Starting phenix.real_space_refine on Wed Feb 4 08:46:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kb8_62220/02_2026/9kb8_62220.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kb8_62220/02_2026/9kb8_62220.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9kb8_62220/02_2026/9kb8_62220.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kb8_62220/02_2026/9kb8_62220.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9kb8_62220/02_2026/9kb8_62220.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kb8_62220/02_2026/9kb8_62220.map" } resolution = 3.25 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= 0.001 sd= 0.017 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: 4 Type Number sf(0) Gaussians S 59 5.16 5 C 6018 2.51 5 N 1579 2.21 5 O 1740 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9396 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 1494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1494 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 11, 'TRANS': 179} Chain: "A" Number of atoms: 5858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 751, 5858 Classifications: {'peptide': 751} Link IDs: {'PCIS': 2, 'PTRANS': 35, 'TRANS': 713} Chain breaks: 1 Chain: "C" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 826 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 4, 'TRANS': 99} Chain: "D" Number of atoms: 1162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1162 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 8, 'TRANS': 142} Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 2.17, per 1000 atoms: 0.23 Number of scatterers: 9396 At special positions: 0 Unit cell: (94.62, 92.13, 156.87, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 59 16.00 O 1740 8.00 N 1579 7.00 C 6018 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 29 " - pdb=" SG CYS A 35 " distance=2.03 Simple disulfide: pdb=" SG CYS A 33 " - pdb=" SG CYS A 43 " distance=2.03 Simple disulfide: pdb=" SG CYS A 339 " - pdb=" SG CYS A 364 " distance=2.03 Simple disulfide: pdb=" SG CYS A 470 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 471 " - pdb=" SG CYS A 532 " distance=2.03 Simple disulfide: pdb=" SG CYS A 618 " - pdb=" SG CYS A 693 " distance=2.03 Simple disulfide: pdb=" SG CYS C 40 " - pdb=" SG CYS C 46 " distance=2.03 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 52 " distance=2.03 Simple disulfide: pdb=" SG CYS C 55 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 78 " - pdb=" SG CYS C 93 " distance=2.03 Simple disulfide: pdb=" SG CYS C 96 " - pdb=" SG CYS C 104 " distance=2.03 Simple disulfide: pdb=" SG CYS C 101 " - pdb=" SG CYS C 110 " distance=2.03 Simple disulfide: pdb=" SG CYS C 113 " - pdb=" SG CYS C 124 " distance=2.03 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 141 " distance=2.03 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 Links applied NAG-ASN " NAG A1001 " - " ASN A 68 " " NAG A1002 " - " ASN A 199 " " NAG A1003 " - " ASN A 294 " " NAG A1004 " - " ASN A 314 " Time building additional restraints: 0.47 Conformation dependent library (CDL) restraints added in 351.2 milliseconds 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2244 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 12 sheets defined 35.5% alpha, 16.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'B' and resid 102 through 107 removed outlier: 3.798A pdb=" N LEU B 106 " --> pdb=" O PRO B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 114 removed outlier: 4.094A pdb=" N GLU B 113 " --> pdb=" O ASN B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 132 Processing helix chain 'B' and resid 138 through 149 Processing helix chain 'B' and resid 162 through 170 removed outlier: 4.192A pdb=" N ASP B 166 " --> pdb=" O PRO B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 198 Processing helix chain 'B' and resid 214 through 247 Processing helix chain 'A' and resid 123 through 128 removed outlier: 3.542A pdb=" N ARG A 126 " --> pdb=" O GLU A 123 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLY A 127 " --> pdb=" O ALA A 124 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU A 128 " --> pdb=" O ILE A 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 123 through 128' Processing helix chain 'A' and resid 169 through 174 Processing helix chain 'A' and resid 241 through 247 Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 452 through 456 removed outlier: 3.830A pdb=" N ASP A 455 " --> pdb=" O ALA A 452 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N PHE A 456 " --> pdb=" O ALA A 453 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 452 through 456' Processing helix chain 'A' and resid 466 through 471 removed outlier: 3.623A pdb=" N CYS A 471 " --> pdb=" O TYR A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 565 Processing helix chain 'A' and resid 571 through 601 removed outlier: 3.769A pdb=" N PHE A 586 " --> pdb=" O VAL A 582 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N MET A 587 " --> pdb=" O SER A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 615 removed outlier: 3.882A pdb=" N PHE A 608 " --> pdb=" O ARG A 604 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ILE A 610 " --> pdb=" O ALA A 606 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N TRP A 611 " --> pdb=" O GLU A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 653 removed outlier: 4.091A pdb=" N LYS A 619 " --> pdb=" O GLY A 615 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N MET A 651 " --> pdb=" O ALA A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 683 Proline residue: A 680 - end of helix removed outlier: 3.747A pdb=" N HIS A 683 " --> pdb=" O PHE A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 732 removed outlier: 3.607A pdb=" N GLY A 705 " --> pdb=" O THR A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 738 removed outlier: 3.618A pdb=" N LEU A 737 " --> pdb=" O LYS A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 769 removed outlier: 4.072A pdb=" N MET A 745 " --> pdb=" O SER A 741 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N CYS A 761 " --> pdb=" O CYS A 757 " (cutoff:3.500A) Proline residue: A 762 - end of helix Processing helix chain 'A' and resid 770 through 772 No H-bonds generated for 'chain 'A' and resid 770 through 772' Processing helix chain 'A' and resid 778 through 790 removed outlier: 3.865A pdb=" N MET A 782 " --> pdb=" O SER A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 791 through 805 Proline residue: A 798 - end of helix removed outlier: 3.741A pdb=" N TYR A 801 " --> pdb=" O ASN A 797 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 822 removed outlier: 3.971A pdb=" N LYS A 809 " --> pdb=" O ASN A 805 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU A 810 " --> pdb=" O PRO A 806 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 107 removed outlier: 3.780A pdb=" N LEU D 106 " --> pdb=" O PRO D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 115 removed outlier: 4.026A pdb=" N GLU D 113 " --> pdb=" O ASN D 110 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LEU D 115 " --> pdb=" O GLU D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 132 Processing helix chain 'D' and resid 138 through 149 Processing helix chain 'D' and resid 163 through 170 Processing helix chain 'D' and resid 185 through 198 Processing sheet with id=AA1, first strand: chain 'B' and resid 58 through 68 removed outlier: 6.455A pdb=" N TRP B 120 " --> pdb=" O ALA B 153 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N ILE B 155 " --> pdb=" O TRP B 120 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N GLY B 122 " --> pdb=" O ILE B 155 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ASP B 157 " --> pdb=" O GLY B 122 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N VAL B 124 " --> pdb=" O ASP B 157 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N LYS B 125 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N ALA B 201 " --> pdb=" O ILE B 98 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 34 through 35 Processing sheet with id=AA3, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'A' and resid 191 through 192 Processing sheet with id=AA5, first strand: chain 'A' and resid 262 through 263 Processing sheet with id=AA6, first strand: chain 'A' and resid 300 through 304 removed outlier: 6.229A pdb=" N LEU A 324 " --> pdb=" O ASP A 349 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU A 462 " --> pdb=" O THR A 523 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 43 through 47 removed outlier: 6.619A pdb=" N CYS C 43 " --> pdb=" O CYS C 55 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N CYS C 55 " --> pdb=" O CYS C 43 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N SER C 45 " --> pdb=" O SER C 53 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 69 through 75 removed outlier: 3.574A pdb=" N CYS C 93 " --> pdb=" O PHE C 61 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N LEU C 63 " --> pdb=" O CYS C 93 " (cutoff:3.500A) removed outlier: 9.220A pdb=" N ARG C 95 " --> pdb=" O LEU C 63 " (cutoff:3.500A) removed outlier: 14.508A pdb=" N ARG C 65 " --> pdb=" O ARG C 95 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 101 through 106 removed outlier: 6.937A pdb=" N CYS C 101 " --> pdb=" O CYS C 113 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N CYS C 113 " --> pdb=" O CYS C 101 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N SER C 103 " --> pdb=" O THR C 111 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N PHE C 109 " --> pdb=" O PHE C 105 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 118 through 120 Processing sheet with id=AB2, first strand: chain 'C' and resid 133 through 135 Processing sheet with id=AB3, first strand: chain 'D' and resid 77 through 80 removed outlier: 6.367A pdb=" N TRP D 120 " --> pdb=" O ALA D 153 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N ILE D 155 " --> pdb=" O TRP D 120 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N GLY D 122 " --> pdb=" O ILE D 155 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ASP D 157 " --> pdb=" O GLY D 122 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N VAL D 124 " --> pdb=" O ASP D 157 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N VAL D 154 " --> pdb=" O VAL D 181 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N VAL D 183 " --> pdb=" O VAL D 154 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N PHE D 156 " --> pdb=" O VAL D 183 " (cutoff:3.500A) 392 hydrogen bonds defined for protein. 1083 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.23 Time building geometry restraints manager: 0.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3035 1.34 - 1.46: 2077 1.46 - 1.58: 4412 1.58 - 1.70: 0 1.70 - 1.82: 77 Bond restraints: 9601 Sorted by residual: bond pdb=" CA GLU C 127 " pdb=" CB GLU C 127 " ideal model delta sigma weight residual 1.533 1.566 -0.032 1.72e-02 3.38e+03 3.56e+00 bond pdb=" CB LYS B 134 " pdb=" CG LYS B 134 " ideal model delta sigma weight residual 1.520 1.562 -0.042 3.00e-02 1.11e+03 1.96e+00 bond pdb=" CB GLU C 127 " pdb=" CG GLU C 127 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.62e+00 bond pdb=" CB GLN C 57 " pdb=" CG GLN C 57 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.60e+00 bond pdb=" CB ASP B 166 " pdb=" CG ASP B 166 " ideal model delta sigma weight residual 1.516 1.548 -0.032 2.50e-02 1.60e+03 1.59e+00 ... (remaining 9596 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 12786 1.83 - 3.65: 177 3.65 - 5.48: 38 5.48 - 7.30: 11 7.30 - 9.13: 7 Bond angle restraints: 13019 Sorted by residual: angle pdb=" CA LYS B 134 " pdb=" CB LYS B 134 " pdb=" CG LYS B 134 " ideal model delta sigma weight residual 114.10 121.35 -7.25 2.00e+00 2.50e-01 1.31e+01 angle pdb=" CA GLN C 57 " pdb=" CB GLN C 57 " pdb=" CG GLN C 57 " ideal model delta sigma weight residual 114.10 121.05 -6.95 2.00e+00 2.50e-01 1.21e+01 angle pdb=" CA GLU C 127 " pdb=" CB GLU C 127 " pdb=" CG GLU C 127 " ideal model delta sigma weight residual 114.10 120.90 -6.80 2.00e+00 2.50e-01 1.15e+01 angle pdb=" CB GLU C 127 " pdb=" CG GLU C 127 " pdb=" CD GLU C 127 " ideal model delta sigma weight residual 112.60 117.78 -5.18 1.70e+00 3.46e-01 9.27e+00 angle pdb=" CB MET B 192 " pdb=" CG MET B 192 " pdb=" SD MET B 192 " ideal model delta sigma weight residual 112.70 121.83 -9.13 3.00e+00 1.11e-01 9.26e+00 ... (remaining 13014 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.33: 5098 17.33 - 34.66: 593 34.66 - 51.98: 142 51.98 - 69.31: 20 69.31 - 86.64: 5 Dihedral angle restraints: 5858 sinusoidal: 2395 harmonic: 3463 Sorted by residual: dihedral pdb=" CB CYS A 29 " pdb=" SG CYS A 29 " pdb=" SG CYS A 35 " pdb=" CB CYS A 35 " ideal model delta sinusoidal sigma weight residual -86.00 -19.62 -66.38 1 1.00e+01 1.00e-02 5.75e+01 dihedral pdb=" CB CYS A 470 " pdb=" SG CYS A 470 " pdb=" SG CYS A 522 " pdb=" CB CYS A 522 " ideal model delta sinusoidal sigma weight residual 93.00 151.72 -58.72 1 1.00e+01 1.00e-02 4.62e+01 dihedral pdb=" CB CYS A 618 " pdb=" SG CYS A 618 " pdb=" SG CYS A 693 " pdb=" CB CYS A 693 " ideal model delta sinusoidal sigma weight residual -86.00 -126.65 40.65 1 1.00e+01 1.00e-02 2.32e+01 ... (remaining 5855 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1004 0.036 - 0.072: 359 0.072 - 0.108: 108 0.108 - 0.143: 27 0.143 - 0.179: 3 Chirality restraints: 1501 Sorted by residual: chirality pdb=" C1 NAG A1003 " pdb=" ND2 ASN A 294 " pdb=" C2 NAG A1003 " pdb=" O5 NAG A1003 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 8.03e-01 chirality pdb=" CA THR A 701 " pdb=" N THR A 701 " pdb=" C THR A 701 " pdb=" CB THR A 701 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.16 2.00e-01 2.50e+01 6.49e-01 chirality pdb=" CB THR A 595 " pdb=" CA THR A 595 " pdb=" OG1 THR A 595 " pdb=" CG2 THR A 595 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.85e-01 ... (remaining 1498 not shown) Planarity restraints: 1671 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS C 128 " -0.021 5.00e-02 4.00e+02 3.27e-02 1.71e+00 pdb=" N PRO C 129 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO C 129 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 129 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 134 " 0.021 5.00e-02 4.00e+02 3.16e-02 1.60e+00 pdb=" N PRO D 135 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO D 135 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO D 135 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 97 " -0.019 5.00e-02 4.00e+02 2.85e-02 1.30e+00 pdb=" N PRO A 98 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO A 98 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 98 " -0.016 5.00e-02 4.00e+02 ... (remaining 1668 not shown) Histogram of nonbonded interaction distances: 2.52 - 3.00: 5094 3.00 - 3.47: 9491 3.47 - 3.95: 14720 3.95 - 4.42: 17011 4.42 - 4.90: 27653 Nonbonded interactions: 73969 Sorted by model distance: nonbonded pdb=" N GLN C 57 " pdb=" OE1 GLN C 57 " model vdw 2.522 3.120 nonbonded pdb=" N GLU D 130 " pdb=" OE1 GLU D 130 " model vdw 2.536 3.120 nonbonded pdb=" O ASP D 132 " pdb=" OD1 ASP D 132 " model vdw 2.539 3.040 nonbonded pdb=" N ASP D 174 " pdb=" OD1 ASP D 174 " model vdw 2.552 3.120 nonbonded pdb=" N GLU D 117 " pdb=" OE1 GLU D 117 " model vdw 2.563 3.120 ... (remaining 73964 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.360 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.560 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 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 : 0.003 0.042 9619 Z= 0.129 Angle : 0.608 9.129 13059 Z= 0.306 Chirality : 0.042 0.179 1501 Planarity : 0.003 0.035 1667 Dihedral : 15.175 86.639 3572 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.63 % Allowed : 19.39 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.59 (0.25), residues: 1187 helix: 1.88 (0.28), residues: 352 sheet: -0.42 (0.37), residues: 222 loop : -0.09 (0.26), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 54 TYR 0.009 0.001 TYR D 116 PHE 0.016 0.001 PHE A 765 TRP 0.008 0.001 TRP A 159 HIS 0.004 0.001 HIS A 293 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 9601) covalent geometry : angle 0.60670 (13019) SS BOND : bond 0.00164 ( 14) SS BOND : angle 0.44352 ( 28) hydrogen bonds : bond 0.16735 ( 392) hydrogen bonds : angle 6.63518 ( 1083) link_NAG-ASN : bond 0.00231 ( 4) link_NAG-ASN : angle 1.66949 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 131 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 66 PHE cc_start: 0.8163 (OUTLIER) cc_final: 0.7898 (m-80) REVERT: B 187 ASP cc_start: 0.8632 (m-30) cc_final: 0.8291 (m-30) REVERT: A 66 MET cc_start: 0.8703 (mmt) cc_final: 0.7582 (mmt) REVERT: A 403 GLU cc_start: 0.8839 (OUTLIER) cc_final: 0.8196 (tm-30) REVERT: A 521 HIS cc_start: 0.8326 (m-70) cc_final: 0.7838 (t70) REVERT: A 596 PHE cc_start: 0.8997 (OUTLIER) cc_final: 0.8706 (m-10) REVERT: A 637 MET cc_start: 0.9466 (ttm) cc_final: 0.9018 (tpp) REVERT: C 95 ARG cc_start: 0.9183 (tpp80) cc_final: 0.8904 (ttm-80) REVERT: C 102 ASP cc_start: 0.8630 (m-30) cc_final: 0.8246 (m-30) REVERT: C 140 GLU cc_start: 0.8528 (pm20) cc_final: 0.7874 (pm20) REVERT: D 62 GLU cc_start: 0.8666 (mm-30) cc_final: 0.8065 (tt0) REVERT: D 137 LEU cc_start: 0.9340 (mt) cc_final: 0.9113 (mt) REVERT: D 144 LYS cc_start: 0.9601 (tptm) cc_final: 0.9321 (tptm) REVERT: D 163 GLU cc_start: 0.9068 (mp0) cc_final: 0.8792 (mp0) REVERT: D 197 LYS cc_start: 0.9292 (mmtp) cc_final: 0.9069 (mmmm) outliers start: 17 outliers final: 11 residues processed: 141 average time/residue: 0.1052 time to fit residues: 19.9614 Evaluate side-chains 134 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 120 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 PHE Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 596 PHE Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 725 TYR Chi-restraints excluded: chain A residue 729 TYR Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 756 ASN Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain D residue 66 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 117 optimal weight: 4.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 244 GLN D 148 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.085134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.058344 restraints weight = 23592.515| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 3.90 r_work: 0.2669 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 9619 Z= 0.298 Angle : 0.641 7.470 13059 Z= 0.326 Chirality : 0.045 0.214 1501 Planarity : 0.004 0.031 1667 Dihedral : 6.116 57.509 1380 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 3.65 % Allowed : 17.85 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.49 (0.25), residues: 1187 helix: 1.75 (0.27), residues: 358 sheet: -0.53 (0.37), residues: 225 loop : -0.12 (0.26), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 54 TYR 0.010 0.001 TYR D 182 PHE 0.019 0.002 PHE A 255 TRP 0.015 0.001 TRP A 159 HIS 0.005 0.001 HIS D 102 Details of bonding type rmsd covalent geometry : bond 0.00691 ( 9601) covalent geometry : angle 0.63883 (13019) SS BOND : bond 0.00424 ( 14) SS BOND : angle 0.63139 ( 28) hydrogen bonds : bond 0.04680 ( 392) hydrogen bonds : angle 5.17022 ( 1083) link_NAG-ASN : bond 0.00625 ( 4) link_NAG-ASN : angle 2.00785 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 115 time to evaluate : 0.374 Fit side-chains revert: symmetry clash REVERT: B 115 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8417 (mm) REVERT: B 187 ASP cc_start: 0.8687 (m-30) cc_final: 0.8394 (m-30) REVERT: A 66 MET cc_start: 0.8821 (OUTLIER) cc_final: 0.7520 (mmt) REVERT: A 271 ASN cc_start: 0.9597 (OUTLIER) cc_final: 0.9364 (m110) REVERT: A 442 VAL cc_start: 0.9343 (OUTLIER) cc_final: 0.9014 (m) REVERT: A 557 LEU cc_start: 0.9528 (mm) cc_final: 0.9084 (mm) REVERT: A 768 PHE cc_start: 0.8368 (OUTLIER) cc_final: 0.7800 (m-10) REVERT: C 95 ARG cc_start: 0.9205 (tpp80) cc_final: 0.8902 (tpp80) REVERT: C 97 ARG cc_start: 0.8966 (OUTLIER) cc_final: 0.8762 (mmp-170) REVERT: C 102 ASP cc_start: 0.8645 (m-30) cc_final: 0.8046 (m-30) REVERT: C 136 GLU cc_start: 0.8881 (mm-30) cc_final: 0.8632 (mm-30) REVERT: C 140 GLU cc_start: 0.8489 (pm20) cc_final: 0.7875 (pm20) REVERT: D 62 GLU cc_start: 0.8668 (mm-30) cc_final: 0.7980 (tt0) REVERT: D 163 GLU cc_start: 0.9054 (mp0) cc_final: 0.8739 (mp0) outliers start: 38 outliers final: 21 residues processed: 147 average time/residue: 0.1065 time to fit residues: 21.4691 Evaluate side-chains 136 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 109 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 PHE Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 91 ASN Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 725 TYR Chi-restraints excluded: chain A residue 729 TYR Chi-restraints excluded: chain A residue 768 PHE Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 97 ARG Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 200 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 67 optimal weight: 0.7980 chunk 78 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 51 optimal weight: 0.5980 chunk 16 optimal weight: 9.9990 chunk 7 optimal weight: 0.0570 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 584 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 = 0.3496 r_free = 0.3496 target = 0.088147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.061293 restraints weight = 23198.869| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 3.97 r_work: 0.2728 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.0962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9619 Z= 0.119 Angle : 0.532 7.403 13059 Z= 0.266 Chirality : 0.042 0.171 1501 Planarity : 0.003 0.038 1667 Dihedral : 4.608 54.548 1362 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.69 % Allowed : 18.91 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.67 (0.25), residues: 1187 helix: 1.94 (0.28), residues: 358 sheet: -0.38 (0.37), residues: 226 loop : -0.05 (0.26), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 87 TYR 0.009 0.001 TYR B 182 PHE 0.025 0.001 PHE B 225 TRP 0.008 0.001 TRP A 159 HIS 0.004 0.001 HIS A 256 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 9601) covalent geometry : angle 0.53047 (13019) SS BOND : bond 0.00200 ( 14) SS BOND : angle 0.37811 ( 28) hydrogen bonds : bond 0.03684 ( 392) hydrogen bonds : angle 4.81171 ( 1083) link_NAG-ASN : bond 0.00274 ( 4) link_NAG-ASN : angle 1.42958 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 130 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 87 ARG cc_start: 0.8964 (OUTLIER) cc_final: 0.8056 (ttt-90) REVERT: B 100 GLN cc_start: 0.6746 (OUTLIER) cc_final: 0.5697 (pm20) REVERT: B 115 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8403 (mm) REVERT: B 187 ASP cc_start: 0.8621 (m-30) cc_final: 0.8331 (m-30) REVERT: A 66 MET cc_start: 0.8701 (OUTLIER) cc_final: 0.8384 (mmt) REVERT: A 521 HIS cc_start: 0.8490 (m-70) cc_final: 0.8030 (t70) REVERT: A 557 LEU cc_start: 0.9522 (mm) cc_final: 0.9085 (mm) REVERT: C 95 ARG cc_start: 0.9215 (tpp80) cc_final: 0.8879 (tpp80) REVERT: C 102 ASP cc_start: 0.8732 (m-30) cc_final: 0.8345 (m-30) REVERT: C 140 GLU cc_start: 0.8523 (pm20) cc_final: 0.8029 (pm20) REVERT: D 62 GLU cc_start: 0.8621 (mm-30) cc_final: 0.7968 (tt0) REVERT: D 93 SER cc_start: 0.9084 (m) cc_final: 0.8833 (p) REVERT: D 117 GLU cc_start: 0.8853 (mp0) cc_final: 0.8514 (pm20) REVERT: D 163 GLU cc_start: 0.9103 (mp0) cc_final: 0.8868 (mp0) outliers start: 28 outliers final: 14 residues processed: 150 average time/residue: 0.1158 time to fit residues: 23.3792 Evaluate side-chains 137 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 119 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 ARG Chi-restraints excluded: chain B residue 100 GLN Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 725 TYR Chi-restraints excluded: chain A residue 729 TYR Chi-restraints excluded: chain A residue 756 ASN Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 194 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 114 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 20.0000 chunk 105 optimal weight: 0.0770 chunk 59 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 79 optimal weight: 7.9990 chunk 17 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 chunk 50 optimal weight: 0.0050 chunk 87 optimal weight: 2.9990 overall best weight: 2.0158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.085830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.059018 restraints weight = 23783.547| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 3.96 r_work: 0.2673 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 9619 Z= 0.259 Angle : 0.615 7.307 13059 Z= 0.309 Chirality : 0.044 0.200 1501 Planarity : 0.004 0.031 1667 Dihedral : 4.621 53.801 1358 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 4.32 % Allowed : 18.71 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 (0.25), residues: 1187 helix: 1.87 (0.28), residues: 359 sheet: -0.50 (0.36), residues: 228 loop : -0.11 (0.27), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 54 TYR 0.010 0.001 TYR D 182 PHE 0.021 0.002 PHE A 576 TRP 0.013 0.001 TRP A 159 HIS 0.004 0.001 HIS A 256 Details of bonding type rmsd covalent geometry : bond 0.00604 ( 9601) covalent geometry : angle 0.61244 (13019) SS BOND : bond 0.00391 ( 14) SS BOND : angle 0.58994 ( 28) hydrogen bonds : bond 0.04239 ( 392) hydrogen bonds : angle 4.90339 ( 1083) link_NAG-ASN : bond 0.00547 ( 4) link_NAG-ASN : angle 1.91224 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 116 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 115 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8412 (mm) REVERT: B 187 ASP cc_start: 0.8759 (m-30) cc_final: 0.8462 (m-30) REVERT: A 66 MET cc_start: 0.8806 (OUTLIER) cc_final: 0.7585 (mmt) REVERT: A 521 HIS cc_start: 0.8552 (m-70) cc_final: 0.8024 (t70) REVERT: C 48 LYS cc_start: 0.9257 (ttpt) cc_final: 0.9001 (tmmt) REVERT: C 102 ASP cc_start: 0.8720 (m-30) cc_final: 0.8168 (m-30) REVERT: C 140 GLU cc_start: 0.8561 (pm20) cc_final: 0.8061 (pm20) REVERT: D 62 GLU cc_start: 0.8669 (mm-30) cc_final: 0.7955 (tt0) REVERT: D 93 SER cc_start: 0.9109 (m) cc_final: 0.8846 (p) REVERT: D 117 GLU cc_start: 0.8866 (mp0) cc_final: 0.8407 (pm20) REVERT: D 163 GLU cc_start: 0.9099 (mp0) cc_final: 0.8868 (mp0) REVERT: D 197 LYS cc_start: 0.9104 (mmtm) cc_final: 0.8888 (mmtp) outliers start: 45 outliers final: 26 residues processed: 150 average time/residue: 0.0961 time to fit residues: 19.7758 Evaluate side-chains 139 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 111 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 ARG Chi-restraints excluded: chain B residue 100 GLN Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 218 ASP Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 91 ASN Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 293 HIS Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 690 SER Chi-restraints excluded: chain A residue 725 TYR Chi-restraints excluded: chain A residue 729 TYR Chi-restraints excluded: chain A residue 756 ASN Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain D residue 194 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 9 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 chunk 19 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 23 optimal weight: 0.4980 chunk 80 optimal weight: 7.9990 chunk 72 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 67 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.087404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.060487 restraints weight = 23436.408| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 3.99 r_work: 0.2708 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9619 Z= 0.138 Angle : 0.549 7.353 13059 Z= 0.274 Chirality : 0.042 0.175 1501 Planarity : 0.003 0.031 1667 Dihedral : 4.371 54.166 1358 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.78 % Allowed : 20.35 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.67 (0.25), residues: 1187 helix: 1.96 (0.28), residues: 358 sheet: -0.41 (0.36), residues: 228 loop : -0.06 (0.26), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 92 TYR 0.009 0.001 TYR B 182 PHE 0.012 0.001 PHE B 85 TRP 0.009 0.001 TRP A 159 HIS 0.004 0.001 HIS A 256 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 9601) covalent geometry : angle 0.54741 (13019) SS BOND : bond 0.00206 ( 14) SS BOND : angle 0.66124 ( 28) hydrogen bonds : bond 0.03689 ( 392) hydrogen bonds : angle 4.72400 ( 1083) link_NAG-ASN : bond 0.00302 ( 4) link_NAG-ASN : angle 1.50428 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 125 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 115 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8402 (mm) REVERT: B 187 ASP cc_start: 0.8724 (m-30) cc_final: 0.8416 (m-30) REVERT: A 66 MET cc_start: 0.8732 (OUTLIER) cc_final: 0.7579 (mmt) REVERT: A 521 HIS cc_start: 0.8501 (m-70) cc_final: 0.7975 (t70) REVERT: A 557 LEU cc_start: 0.9498 (mm) cc_final: 0.9041 (mm) REVERT: A 596 PHE cc_start: 0.8968 (OUTLIER) cc_final: 0.8605 (m-80) REVERT: C 102 ASP cc_start: 0.8718 (m-30) cc_final: 0.8157 (m-30) REVERT: C 140 GLU cc_start: 0.8588 (pm20) cc_final: 0.8075 (pm20) REVERT: D 62 GLU cc_start: 0.8669 (mm-30) cc_final: 0.7996 (tt0) REVERT: D 93 SER cc_start: 0.9089 (m) cc_final: 0.8811 (p) REVERT: D 117 GLU cc_start: 0.8853 (mp0) cc_final: 0.8379 (pm20) REVERT: D 163 GLU cc_start: 0.9074 (mp0) cc_final: 0.8638 (mp0) REVERT: D 167 GLN cc_start: 0.9140 (mt0) cc_final: 0.8816 (mp10) outliers start: 29 outliers final: 19 residues processed: 147 average time/residue: 0.1143 time to fit residues: 22.5729 Evaluate side-chains 139 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 117 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 ARG Chi-restraints excluded: chain B residue 100 GLN Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 218 ASP Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 293 HIS Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 596 PHE Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 690 SER Chi-restraints excluded: chain A residue 725 TYR Chi-restraints excluded: chain A residue 729 TYR Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain D residue 194 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 110 optimal weight: 2.9990 chunk 80 optimal weight: 8.9990 chunk 29 optimal weight: 2.9990 chunk 95 optimal weight: 0.4980 chunk 12 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 52 optimal weight: 0.0770 chunk 30 optimal weight: 3.9990 chunk 74 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 overall best weight: 1.0342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 128 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.087327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.060498 restraints weight = 23509.233| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 3.98 r_work: 0.2703 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9619 Z= 0.151 Angle : 0.561 7.342 13059 Z= 0.278 Chirality : 0.043 0.175 1501 Planarity : 0.003 0.031 1667 Dihedral : 4.336 53.891 1358 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.17 % Allowed : 19.96 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 (0.25), residues: 1187 helix: 2.00 (0.28), residues: 357 sheet: -0.34 (0.36), residues: 228 loop : -0.06 (0.26), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 54 TYR 0.014 0.001 TYR D 77 PHE 0.030 0.001 PHE B 225 TRP 0.010 0.001 TRP A 159 HIS 0.004 0.001 HIS A 256 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 9601) covalent geometry : angle 0.55988 (13019) SS BOND : bond 0.00241 ( 14) SS BOND : angle 0.52517 ( 28) hydrogen bonds : bond 0.03679 ( 392) hydrogen bonds : angle 4.68631 ( 1083) link_NAG-ASN : bond 0.00307 ( 4) link_NAG-ASN : angle 1.53099 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 117 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 87 ARG cc_start: 0.8913 (OUTLIER) cc_final: 0.8704 (mtp-110) REVERT: B 115 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8414 (mm) REVERT: B 187 ASP cc_start: 0.8811 (m-30) cc_final: 0.8460 (m-30) REVERT: A 66 MET cc_start: 0.8747 (OUTLIER) cc_final: 0.7568 (mmt) REVERT: A 521 HIS cc_start: 0.8523 (m-70) cc_final: 0.7999 (t70) REVERT: A 557 LEU cc_start: 0.9541 (mm) cc_final: 0.9141 (mm) REVERT: A 596 PHE cc_start: 0.8978 (OUTLIER) cc_final: 0.8609 (m-80) REVERT: A 637 MET cc_start: 0.9226 (ttt) cc_final: 0.8961 (ttm) REVERT: C 102 ASP cc_start: 0.8699 (m-30) cc_final: 0.8141 (m-30) REVERT: C 140 GLU cc_start: 0.8568 (pm20) cc_final: 0.8073 (pm20) REVERT: D 93 SER cc_start: 0.9084 (m) cc_final: 0.8811 (p) REVERT: D 117 GLU cc_start: 0.8868 (mp0) cc_final: 0.8416 (pm20) REVERT: D 167 GLN cc_start: 0.9101 (mt0) cc_final: 0.8753 (mp10) outliers start: 33 outliers final: 21 residues processed: 143 average time/residue: 0.1188 time to fit residues: 22.8428 Evaluate side-chains 139 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 114 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 ARG Chi-restraints excluded: chain B residue 100 GLN Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 218 ASP Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 596 PHE Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 690 SER Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 725 TYR Chi-restraints excluded: chain A residue 729 TYR Chi-restraints excluded: chain A residue 756 ASN Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain D residue 194 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 1 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 103 optimal weight: 0.0970 chunk 115 optimal weight: 0.2980 chunk 7 optimal weight: 0.0170 chunk 63 optimal weight: 0.0370 chunk 30 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 91 optimal weight: 0.4980 overall best weight: 0.1894 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 148 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.089575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.063012 restraints weight = 23219.283| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 3.91 r_work: 0.2784 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9619 Z= 0.095 Angle : 0.548 8.130 13059 Z= 0.265 Chirality : 0.042 0.256 1501 Planarity : 0.003 0.031 1667 Dihedral : 4.086 54.341 1358 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.73 % Allowed : 21.31 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 (0.25), residues: 1187 helix: 2.07 (0.28), residues: 358 sheet: -0.16 (0.36), residues: 225 loop : -0.05 (0.26), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 54 TYR 0.009 0.001 TYR B 182 PHE 0.029 0.001 PHE B 225 TRP 0.007 0.001 TRP B 120 HIS 0.004 0.000 HIS A 293 Details of bonding type rmsd covalent geometry : bond 0.00209 ( 9601) covalent geometry : angle 0.54797 (13019) SS BOND : bond 0.00103 ( 14) SS BOND : angle 0.38902 ( 28) hydrogen bonds : bond 0.03158 ( 392) hydrogen bonds : angle 4.50739 ( 1083) link_NAG-ASN : bond 0.00260 ( 4) link_NAG-ASN : angle 1.13058 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 130 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 115 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8321 (mm) REVERT: B 187 ASP cc_start: 0.8654 (m-30) cc_final: 0.8353 (m-30) REVERT: A 66 MET cc_start: 0.8750 (mmt) cc_final: 0.7796 (mmt) REVERT: A 344 MET cc_start: 0.8957 (mpp) cc_final: 0.8588 (mtp) REVERT: A 403 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.8189 (tm-30) REVERT: A 521 HIS cc_start: 0.8406 (m-70) cc_final: 0.8068 (t70) REVERT: A 557 LEU cc_start: 0.9541 (mm) cc_final: 0.9117 (mm) REVERT: A 596 PHE cc_start: 0.8724 (OUTLIER) cc_final: 0.8417 (m-10) REVERT: A 637 MET cc_start: 0.9201 (ttt) cc_final: 0.8819 (tpp) REVERT: C 73 GLU cc_start: 0.8673 (tt0) cc_final: 0.8378 (mt-10) REVERT: C 102 ASP cc_start: 0.8814 (m-30) cc_final: 0.8219 (m-30) REVERT: C 118 TYR cc_start: 0.8197 (m-10) cc_final: 0.7637 (m-10) REVERT: C 140 GLU cc_start: 0.8490 (pm20) cc_final: 0.7996 (pm20) REVERT: D 87 ARG cc_start: 0.9175 (ttm110) cc_final: 0.8697 (mtp-110) REVERT: D 93 SER cc_start: 0.9122 (m) cc_final: 0.8790 (p) REVERT: D 117 GLU cc_start: 0.8840 (mp0) cc_final: 0.8558 (pm20) REVERT: D 145 ARG cc_start: 0.8303 (tpt170) cc_final: 0.8089 (tpt170) REVERT: D 149 ARG cc_start: 0.9339 (mmm-85) cc_final: 0.9078 (mmm-85) REVERT: D 167 GLN cc_start: 0.9074 (mt0) cc_final: 0.8738 (mp10) REVERT: D 170 GLN cc_start: 0.8895 (pp30) cc_final: 0.8681 (pp30) outliers start: 18 outliers final: 12 residues processed: 144 average time/residue: 0.1143 time to fit residues: 21.9313 Evaluate side-chains 138 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 123 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 596 PHE Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 725 TYR Chi-restraints excluded: chain A residue 729 TYR Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 756 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 80 optimal weight: 2.9990 chunk 68 optimal weight: 0.2980 chunk 57 optimal weight: 1.9990 chunk 22 optimal weight: 6.9990 chunk 92 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 23 optimal weight: 0.2980 chunk 118 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.087351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.060614 restraints weight = 23312.779| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 3.89 r_work: 0.2721 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9619 Z= 0.178 Angle : 0.603 9.590 13059 Z= 0.294 Chirality : 0.044 0.233 1501 Planarity : 0.003 0.033 1667 Dihedral : 4.264 53.845 1358 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.30 % Allowed : 21.69 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.75 (0.25), residues: 1187 helix: 2.02 (0.28), residues: 358 sheet: -0.23 (0.36), residues: 229 loop : -0.06 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 54 TYR 0.013 0.001 TYR D 77 PHE 0.031 0.001 PHE B 225 TRP 0.012 0.001 TRP A 159 HIS 0.004 0.001 HIS A 256 Details of bonding type rmsd covalent geometry : bond 0.00416 ( 9601) covalent geometry : angle 0.60169 (13019) SS BOND : bond 0.00254 ( 14) SS BOND : angle 0.48966 ( 28) hydrogen bonds : bond 0.03718 ( 392) hydrogen bonds : angle 4.57014 ( 1083) link_NAG-ASN : bond 0.00357 ( 4) link_NAG-ASN : angle 1.53814 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 115 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: B 115 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8369 (mm) REVERT: B 187 ASP cc_start: 0.8795 (m-30) cc_final: 0.8482 (m-30) REVERT: A 521 HIS cc_start: 0.8476 (m-70) cc_final: 0.8030 (t70) REVERT: A 596 PHE cc_start: 0.8951 (OUTLIER) cc_final: 0.8583 (m-80) REVERT: A 637 MET cc_start: 0.9206 (ttt) cc_final: 0.8963 (ttm) REVERT: C 95 ARG cc_start: 0.9341 (tpp-160) cc_final: 0.8983 (ttm-80) REVERT: C 102 ASP cc_start: 0.8814 (m-30) cc_final: 0.8224 (m-30) REVERT: C 118 TYR cc_start: 0.8237 (m-10) cc_final: 0.7584 (m-10) REVERT: C 140 GLU cc_start: 0.8544 (pm20) cc_final: 0.8036 (pm20) REVERT: D 87 ARG cc_start: 0.9210 (ttm110) cc_final: 0.8674 (mtp-110) REVERT: D 93 SER cc_start: 0.9100 (m) cc_final: 0.8793 (p) REVERT: D 117 GLU cc_start: 0.8867 (mp0) cc_final: 0.8434 (pm20) REVERT: D 149 ARG cc_start: 0.9381 (mmm-85) cc_final: 0.9163 (mmm-85) REVERT: D 167 GLN cc_start: 0.9078 (mt0) cc_final: 0.8749 (mp10) outliers start: 24 outliers final: 15 residues processed: 134 average time/residue: 0.1220 time to fit residues: 21.9545 Evaluate side-chains 131 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 GLN Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 596 PHE Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 725 TYR Chi-restraints excluded: chain A residue 729 TYR Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain C residue 80 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 18 optimal weight: 10.0000 chunk 14 optimal weight: 3.9990 chunk 56 optimal weight: 0.2980 chunk 97 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 chunk 65 optimal weight: 0.0770 chunk 54 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 110 optimal weight: 0.7980 chunk 76 optimal weight: 9.9990 chunk 118 optimal weight: 2.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 584 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 = 0.3520 r_free = 0.3520 target = 0.089049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.062217 restraints weight = 23120.323| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 3.91 r_work: 0.2756 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9619 Z= 0.113 Angle : 0.581 9.518 13059 Z= 0.280 Chirality : 0.042 0.167 1501 Planarity : 0.003 0.036 1667 Dihedral : 4.145 54.208 1358 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.82 % Allowed : 21.79 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.78 (0.25), residues: 1187 helix: 2.01 (0.28), residues: 358 sheet: -0.17 (0.37), residues: 223 loop : -0.05 (0.26), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 54 TYR 0.008 0.001 TYR B 182 PHE 0.031 0.001 PHE B 225 TRP 0.007 0.001 TRP A 159 HIS 0.004 0.001 HIS A 293 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 9601) covalent geometry : angle 0.58022 (13019) SS BOND : bond 0.00186 ( 14) SS BOND : angle 0.39410 ( 28) hydrogen bonds : bond 0.03402 ( 392) hydrogen bonds : angle 4.49245 ( 1083) link_NAG-ASN : bond 0.00245 ( 4) link_NAG-ASN : angle 1.26370 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 115 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8347 (mm) REVERT: B 187 ASP cc_start: 0.8691 (m-30) cc_final: 0.8388 (m-30) REVERT: B 199 LYS cc_start: 0.7156 (tptt) cc_final: 0.6860 (tppt) REVERT: A 66 MET cc_start: 0.8758 (mmt) cc_final: 0.8479 (mmt) REVERT: A 521 HIS cc_start: 0.8452 (m-70) cc_final: 0.8030 (t70) REVERT: A 557 LEU cc_start: 0.9491 (mm) cc_final: 0.9073 (mm) REVERT: A 596 PHE cc_start: 0.8758 (OUTLIER) cc_final: 0.8416 (m-10) REVERT: A 637 MET cc_start: 0.9210 (ttt) cc_final: 0.8891 (tpp) REVERT: A 782 MET cc_start: 0.8947 (ptp) cc_final: 0.8503 (pmm) REVERT: C 95 ARG cc_start: 0.9378 (tpp-160) cc_final: 0.9022 (tpp80) REVERT: C 102 ASP cc_start: 0.8825 (m-30) cc_final: 0.8242 (m-30) REVERT: C 118 TYR cc_start: 0.8300 (m-10) cc_final: 0.7747 (m-10) REVERT: C 140 GLU cc_start: 0.8509 (pm20) cc_final: 0.7932 (pm20) REVERT: D 87 ARG cc_start: 0.9210 (ttm110) cc_final: 0.8673 (mtp-110) REVERT: D 93 SER cc_start: 0.9080 (m) cc_final: 0.8727 (p) REVERT: D 117 GLU cc_start: 0.8852 (mp0) cc_final: 0.8413 (pm20) REVERT: D 167 GLN cc_start: 0.9065 (mt0) cc_final: 0.8734 (mp10) REVERT: D 170 GLN cc_start: 0.8872 (pp30) cc_final: 0.8627 (pp30) outliers start: 19 outliers final: 16 residues processed: 140 average time/residue: 0.1198 time to fit residues: 22.5102 Evaluate side-chains 139 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 GLN Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain A residue 293 HIS Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 596 PHE Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 690 SER Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 725 TYR Chi-restraints excluded: chain A residue 729 TYR Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain C residue 80 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 63 optimal weight: 0.4980 chunk 73 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 chunk 3 optimal weight: 5.9990 chunk 27 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.088351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.061483 restraints weight = 23301.362| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 3.96 r_work: 0.2744 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9619 Z= 0.133 Angle : 0.601 10.476 13059 Z= 0.289 Chirality : 0.043 0.170 1501 Planarity : 0.003 0.037 1667 Dihedral : 4.174 54.289 1358 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.92 % Allowed : 21.98 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.78 (0.25), residues: 1187 helix: 2.00 (0.28), residues: 358 sheet: -0.18 (0.36), residues: 230 loop : -0.03 (0.26), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 54 TYR 0.016 0.001 TYR D 77 PHE 0.031 0.001 PHE B 225 TRP 0.010 0.001 TRP A 159 HIS 0.004 0.001 HIS A 256 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 9601) covalent geometry : angle 0.60048 (13019) SS BOND : bond 0.00198 ( 14) SS BOND : angle 0.39684 ( 28) hydrogen bonds : bond 0.03490 ( 392) hydrogen bonds : angle 4.50522 ( 1083) link_NAG-ASN : bond 0.00246 ( 4) link_NAG-ASN : angle 1.34702 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 118 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 115 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8365 (mm) REVERT: B 187 ASP cc_start: 0.8756 (m-30) cc_final: 0.8464 (m-30) REVERT: B 199 LYS cc_start: 0.7187 (tptt) cc_final: 0.6892 (tppt) REVERT: A 521 HIS cc_start: 0.8446 (m-70) cc_final: 0.8033 (t70) REVERT: A 557 LEU cc_start: 0.9504 (mm) cc_final: 0.9081 (mm) REVERT: A 596 PHE cc_start: 0.8776 (OUTLIER) cc_final: 0.8434 (m-80) REVERT: A 637 MET cc_start: 0.9215 (ttt) cc_final: 0.8946 (tpp) REVERT: A 782 MET cc_start: 0.8929 (ptp) cc_final: 0.8464 (pmm) REVERT: C 95 ARG cc_start: 0.9366 (tpp-160) cc_final: 0.9014 (tpp80) REVERT: C 102 ASP cc_start: 0.8826 (m-30) cc_final: 0.8245 (m-30) REVERT: C 118 TYR cc_start: 0.8311 (m-10) cc_final: 0.7689 (m-10) REVERT: C 140 GLU cc_start: 0.8536 (pm20) cc_final: 0.7971 (pm20) REVERT: D 87 ARG cc_start: 0.9222 (ttm110) cc_final: 0.8678 (mtp-110) REVERT: D 93 SER cc_start: 0.9093 (m) cc_final: 0.8749 (p) REVERT: D 117 GLU cc_start: 0.8855 (mp0) cc_final: 0.8435 (pm20) REVERT: D 167 GLN cc_start: 0.9058 (mt0) cc_final: 0.8727 (mp10) REVERT: D 192 MET cc_start: 0.8841 (mmm) cc_final: 0.8408 (mmp) outliers start: 20 outliers final: 17 residues processed: 134 average time/residue: 0.1180 time to fit residues: 21.3558 Evaluate side-chains 136 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 117 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 GLN Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 293 HIS Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 596 PHE Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 690 SER Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 725 TYR Chi-restraints excluded: chain A residue 729 TYR Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain C residue 80 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 59 optimal weight: 0.5980 chunk 89 optimal weight: 5.9990 chunk 71 optimal weight: 0.4980 chunk 98 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 16 optimal weight: 8.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.088572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.061946 restraints weight = 23097.224| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 3.84 r_work: 0.2748 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9619 Z= 0.129 Angle : 0.605 10.490 13059 Z= 0.290 Chirality : 0.043 0.164 1501 Planarity : 0.003 0.037 1667 Dihedral : 4.164 54.705 1358 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.82 % Allowed : 22.46 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.77 (0.25), residues: 1187 helix: 2.00 (0.28), residues: 358 sheet: -0.17 (0.36), residues: 231 loop : -0.06 (0.26), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 149 TYR 0.008 0.001 TYR B 182 PHE 0.031 0.001 PHE B 225 TRP 0.009 0.001 TRP A 159 HIS 0.004 0.001 HIS A 256 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 9601) covalent geometry : angle 0.60434 (13019) SS BOND : bond 0.00191 ( 14) SS BOND : angle 0.38065 ( 28) hydrogen bonds : bond 0.03451 ( 392) hydrogen bonds : angle 4.49680 ( 1083) link_NAG-ASN : bond 0.00250 ( 4) link_NAG-ASN : angle 1.30970 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2390.96 seconds wall clock time: 41 minutes 41.12 seconds (2501.12 seconds total)