Starting phenix.real_space_refine on Thu Aug 6 18:49:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jo5_61644/08_2026/9jo5_61644.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jo5_61644/08_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_61644/08_2026/9jo5_61644.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jo5_61644/08_2026/9jo5_61644.map" model { file = "/net/cci-nas-00/data/ceres_data/9jo5_61644/08_2026/9jo5_61644.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jo5_61644/08_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-2.2rc3-6140/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: 2.93, per 1000 atoms: 0.17 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: 1.16 Conformation dependent library (CDL) restraints added in 483.2 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: 1.78 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: 4.57 Time building geometry restraints manager: 1.63 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: 24773 2.38 - 4.77: 655 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: 2.820 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: 0.030 Process input model: 16.610 Find NCS groups from input model: 0.180 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:7.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.160 ------------------------------------------------------------------------------- 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= 0.843 Angle : 0.909 11.919 25470 Z= 0.728 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 0.90859 / 0.73 (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 : 0.368 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: 0.8025 (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: 0.7531 time to fit residues: 136.2254 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 : 0.381 ------------------------------------------------------------------------------- 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: 9.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 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: 1.7684 ------------------------------------------------------------------------------- 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 = 0.3823 r_free = 0.3823 target = 0.096248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.063963 restraints weight = 47019.014| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 2.18 r_work: 0.3032 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17932 Z= 0.205 Angle : 0.765 10.178 25470 Z= 0.419 Chirality : 0.052 0.431 2883 Planarity : 0.005 0.043 2222 Dihedral : 29.840 179.884 4721 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.36 % Allowed : 9.78 % 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: -0.01 (0.23), residues: 1357 helix: 1.07 (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 0.021 0.002 TYR K 499 PHE 0.017 0.002 PHE K 574 TRP 0.023 0.002 TRP K 384 HIS 0.005 0.001 HIS K 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.20 (17932) covalent geometry : angle 0.76473 / 0.42 (25470) hydrogen bonds : bond 0.06827 / 4.59 ( 932) hydrogen bonds : angle 3.92733 / 2.83 ( 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: 16 poor density : 151 time to evaluate : 0.432 Fit side-chains revert: symmetry clash REVERT: A 56 LYS cc_start: 0.9412 (OUTLIER) cc_final: 0.9182 (ttpt) REVERT: A 79 LYS cc_start: 0.9377 (tttt) cc_final: 0.9109 (tttm) REVERT: C 64 GLU cc_start: 0.8445 (tp30) cc_final: 0.8242 (tp30) REVERT: D 65 ASP cc_start: 0.8880 (t70) cc_final: 0.8384 (t0) REVERT: D 90 GLU cc_start: 0.8926 (mp0) cc_final: 0.8682 (mp0) REVERT: D 102 GLU cc_start: 0.8715 (mm-30) cc_final: 0.8490 (mm-30) REVERT: F 95 ARG cc_start: 0.8720 (OUTLIER) cc_final: 0.7550 (mtp85) REVERT: K 294 CYS cc_start: 0.8245 (m) cc_final: 0.8037 (m) REVERT: K 418 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7062 (pp20) REVERT: K 433 MET cc_start: 0.7233 (tmm) cc_final: 0.6942 (tmm) REVERT: K 470 MET cc_start: 0.9447 (tpp) cc_final: 0.9235 (tpp) REVERT: K 524 PHE cc_start: 0.8126 (m-80) cc_final: 0.7289 (t80) REVERT: K 527 MET cc_start: 0.8916 (tmm) cc_final: 0.8640 (tmt) REVERT: K 674 MET cc_start: 0.7991 (tpt) cc_final: 0.7703 (tpt) outliers start: 16 outliers final: 2 residues processed: 159 average time/residue: 0.7561 time to fit residues: 129.6329 Evaluate side-chains 144 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 139 time to evaluate : 0.341 ------------------------------------------------------------------------------- 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: 10.0000 chunk 141 optimal weight: 7.9990 chunk 38 optimal weight: 0.0970 chunk 55 optimal weight: 0.0470 chunk 136 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 3 optimal weight: 0.5980 chunk 27 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 overall best weight: 0.4876 ------------------------------------------------------------------------------- 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 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.098470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.066870 restraints weight = 47368.435| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.20 r_work: 0.3090 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 17932 Z= 0.150 Angle : 0.671 8.611 25470 Z= 0.377 Chirality : 0.047 0.401 2883 Planarity : 0.004 0.039 2222 Dihedral : 29.459 179.764 4719 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.45 % Allowed : 11.82 % Favored : 86.73 % 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: 0.45 (0.23), residues: 1357 helix: 1.44 (0.18), residues: 834 sheet: -2.47 (0.65), residues: 50 loop : -1.49 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 96 TYR 0.016 0.001 TYR K 499 PHE 0.018 0.002 PHE K 737 TRP 0.021 0.002 TRP K 364 HIS 0.005 0.001 HIS K 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.15 (17932) covalent geometry : angle 0.67071 / 0.38 (25470) hydrogen bonds : bond 0.05503 / 3.69 ( 932) hydrogen bonds : angle 3.58763 / 2.58 ( 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 173 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 156 time to evaluate : 0.405 Fit side-chains REVERT: A 56 LYS cc_start: 0.9443 (OUTLIER) cc_final: 0.9195 (ttpt) REVERT: A 79 LYS cc_start: 0.9339 (tttt) cc_final: 0.9096 (tttm) REVERT: D 65 ASP cc_start: 0.8815 (t70) cc_final: 0.8304 (t0) REVERT: D 90 GLU cc_start: 0.8932 (mp0) cc_final: 0.8657 (mp0) REVERT: D 102 GLU cc_start: 0.8655 (mm-30) cc_final: 0.8435 (mm-30) REVERT: E 87 SER cc_start: 0.8868 (OUTLIER) cc_final: 0.8603 (t) REVERT: F 95 ARG cc_start: 0.8710 (OUTLIER) cc_final: 0.7551 (mtp85) REVERT: G 64 GLU cc_start: 0.8681 (tm-30) cc_final: 0.8033 (tp30) REVERT: H 90 GLU cc_start: 0.8945 (mm-30) cc_final: 0.7971 (mp0) REVERT: H 102 GLU cc_start: 0.7982 (mm-30) cc_final: 0.7729 (mm-30) REVERT: K 294 CYS cc_start: 0.8143 (m) cc_final: 0.7926 (m) REVERT: K 349 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7913 (tp) REVERT: K 433 MET cc_start: 0.7427 (tmm) cc_final: 0.7094 (tmm) REVERT: K 524 PHE cc_start: 0.8208 (m-80) cc_final: 0.7467 (t80) REVERT: K 609 MET cc_start: 0.9071 (ptm) cc_final: 0.8614 (ppp) REVERT: K 674 MET cc_start: 0.7830 (tpt) cc_final: 0.7509 (tpt) outliers start: 17 outliers final: 2 residues processed: 168 average time/residue: 0.7460 time to fit residues: 135.6720 Evaluate side-chains 152 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 146 time to evaluate : 0.411 ------------------------------------------------------------------------------- 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: 5.9990 chunk 94 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 chunk 101 optimal weight: 0.4980 chunk 95 optimal weight: 10.0000 chunk 64 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 85 optimal weight: 9.9990 chunk 139 optimal weight: 6.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.097723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.065865 restraints weight = 47261.625| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 2.17 r_work: 0.3047 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17932 Z= 0.166 Angle : 0.667 8.786 25470 Z= 0.373 Chirality : 0.046 0.415 2883 Planarity : 0.004 0.038 2222 Dihedral : 29.419 179.754 4716 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 1.19 % Allowed : 14.29 % Favored : 84.52 % 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: 0.65 (0.23), residues: 1357 helix: 1.61 (0.18), residues: 834 sheet: -2.34 (0.66), residues: 50 loop : -1.43 (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 0.012 0.001 PHE K 574 TRP 0.020 0.002 TRP K 364 HIS 0.004 0.001 HIS K 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.17 (17932) covalent geometry : angle 0.66721 / 0.37 (25470) hydrogen bonds : bond 0.05681 / 3.83 ( 932) hydrogen bonds : angle 3.53650 / 2.55 ( 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 162 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 148 time to evaluate : 0.372 Fit side-chains REVERT: D 65 ASP cc_start: 0.8792 (t70) cc_final: 0.8290 (t0) REVERT: D 90 GLU cc_start: 0.9000 (mp0) cc_final: 0.8731 (mp0) REVERT: D 102 GLU cc_start: 0.8684 (mm-30) cc_final: 0.8423 (mm-30) REVERT: D 105 LYS cc_start: 0.8785 (ttmm) cc_final: 0.8408 (tttp) REVERT: E 87 SER cc_start: 0.8881 (OUTLIER) cc_final: 0.8629 (t) REVERT: F 95 ARG cc_start: 0.8713 (OUTLIER) cc_final: 0.7518 (mtp85) REVERT: G 61 GLU cc_start: 0.8379 (tp30) cc_final: 0.7892 (tp30) REVERT: G 64 GLU cc_start: 0.8691 (tm-30) cc_final: 0.8030 (tp30) REVERT: H 31 LYS cc_start: 0.8977 (ttmm) cc_final: 0.8288 (mtmm) REVERT: H 90 GLU cc_start: 0.8936 (mm-30) cc_final: 0.7861 (mp0) REVERT: H 96 ARG cc_start: 0.8861 (mpt-90) cc_final: 0.8660 (mtt-85) REVERT: H 102 GLU cc_start: 0.7976 (mm-30) cc_final: 0.7557 (mm-30) REVERT: K 294 CYS cc_start: 0.8165 (m) cc_final: 0.7952 (m) REVERT: K 433 MET cc_start: 0.7463 (tmm) cc_final: 0.7152 (tmm) REVERT: K 524 PHE cc_start: 0.8312 (m-80) cc_final: 0.7650 (t80) REVERT: K 674 MET cc_start: 0.7835 (tpt) cc_final: 0.7505 (tpt) outliers start: 14 outliers final: 4 residues processed: 157 average time/residue: 0.9100 time to fit residues: 153.9493 Evaluate side-chains 149 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 143 time to evaluate : 0.498 ------------------------------------------------------------------------------- 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 95 ARG Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain K residue 298 VAL 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: 5.9990 chunk 106 optimal weight: 5.9990 chunk 109 optimal weight: 6.9990 chunk 112 optimal weight: 5.9990 chunk 127 optimal weight: 9.9990 chunk 148 optimal weight: 6.9990 chunk 14 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 2 optimal weight: 5.9990 chunk 140 optimal weight: 2.9990 chunk 76 optimal weight: 9.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 73 ASN ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 86 ASN ** K 496 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3808 r_free = 0.3808 target = 0.095458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.062945 restraints weight = 47081.640| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.20 r_work: 0.2998 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 17932 Z= 0.295 Angle : 0.752 9.593 25470 Z= 0.408 Chirality : 0.051 0.507 2883 Planarity : 0.005 0.038 2222 Dihedral : 29.642 179.355 4716 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.55 % Allowed : 14.88 % Favored : 82.57 % 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: 0.44 (0.23), residues: 1357 helix: 1.46 (0.18), residues: 835 sheet: -2.56 (0.58), residues: 64 loop : -1.49 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 579 TYR 0.014 0.002 TYR E 54 PHE 0.021 0.002 PHE G 25 TRP 0.031 0.003 TRP K 384 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00626 / 0.30 (17932) covalent geometry : angle 0.75155 / 0.41 (25470) hydrogen bonds : bond 0.07506 / 5.10 ( 932) hydrogen bonds : angle 3.71559 / 2.67 ( 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 171 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 141 time to evaluate : 0.502 Fit side-chains REVERT: D 65 ASP cc_start: 0.8823 (t70) cc_final: 0.8336 (t0) REVERT: D 90 GLU cc_start: 0.9045 (mp0) cc_final: 0.8577 (mp0) REVERT: F 92 ARG cc_start: 0.9291 (OUTLIER) cc_final: 0.8845 (mtp-110) REVERT: F 93 GLN cc_start: 0.9040 (OUTLIER) cc_final: 0.8066 (mp10) REVERT: F 95 ARG cc_start: 0.8861 (OUTLIER) cc_final: 0.7581 (mtp85) REVERT: G 61 GLU cc_start: 0.8491 (tp30) cc_final: 0.7980 (tp30) REVERT: G 64 GLU cc_start: 0.8695 (tm-30) cc_final: 0.8056 (tp30) REVERT: H 90 GLU cc_start: 0.8962 (mm-30) cc_final: 0.7877 (mp0) REVERT: H 102 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7840 (mm-30) REVERT: K 294 CYS cc_start: 0.8315 (m) cc_final: 0.8079 (m) REVERT: K 433 MET cc_start: 0.7500 (tmm) cc_final: 0.7197 (tmm) REVERT: K 524 PHE cc_start: 0.8344 (m-80) cc_final: 0.7874 (t80) REVERT: K 674 MET cc_start: 0.7833 (tpt) cc_final: 0.7579 (tpt) outliers start: 30 outliers final: 10 residues processed: 164 average time/residue: 0.8833 time to fit residues: 156.5729 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 : 0.501 ------------------------------------------------------------------------------- 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 92 ARG 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 409 LEU Chi-restraints excluded: chain K residue 507 LEU Chi-restraints excluded: chain K residue 546 CYS Chi-restraints excluded: chain K residue 578 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 140 optimal weight: 4.9990 chunk 149 optimal weight: 3.9990 chunk 148 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 155 optimal weight: 0.0010 chunk 81 optimal weight: 8.9990 chunk 139 optimal weight: 10.0000 chunk 120 optimal weight: 0.8980 chunk 150 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 overall best weight: 1.1792 ------------------------------------------------------------------------------- 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** ** K 607 GLN ** 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 = 0.3843 r_free = 0.3843 target = 0.097423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.065394 restraints weight = 46900.061| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 2.18 r_work: 0.3037 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17932 Z= 0.159 Angle : 0.683 10.606 25470 Z= 0.374 Chirality : 0.047 0.428 2883 Planarity : 0.004 0.043 2222 Dihedral : 29.480 179.008 4716 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 1.19 % Allowed : 17.60 % Favored : 81.21 % 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: 0.72 (0.23), residues: 1357 helix: 1.74 (0.18), residues: 828 sheet: -2.46 (0.66), residues: 50 loop : -1.49 (0.27), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG K 579 TYR 0.014 0.001 TYR E 54 PHE 0.012 0.001 PHE K 574 TRP 0.030 0.002 TRP K 384 HIS 0.004 0.001 HIS K 478 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.16 (17932) covalent geometry : angle 0.68336 / 0.37 (25470) hydrogen bonds : bond 0.05533 / 3.73 ( 932) hydrogen bonds : angle 3.47269 / 2.50 ( 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 165 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 151 time to evaluate : 0.427 Fit side-chains revert: symmetry clash REVERT: C 92 GLU cc_start: 0.8782 (mm-30) cc_final: 0.8508 (mm-30) REVERT: D 65 ASP cc_start: 0.8789 (t70) cc_final: 0.8310 (t0) REVERT: D 90 GLU cc_start: 0.8995 (mp0) cc_final: 0.8658 (mp0) REVERT: D 105 LYS cc_start: 0.8756 (ttmm) cc_final: 0.8399 (tttp) REVERT: E 87 SER cc_start: 0.8902 (OUTLIER) cc_final: 0.8666 (t) REVERT: F 93 GLN cc_start: 0.9018 (OUTLIER) cc_final: 0.8071 (mp10) REVERT: F 95 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.7487 (mtp85) REVERT: G 61 GLU cc_start: 0.8430 (tp30) cc_final: 0.7907 (tp30) REVERT: G 64 GLU cc_start: 0.8655 (tm-30) cc_final: 0.8031 (tp30) REVERT: H 31 LYS cc_start: 0.9002 (ttmm) cc_final: 0.8541 (mtmm) REVERT: H 90 GLU cc_start: 0.8966 (mm-30) cc_final: 0.7863 (mp0) REVERT: H 102 GLU cc_start: 0.8105 (mm-30) cc_final: 0.7822 (mm-30) REVERT: K 294 CYS cc_start: 0.8261 (m) cc_final: 0.8020 (m) REVERT: K 433 MET cc_start: 0.7495 (tmm) cc_final: 0.7181 (tmm) REVERT: K 524 PHE cc_start: 0.8417 (m-80) cc_final: 0.7845 (t80) REVERT: K 609 MET cc_start: 0.8983 (ptm) cc_final: 0.8514 (ppp) REVERT: K 674 MET cc_start: 0.7750 (tpt) cc_final: 0.7480 (tpt) outliers start: 14 outliers final: 5 residues processed: 159 average time/residue: 0.8287 time to fit residues: 142.1262 Evaluate side-chains 152 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 144 time to evaluate : 0.443 ------------------------------------------------------------------------------- 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 344 THR 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: 2.9990 chunk 7 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 86 optimal weight: 20.0000 chunk 137 optimal weight: 20.0000 chunk 117 optimal weight: 3.9990 chunk 98 optimal weight: 9.9990 chunk 9 optimal weight: 7.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- 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** ** K 607 GLN ** 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 = 0.3817 r_free = 0.3817 target = 0.095996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.063615 restraints weight = 46731.378| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 2.19 r_work: 0.3014 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 17932 Z= 0.264 Angle : 0.737 11.622 25470 Z= 0.398 Chirality : 0.050 0.479 2883 Planarity : 0.004 0.038 2222 Dihedral : 29.538 179.388 4716 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 1.96 % Allowed : 17.18 % Favored : 80.87 % 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: 0.57 (0.23), residues: 1357 helix: 1.64 (0.18), residues: 829 sheet: -2.49 (0.61), residues: 64 loop : -1.54 (0.28), residues: 464 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 0.014 0.002 PHE G 25 TRP 0.029 0.002 TRP K 384 HIS 0.004 0.001 HIS F 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00558 / 0.26 (17932) covalent geometry : angle 0.73656 / 0.40 (25470) hydrogen bonds : bond 0.06847 / 4.64 ( 932) hydrogen bonds : angle 3.61950 / 2.60 ( 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 168 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 145 time to evaluate : 0.316 Fit side-chains REVERT: D 65 ASP cc_start: 0.8835 (t70) cc_final: 0.8343 (t0) REVERT: D 90 GLU cc_start: 0.9050 (mp0) cc_final: 0.8565 (mp0) REVERT: D 105 LYS cc_start: 0.8873 (ttmm) cc_final: 0.8495 (tttp) REVERT: F 93 GLN cc_start: 0.9027 (OUTLIER) cc_final: 0.8092 (mp10) REVERT: F 95 ARG cc_start: 0.8824 (OUTLIER) cc_final: 0.7576 (mtp85) REVERT: G 61 GLU cc_start: 0.8488 (tp30) cc_final: 0.7954 (tp30) REVERT: G 64 GLU cc_start: 0.8655 (tm-30) cc_final: 0.8067 (tp30) REVERT: H 31 LYS cc_start: 0.9089 (ttmm) cc_final: 0.8596 (mtmm) REVERT: H 90 GLU cc_start: 0.8965 (mm-30) cc_final: 0.7897 (mp0) REVERT: H 102 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7888 (mm-30) REVERT: K 294 CYS cc_start: 0.8331 (m) cc_final: 0.8085 (m) REVERT: K 433 MET cc_start: 0.7507 (tmm) cc_final: 0.7180 (tmm) REVERT: K 524 PHE cc_start: 0.8362 (m-80) cc_final: 0.7846 (t80) REVERT: K 609 MET cc_start: 0.9006 (ptm) cc_final: 0.8523 (ppp) REVERT: K 674 MET cc_start: 0.7732 (tpt) cc_final: 0.7442 (tpt) outliers start: 23 outliers final: 13 residues processed: 160 average time/residue: 0.8325 time to fit residues: 143.8083 Evaluate side-chains 157 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 142 time to evaluate : 0.451 ------------------------------------------------------------------------------- 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 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 401 LEU Chi-restraints excluded: chain K residue 409 LEU Chi-restraints excluded: chain K residue 546 CYS Chi-restraints excluded: chain K residue 578 THR 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: 7.9990 chunk 87 optimal weight: 20.0000 chunk 143 optimal weight: 0.9990 chunk 139 optimal weight: 6.9990 chunk 51 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 130 optimal weight: 7.9990 chunk 16 optimal weight: 0.1980 chunk 58 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 106 HIS 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** ** 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 = 0.3850 r_free = 0.3850 target = 0.097785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.065831 restraints weight = 47139.033| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.22 r_work: 0.3074 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 17932 Z= 0.150 Angle : 0.684 11.558 25470 Z= 0.375 Chirality : 0.046 0.401 2883 Planarity : 0.004 0.055 2222 Dihedral : 29.379 179.358 4716 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 1.70 % Allowed : 18.20 % 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: 0.74 (0.23), residues: 1357 helix: 1.76 (0.18), residues: 835 sheet: -2.61 (0.64), residues: 57 loop : -1.49 (0.28), residues: 465 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 0.013 0.001 PHE K 574 TRP 0.035 0.002 TRP K 384 HIS 0.003 0.001 HIS K 478 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.15 (17932) covalent geometry : angle 0.68429 / 0.37 (25470) hydrogen bonds : bond 0.05283 / 3.56 ( 932) hydrogen bonds : angle 3.42745 / 2.47 ( 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: 20 poor density : 147 time to evaluate : 0.526 Fit side-chains REVERT: C 92 GLU cc_start: 0.8774 (mm-30) cc_final: 0.8356 (mm-30) REVERT: D 65 ASP cc_start: 0.8806 (t70) cc_final: 0.8333 (t0) REVERT: D 90 GLU cc_start: 0.8951 (mp0) cc_final: 0.8719 (mp0) REVERT: D 105 LYS cc_start: 0.8772 (ttmm) cc_final: 0.8368 (tttp) REVERT: E 87 SER cc_start: 0.8888 (OUTLIER) cc_final: 0.8631 (t) REVERT: F 84 MET cc_start: 0.9424 (mmm) cc_final: 0.9172 (mmp) REVERT: F 93 GLN cc_start: 0.9009 (OUTLIER) cc_final: 0.8068 (mp10) REVERT: F 95 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.7496 (mtp85) REVERT: G 61 GLU cc_start: 0.8444 (tp30) cc_final: 0.7920 (tp30) REVERT: G 64 GLU cc_start: 0.8630 (tm-30) cc_final: 0.8045 (tp30) REVERT: H 31 LYS cc_start: 0.9004 (ttmm) cc_final: 0.8591 (mtmm) REVERT: H 65 ASP cc_start: 0.8932 (t0) cc_final: 0.8720 (t0) REVERT: H 90 GLU cc_start: 0.8968 (mm-30) cc_final: 0.7883 (mp0) REVERT: H 102 GLU cc_start: 0.8103 (mm-30) cc_final: 0.7787 (mm-30) REVERT: K 294 CYS cc_start: 0.8270 (m) cc_final: 0.8024 (m) REVERT: K 433 MET cc_start: 0.7350 (OUTLIER) cc_final: 0.6949 (tmm) REVERT: K 524 PHE cc_start: 0.8318 (m-80) cc_final: 0.7857 (t80) REVERT: K 609 MET cc_start: 0.8968 (ptm) cc_final: 0.8480 (ppp) REVERT: K 674 MET cc_start: 0.7765 (tpt) cc_final: 0.7462 (tpt) outliers start: 20 outliers final: 9 residues processed: 159 average time/residue: 0.8576 time to fit residues: 146.9231 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 : 0.404 ------------------------------------------------------------------------------- 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 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 409 LEU Chi-restraints excluded: chain K residue 433 MET Chi-restraints excluded: chain K residue 546 CYS Chi-restraints excluded: chain K residue 578 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 114 optimal weight: 0.0070 chunk 90 optimal weight: 10.0000 chunk 7 optimal weight: 0.9980 chunk 121 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 148 optimal weight: 7.9990 chunk 22 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 93 optimal weight: 9.9990 chunk 4 optimal weight: 0.6980 overall best weight: 0.7000 ------------------------------------------------------------------------------- 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** K 607 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.098326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.066422 restraints weight = 47101.259| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.20 r_work: 0.3088 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17932 Z= 0.143 Angle : 0.672 12.429 25470 Z= 0.369 Chirality : 0.045 0.392 2883 Planarity : 0.004 0.071 2222 Dihedral : 29.271 179.322 4716 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 1.45 % Allowed : 18.79 % Favored : 79.76 % 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: 0.92 (0.24), residues: 1357 helix: 1.90 (0.18), residues: 835 sheet: -2.52 (0.64), residues: 57 loop : -1.41 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG K 579 TYR 0.012 0.001 TYR K 499 PHE 0.012 0.001 PHE K 574 TRP 0.038 0.003 TRP K 384 HIS 0.004 0.001 HIS K 478 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.14 (17932) covalent geometry : angle 0.67212 / 0.37 (25470) hydrogen bonds : bond 0.05105 / 3.43 ( 932) hydrogen bonds : angle 3.35849 / 2.42 ( 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 163 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 146 time to evaluate : 0.544 Fit side-chains REVERT: C 111 ILE cc_start: 0.8825 (pt) cc_final: 0.8591 (mt) REVERT: D 65 ASP cc_start: 0.8776 (t70) cc_final: 0.8307 (t0) REVERT: D 90 GLU cc_start: 0.8980 (mp0) cc_final: 0.8498 (mp0) REVERT: D 105 LYS cc_start: 0.8784 (ttmm) cc_final: 0.8399 (tttp) REVERT: E 87 SER cc_start: 0.8864 (OUTLIER) cc_final: 0.8600 (t) REVERT: F 84 MET cc_start: 0.9423 (mmm) cc_final: 0.9181 (mmp) REVERT: F 93 GLN cc_start: 0.8993 (OUTLIER) cc_final: 0.8049 (mp10) REVERT: F 95 ARG cc_start: 0.8782 (OUTLIER) cc_final: 0.7554 (mtp85) REVERT: G 61 GLU cc_start: 0.8418 (tp30) cc_final: 0.7875 (tp30) REVERT: G 64 GLU cc_start: 0.8645 (tm-30) cc_final: 0.8017 (tp30) REVERT: H 31 LYS cc_start: 0.8979 (ttmm) cc_final: 0.8550 (mtmm) REVERT: H 65 ASP cc_start: 0.8927 (t0) cc_final: 0.8687 (t0) REVERT: H 90 GLU cc_start: 0.8958 (mm-30) cc_final: 0.7869 (mp0) REVERT: K 294 CYS cc_start: 0.8265 (m) cc_final: 0.8018 (m) REVERT: K 433 MET cc_start: 0.7327 (tmm) cc_final: 0.6922 (tmm) REVERT: K 524 PHE cc_start: 0.8326 (m-80) cc_final: 0.7855 (t80) REVERT: K 609 MET cc_start: 0.8957 (ptm) cc_final: 0.8463 (ppp) REVERT: K 674 MET cc_start: 0.7732 (tpt) cc_final: 0.7424 (tpt) outliers start: 17 outliers final: 10 residues processed: 156 average time/residue: 0.7982 time to fit residues: 134.8515 Evaluate side-chains 156 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 143 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain B residue 24 ASP 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 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 409 LEU 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: 4.9990 chunk 18 optimal weight: 0.0980 chunk 118 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 74 optimal weight: 10.0000 chunk 16 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 93 optimal weight: 9.9990 chunk 40 optimal weight: 2.9990 chunk 90 optimal weight: 10.0000 chunk 0 optimal weight: 4.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- 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 = 0.3835 r_free = 0.3835 target = 0.096936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.065050 restraints weight = 46751.483| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.14 r_work: 0.3046 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.2035 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= 0.227 Angle : 0.719 12.765 25470 Z= 0.388 Chirality : 0.047 0.441 2883 Planarity : 0.004 0.065 2222 Dihedral : 29.362 179.027 4716 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 1.36 % Allowed : 19.13 % 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: 0.81 (0.24), residues: 1357 helix: 1.82 (0.18), residues: 835 sheet: -2.60 (0.63), residues: 57 loop : -1.48 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG K 579 TYR 0.012 0.001 TYR E 54 PHE 0.011 0.001 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 0.00476 / 0.23 (17932) covalent geometry : angle 0.71861 / 0.39 (25470) hydrogen bonds : bond 0.06073 / 4.11 ( 932) hydrogen bonds : angle 3.47195 / 2.51 ( 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: 16 poor density : 145 time to evaluate : 0.464 Fit side-chains REVERT: C 92 GLU cc_start: 0.8772 (mm-30) cc_final: 0.8517 (mm-30) REVERT: C 111 ILE cc_start: 0.8896 (pt) cc_final: 0.8595 (mt) REVERT: D 65 ASP cc_start: 0.8818 (t70) cc_final: 0.8336 (t0) REVERT: D 90 GLU cc_start: 0.9039 (mp0) cc_final: 0.8567 (mp0) REVERT: D 105 LYS cc_start: 0.8798 (ttmm) cc_final: 0.8410 (tttp) REVERT: E 87 SER cc_start: 0.8941 (OUTLIER) cc_final: 0.8694 (t) REVERT: F 93 GLN cc_start: 0.9013 (OUTLIER) cc_final: 0.8069 (mp10) REVERT: F 95 ARG cc_start: 0.8788 (OUTLIER) cc_final: 0.7513 (mtp85) REVERT: G 61 GLU cc_start: 0.8487 (tp30) cc_final: 0.7948 (tp30) REVERT: G 64 GLU cc_start: 0.8638 (tm-30) cc_final: 0.8025 (tp30) REVERT: H 90 GLU cc_start: 0.8950 (mm-30) cc_final: 0.7804 (mp0) REVERT: H 102 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7762 (mm-30) REVERT: K 294 CYS cc_start: 0.8323 (m) cc_final: 0.8072 (m) REVERT: K 433 MET cc_start: 0.7318 (OUTLIER) cc_final: 0.6910 (tmm) REVERT: K 524 PHE cc_start: 0.8368 (m-80) cc_final: 0.7923 (t80) REVERT: K 609 MET cc_start: 0.8984 (ptm) cc_final: 0.8487 (ppp) REVERT: K 674 MET cc_start: 0.7768 (tpt) cc_final: 0.7451 (tpt) outliers start: 16 outliers final: 10 residues processed: 153 average time/residue: 0.8301 time to fit residues: 137.0851 Evaluate side-chains 158 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 144 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU 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 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 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: 0.9990 chunk 83 optimal weight: 10.0000 chunk 37 optimal weight: 0.8980 chunk 158 optimal weight: 6.9990 chunk 151 optimal weight: 9.9990 chunk 86 optimal weight: 20.0000 chunk 113 optimal weight: 6.9990 chunk 115 optimal weight: 0.7980 chunk 146 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3851 r_free = 0.3851 target = 0.097867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.065925 restraints weight = 47083.477| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.19 r_work: 0.3072 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 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 0.046 17932 Z= 0.147 Angle : 0.688 12.962 25470 Z= 0.373 Chirality : 0.046 0.407 2883 Planarity : 0.004 0.064 2222 Dihedral : 29.345 179.272 4716 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 1.28 % Allowed : 18.96 % Favored : 79.76 % 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: 0.89 (0.24), residues: 1357 helix: 1.87 (0.18), residues: 835 sheet: -2.48 (0.64), residues: 57 loop : -1.44 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG K 579 TYR 0.012 0.001 TYR K 499 PHE 0.011 0.001 PHE K 381 TRP 0.040 0.003 TRP K 384 HIS 0.005 0.001 HIS H 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.15 (17932) covalent geometry : angle 0.68820 / 0.37 (25470) hydrogen bonds : bond 0.05404 / 3.64 ( 932) hydrogen bonds : angle 3.39679 / 2.45 ( 2404) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5194.81 seconds wall clock time: 89 minutes 12.69 seconds (5352.69 seconds total)