 Evaluate side-chains 151 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 141 time to evaluate : 0.496 ------------------------------------------------------------------------------- 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 401 LEU Chi-restraints excluded: chain K residue 409 LEU Chi-restraints excluded: chain K residue 546 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 140 optimal weight: 5.9990 chunk 149 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 122 optimal weight: 6.9990 chunk 155 optimal weight: 0.0980 chunk 81 optimal weight: 9.9990 chunk 139 optimal weight: 6.9990 chunk 120 optimal weight: 0.2980 chunk 150 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.096630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.064426 restraints weight = 46913.774| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.23 r_work: 0.3031 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 17932 Z= 0.220 Angle : 0.690 10.537 25470 Z= 0.379 Chirality : 0.047 0.417 2883 Planarity : 0.004 0.041 2222 Dihedral : 29.532 179.961 4716 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 1.79 % Allowed : 16.58 % Favored : 81.63 % 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 are not related in a simple way. whole: 0.71 (0.23), residues: 1357 helix: 1.73 (0.18), residues: 827 sheet: -2.43 (0.66), residues: 50 loop : -1.47 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 96 TYR 0.014 0.001 TYR E 54 PHE 0.013 0.002 PHE G 25 TRP 0.030 0.002 TRP K 384 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.22 (17932) covalent geometry : angle 0.68978 / 0.38 (25470) hydrogen bonds : bond 0.06325 / 4.28 ( 932) hydrogen bonds : angle 3.54098 / 2.54 ( 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 164 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 143 time to evaluate : 0.326 Fit side-chains REVERT: A 79 LYS cc_start: 0.9345 (tttt) cc_final: 0.9141 (tttm) REVERT: C 92 GLU cc_start: 0.8813 (mm-30) cc_final: 0.8530 (mm-30) REVERT: C 99 ARG cc_start: 0.8687 (mmm160) cc_final: 0.8473 (mmm160) REVERT: D 65 ASP cc_start: 0.8805 (t70) cc_final: 0.8311 (t0) REVERT: D 90 GLU cc_start: 0.9035 (mp0) cc_final: 0.8681 (mp0) REVERT: D 102 GLU cc_start: 0.8737 (mm-30) cc_final: 0.8473 (mm-30) REVERT: D 105 LYS cc_start: 0.8799 (ttmm) cc_final: 0.8421 (tttp) REVERT: E 87 SER cc_start: 0.8943 (OUTLIER) cc_final: 0.8712 (t) REVERT: F 84 MET cc_start: 0.9426 (mmm) cc_final: 0.9177 (mmp) REVERT: F 93 GLN cc_start: 0.9028 (OUTLIER) cc_final: 0.8099 (mp10) REVERT: F 95 ARG cc_start: 0.8804 (OUTLIER) cc_final: 0.7567 (mtp85) REVERT: G 61 GLU cc_start: 0.8450 (tp30) cc_final: 0.7926 (tp30) REVERT: G 64 GLU cc_start: 0.8655 (tm-30) cc_final: 0.8051 (tp30) REVERT: H 31 LYS cc_start: 0.8960 (ttmm) cc_final: 0.8378 (mtmm) REVERT: H 39 TYR cc_start: 0.8157 (t80) cc_final: 0.7845 (t80) REVERT: H 83 ARG cc_start: 0.8958 (mmt-90) cc_final: 0.8516 (mmt90) REVERT: H 90 GLU cc_start: 0.8955 (mm-30) cc_final: 0.7856 (mp0) REVERT: H 102 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7774 (mm-30) REVERT: K 294 CYS cc_start: 0.8295 (m) cc_final: 0.8070 (m) REVERT: K 349 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8150 (tp) REVERT: K 433 MET cc_start: 0.7485 (tmm) cc_final: 0.7168 (tmm) REVERT: K 524 PHE cc_start: 0.8456 (m-80) cc_final: 0.7796 (t80) REVERT: K 674 MET cc_start: 0.7762 (tpt) cc_final: 0.7495 (tpt) outliers start: 21 outliers final: 9 residues processed: 155 average time/residue: 0.7838 time to fit residues: 131.3805 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 : 0.435 ------------------------------------------------------------------------------- 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 115 LYS Chi-restraints excluded: chain F residue 50 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 401 LEU Chi-restraints excluded: chain K residue 409 LEU Chi-restraints excluded: chain K residue 546 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 145 optimal weight: 5.9990 chunk 111 optimal weight: 9.9990 chunk 101 optimal weight: 5.9990 chunk 7 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 86 optimal weight: 20.0000 chunk 137 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 98 optimal weight: 10.0000 chunk 9 optimal weight: 6.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.096185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.063929 restraints weight = 46704.730| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.21 r_work: 0.3022 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 17932 Z= 0.241 Angle : 0.709 10.455 25470 Z= 0.388 Chirality : 0.048 0.437 2883 Planarity : 0.004 0.039 2222 Dihedral : 29.608 179.057 4716 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.13 % Allowed : 16.92 % Favored : 80.95 % 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 are not related in a simple way. whole: 0.58 (0.23), residues: 1357 helix: 1.63 (0.18), residues: 833 sheet: -2.35 (0.63), residues: 61 loop : -1.59 (0.27), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 96 TYR 0.015 0.002 TYR E 54 PHE 0.015 0.002 PHE K 574 TRP 0.033 0.002 TRP K 384 HIS 0.003 0.001 HIS F 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00503 / 0.24 (17932) covalent geometry : angle 0.70886 / 0.39 (25470) hydrogen bonds : bond 0.06474 / 4.39 ( 932) hydrogen bonds : angle 3.57103 / 2.57 ( 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 167 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 142 time to evaluate : 0.430 Fit side-chains REVERT: A 79 LYS cc_start: 0.9342 (tttt) cc_final: 0.9030 (tttm) REVERT: C 92 GLU cc_start: 0.8811 (mm-30) cc_final: 0.8538 (mm-30) REVERT: C 99 ARG cc_start: 0.8687 (mmm160) cc_final: 0.8478 (mmm160) REVERT: D 65 ASP cc_start: 0.8811 (t70) cc_final: 0.8333 (t0) REVERT: D 90 GLU cc_start: 0.9042 (mp0) cc_final: 0.8557 (mp0) REVERT: D 102 GLU cc_start: 0.8744 (mm-30) cc_final: 0.8466 (mm-30) REVERT: D 105 LYS cc_start: 0.8869 (ttmm) cc_final: 0.8505 (tttp) REVERT: F 84 MET cc_start: 0.9438 (mmm) cc_final: 0.9092 (mmp) REVERT: F 93 GLN cc_start: 0.9039 (OUTLIER) cc_final: 0.8103 (mp10) REVERT: F 95 ARG cc_start: 0.8815 (OUTLIER) cc_final: 0.7635 (mtp85) REVERT: G 61 GLU cc_start: 0.8492 (tp30) cc_final: 0.7961 (tp30) REVERT: G 64 GLU cc_start: 0.8652 (tm-30) cc_final: 0.8044 (tp30) REVERT: H 39 TYR cc_start: 0.8158 (t80) cc_final: 0.7862 (t80) REVERT: H 83 ARG cc_start: 0.8961 (mmt-90) cc_final: 0.8519 (mmt90) REVERT: H 90 GLU cc_start: 0.8961 (mm-30) cc_final: 0.7902 (mp0) REVERT: H 102 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7868 (mm-30) REVERT: K 294 CYS cc_start: 0.8343 (m) cc_final: 0.8079 (m) REVERT: K 349 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8240 (tp) REVERT: K 433 MET cc_start: 0.7500 (tmm) cc_final: 0.7165 (tmm) REVERT: K 524 PHE cc_start: 0.8438 (m-80) cc_final: 0.7854 (t80) REVERT: K 609 MET cc_start: 0.9036 (ptm) cc_final: 0.8552 (ppp) REVERT: K 674 MET cc_start: 0.7726 (tpt) cc_final: 0.7401 (tpt) outliers start: 25 outliers final: 11 residues processed: 156 average time/residue: 0.7892 time to fit residues: 133.1338 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 : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 50 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 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 401 LEU Chi-restraints excluded: chain K residue 546 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 73 optimal weight: 20.0000 chunk 131 optimal weight: 1.9990 chunk 87 optimal weight: 20.0000 chunk 143 optimal weight: 0.9980 chunk 139 optimal weight: 7.9990 chunk 51 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 130 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3845 r_free = 0.3845 target = 0.097436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.065471 restraints weight = 47066.636| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 2.20 r_work: 0.3037 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17932 Z= 0.158 Angle : 0.671 12.352 25470 Z= 0.369 Chirality : 0.045 0.375 2883 Planarity : 0.004 0.053 2222 Dihedral : 29.480 179.146 4716 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 1.96 % Allowed : 17.94 % 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 are not related in a simple way. whole: 0.79 (0.23), residues: 1357 helix: 1.79 (0.18), residues: 835 sheet: -2.35 (0.68), residues: 50 loop : -1.50 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG H 96 TYR 0.012 0.001 TYR K 499 PHE 0.013 0.001 PHE K 574 TRP 0.035 0.002 TRP K 384 HIS 0.004 0.001 HIS K 478 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.16 (17932) covalent geometry : angle 0.67119 / 0.37 (25470) hydrogen bonds : bond 0.05463 / 3.69 ( 932) hydrogen bonds : angle 3.41504 / 2.46 ( 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 167 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 144 time to evaluate : 0.558 Fit side-chains REVERT: C 92 GLU cc_start: 0.8776 (mm-30) cc_final: 0.8368 (mm-30) REVERT: D 65 ASP cc_start: 0.8784 (t70) cc_final: 0.8303 (t0) REVERT: D 90 GLU cc_start: 0.8986 (mp0) cc_final: 0.8495 (mp0) REVERT: D 102 GLU cc_start: 0.8708 (mm-30) cc_final: 0.8444 (mm-30) REVERT: D 105 LYS cc_start: 0.8760 (ttmm) cc_final: 0.8371 (tttp) REVERT: E 87 SER cc_start: 0.8902 (OUTLIER) cc_final: 0.8659 (t) REVERT: F 84 MET cc_start: 0.9413 (mmm) cc_final: 0.9087 (mmp) REVERT: F 93 GLN cc_start: 0.9011 (OUTLIER) cc_final: 0.8061 (mp10) REVERT: F 95 ARG cc_start: 0.8753 (OUTLIER) cc_final: 0.7483 (mtp85) REVERT: G 61 GLU cc_start: 0.8461 (tp30) cc_final: 0.7934 (tp30) REVERT: G 64 GLU cc_start: 0.8639 (tm-30) cc_final: 0.8035 (tp30) REVERT: H 39 TYR cc_start: 0.8092 (t80) cc_final: 0.7810 (t80) REVERT: H 65 ASP cc_start: 0.8954 (t0) cc_final: 0.8735 (t0) REVERT: H 83 ARG cc_start: 0.8929 (mmt-90) cc_final: 0.8519 (mmt90) REVERT: H 90 GLU cc_start: 0.8955 (mm-30) cc_final: 0.7858 (mp0) REVERT: H 102 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7762 (mm-30) REVERT: K 294 CYS cc_start: 0.8290 (m) cc_final: 0.8028 (m) REVERT: K 349 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.8131 (tp) REVERT: K 433 MET cc_start: 0.7326 (OUTLIER) cc_final: 0.6922 (tmm) REVERT: K 524 PHE cc_start: 0.8395 (m-80) cc_final: 0.7849 (t80) REVERT: K 609 MET cc_start: 0.9010 (ptm) cc_final: 0.8526 (ppp) REVERT: K 674 MET cc_start: 0.7717 (tpt) cc_final: 0.7438 (tpt) outliers start: 23 outliers final: 8 residues processed: 157 average time/residue: 0.8092 time to fit residues: 137.0357 Evaluate side-chains 153 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 140 time to evaluate : 0.514 ------------------------------------------------------------------------------- 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 93 GLN Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain K residue 223 MET 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 114 optimal weight: 0.0020 chunk 90 optimal weight: 10.0000 chunk 7 optimal weight: 0.7980 chunk 121 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 18 optimal weight: 0.0970 chunk 148 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 113 optimal weight: 0.9980 chunk 93 optimal weight: 10.0000 chunk 4 optimal weight: 0.8980 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 76 GLN ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 496 HIS ** K 565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.098766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.067253 restraints weight = 47193.953| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.22 r_work: 0.3090 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.159 17932 Z= 0.142 Angle : 0.664 11.932 25470 Z= 0.367 Chirality : 0.044 0.341 2883 Planarity : 0.004 0.061 2222 Dihedral : 29.331 179.785 4716 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.53 % Allowed : 18.54 % Favored : 79.93 % 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 are not related in a simple way. whole: 0.97 (0.24), residues: 1357 helix: 1.94 (0.18), residues: 833 sheet: -2.21 (0.69), residues: 50 loop : -1.44 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG H 96 TYR 0.013 0.001 TYR K 499 PHE 0.021 0.001 PHE K 119 TRP 0.043 0.003 TRP K 384 HIS 0.004 0.001 HIS K 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.14 (17932) covalent geometry : angle 0.66378 / 0.37 (25470) hydrogen bonds : bond 0.05024 / 3.38 ( 932) hydrogen bonds : angle 3.32857 / 2.40 ( 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 169 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 151 time to evaluate : 0.367 Fit side-chains REVERT: B 22 LEU cc_start: 0.9139 (pt) cc_final: 0.8939 (pp) REVERT: D 65 ASP cc_start: 0.8766 (t70) cc_final: 0.8292 (t0) REVERT: D 90 GLU cc_start: 0.8967 (mp0) cc_final: 0.8481 (mp0) REVERT: D 102 GLU cc_start: 0.8677 (mm-30) cc_final: 0.8438 (mm-30) REVERT: D 105 LYS cc_start: 0.8758 (ttmm) cc_final: 0.8390 (tttp) REVERT: E 87 SER cc_start: 0.8852 (OUTLIER) cc_final: 0.8586 (t) REVERT: F 84 MET cc_start: 0.9365 (mmm) cc_final: 0.9069 (mmp) REVERT: F 93 GLN cc_start: 0.8989 (OUTLIER) cc_final: 0.8044 (mp10) REVERT: F 95 ARG cc_start: 0.8776 (OUTLIER) cc_final: 0.7552 (mtp85) REVERT: G 61 GLU cc_start: 0.8406 (tp30) cc_final: 0.7862 (tp30) REVERT: G 64 GLU cc_start: 0.8628 (tm-30) cc_final: 0.8033 (tp30) REVERT: H 31 LYS cc_start: 0.8874 (ttmm) cc_final: 0.8193 (mtmm) REVERT: H 39 TYR cc_start: 0.8088 (t80) cc_final: 0.7798 (t80) REVERT: H 65 ASP cc_start: 0.8933 (t0) cc_final: 0.8681 (t0) REVERT: H 83 ARG cc_start: 0.8880 (mmt-90) cc_final: 0.8482 (mmt90) REVERT: H 90 GLU cc_start: 0.8948 (mm-30) cc_final: 0.7883 (mp0) REVERT: H 102 GLU cc_start: 0.8066 (mm-30) cc_final: 0.7747 (mm-30) REVERT: K 294 CYS cc_start: 0.8314 (m) cc_final: 0.8087 (m) REVERT: K 349 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.8022 (tp) REVERT: K 433 MET cc_start: 0.7320 (OUTLIER) cc_final: 0.6913 (tmm) REVERT: K 524 PHE cc_start: 0.8371 (m-80) cc_final: 0.7847 (t80) REVERT: K 609 MET cc_start: 0.8964 (ptm) cc_final: 0.8483 (ppp) REVERT: K 674 MET cc_start: 0.7737 (tpt) cc_final: 0.7455 (tpt) outliers start: 18 outliers final: 7 residues processed: 159 average time/residue: 0.8013 time to fit residues: 137.9202 Evaluate side-chains 153 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 141 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 48 ASP 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 409 LEU Chi-restraints excluded: chain K residue 433 MET Chi-restraints excluded: chain K residue 546 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 160 optimal weight: 10.0000 chunk 18 optimal weight: 0.6980 chunk 118 optimal weight: 7.9990 chunk 25 optimal weight: 0.8980 chunk 74 optimal weight: 9.9990 chunk 16 optimal weight: 0.5980 chunk 68 optimal weight: 3.9990 chunk 93 optimal weight: 10.0000 chunk 40 optimal weight: 2.9990 chunk 90 optimal weight: 10.0000 chunk 0 optimal weight: 4.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3843 r_free = 0.3843 target = 0.097405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.065493 restraints weight = 46864.033| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.20 r_work: 0.3036 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 17932 Z= 0.192 Angle : 0.683 12.816 25470 Z= 0.375 Chirality : 0.045 0.378 2883 Planarity : 0.004 0.041 2222 Dihedral : 29.370 179.791 4716 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 1.53 % Allowed : 19.05 % Favored : 79.42 % 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 are not related in a simple way. whole: 0.93 (0.24), residues: 1357 helix: 1.90 (0.18), residues: 835 sheet: -2.32 (0.67), residues: 50 loop : -1.45 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 96 TYR 0.012 0.001 TYR K 499 PHE 0.012 0.001 PHE K 574 TRP 0.039 0.003 TRP K 384 HIS 0.006 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.19 (17932) covalent geometry : angle 0.68344 / 0.37 (25470) hydrogen bonds : bond 0.05652 / 3.82 ( 932) hydrogen bonds : angle 3.38712 / 2.44 ( 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 161 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 143 time to evaluate : 0.546 Fit side-chains REVERT: D 65 ASP cc_start: 0.8791 (t70) cc_final: 0.8314 (t0) REVERT: D 90 GLU cc_start: 0.9002 (mp0) cc_final: 0.8515 (mp0) REVERT: D 102 GLU cc_start: 0.8700 (mm-30) cc_final: 0.8449 (mm-30) REVERT: D 105 LYS cc_start: 0.8788 (ttmm) cc_final: 0.8416 (tttp) REVERT: E 87 SER cc_start: 0.8929 (OUTLIER) cc_final: 0.8672 (t) REVERT: F 93 GLN cc_start: 0.9006 (OUTLIER) cc_final: 0.8056 (mp10) REVERT: F 95 ARG cc_start: 0.8789 (OUTLIER) cc_final: 0.7527 (mtp85) REVERT: G 61 GLU cc_start: 0.8455 (tp30) cc_final: 0.7914 (tp30) REVERT: G 64 GLU cc_start: 0.8647 (tm-30) cc_final: 0.8030 (tp30) REVERT: H 39 TYR cc_start: 0.8149 (t80) cc_final: 0.7831 (t80) REVERT: H 83 ARG cc_start: 0.8926 (mmt-90) cc_final: 0.8516 (mmt90) REVERT: H 90 GLU cc_start: 0.8958 (mm-30) cc_final: 0.7874 (mp0) REVERT: H 102 GLU cc_start: 0.8088 (mm-30) cc_final: 0.7875 (mm-30) REVERT: K 294 CYS cc_start: 0.8322 (m) cc_final: 0.8055 (m) REVERT: K 349 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.8108 (tp) REVERT: K 433 MET cc_start: 0.7309 (OUTLIER) cc_final: 0.6905 (tmm) REVERT: K 524 PHE cc_start: 0.8395 (m-80) cc_final: 0.7887 (t80) REVERT: K 609 MET cc_start: 0.8969 (ptm) cc_final: 0.8498 (ppp) REVERT: K 674 MET cc_start: 0.7737 (tpt) cc_final: 0.7428 (tpt) outliers start: 18 outliers final: 10 residues processed: 154 average time/residue: 0.7677 time to fit residues: 127.7550 Evaluate side-chains 158 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 143 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 87 SER 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 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 356 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 79 optimal weight: 9.9990 chunk 125 optimal weight: 0.9980 chunk 83 optimal weight: 10.0000 chunk 37 optimal weight: 0.7980 chunk 158 optimal weight: 7.9990 chunk 151 optimal weight: 6.9990 chunk 86 optimal weight: 20.0000 chunk 113 optimal weight: 4.9990 chunk 115 optimal weight: 8.9990 chunk 146 optimal weight: 9.9990 chunk 59 optimal weight: 1.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3814 r_free = 0.3814 target = 0.095726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.063394 restraints weight = 46976.407| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.22 r_work: 0.3009 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 17932 Z= 0.284 Angle : 0.753 12.785 25470 Z= 0.406 Chirality : 0.050 0.452 2883 Planarity : 0.005 0.043 2222 Dihedral : 29.599 179.784 4716 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 1.53 % Allowed : 18.96 % 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 are not related in a simple way. whole: 0.62 (0.23), residues: 1357 helix: 1.66 (0.18), residues: 839 sheet: -2.48 (0.59), residues: 61 loop : -1.57 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 96 TYR 0.011 0.002 TYR K 499 PHE 0.015 0.002 PHE G 25 TRP 0.039 0.003 TRP K 384 HIS 0.006 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00606 / 0.28 (17932) covalent geometry : angle 0.75277 / 0.41 (25470) hydrogen bonds : bond 0.07179 / 4.89 ( 932) hydrogen bonds : angle 3.58361 / 2.59 ( 2404) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5111.16 seconds wall clock time: 87 minutes 46.40 seconds (5266.40 seconds total)