Starting phenix.real_space_refine on Thu Mar 6 03:28:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d6f_46596/03_2025/9d6f_46596.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d6f_46596/03_2025/9d6f_46596.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9d6f_46596/03_2025/9d6f_46596.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d6f_46596/03_2025/9d6f_46596.map" model { file = "/net/cci-nas-00/data/ceres_data/9d6f_46596/03_2025/9d6f_46596.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d6f_46596/03_2025/9d6f_46596.cif" } resolution = 4.24 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.015 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 18 5.16 5 C 2967 2.51 5 N 772 2.21 5 O 915 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 4672 Number of models: 1 Model: "" Number of chains: 5 Chain: "L" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 832 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain breaks: 1 Chain: "H" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 934 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain breaks: 1 Chain: "A" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 884 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 107} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 796 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 4, 'TRANS': 100} Chain: "D" Number of atoms: 1226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1226 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 10, 'TRANS': 153} Time building chain proxies: 4.66, per 1000 atoms: 1.00 Number of scatterers: 4672 At special positions: 0 Unit cell: (107.01, 106.14, 72.21, 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 18 16.00 O 915 8.00 N 772 7.00 C 2967 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 93 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 3 " - pdb=" SG CYS D 44 " 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 Time building additional restraints: 0.93 Conformation dependent library (CDL) restraints added in 529.0 milliseconds 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1102 Finding SS restraints... Secondary structure from input PDB file: 2 helices and 17 sheets defined 1.6% alpha, 27.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'L' and resid 84 through 88 removed outlier: 3.739A pdb=" N VAL L 88 " --> pdb=" O THR L 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 91 removed outlier: 3.632A pdb=" N ASP A 90 " --> pdb=" O THR A 87 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER A 91 " --> pdb=" O PHE A 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 87 through 91' Processing sheet with id=AA1, first strand: chain 'L' and resid 4 through 5 removed outlier: 3.844A pdb=" N THR L 5 " --> pdb=" O SER L 24 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER L 24 " --> pdb=" O THR L 5 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'L' and resid 58 through 59 removed outlier: 3.663A pdb=" N ASN L 58 " --> pdb=" O TYR L 54 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TYR L 54 " --> pdb=" O ASN L 58 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N TRP L 40 " --> pdb=" O LEU L 52 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N TYR L 54 " --> pdb=" O LEU L 38 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N LEU L 38 " --> pdb=" O TYR L 54 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN L 95 " --> pdb=" O THR L 102 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N THR L 102 " --> pdb=" O GLN L 95 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 58 through 59 removed outlier: 3.663A pdb=" N ASN L 58 " --> pdb=" O TYR L 54 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TYR L 54 " --> pdb=" O ASN L 58 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N TRP L 40 " --> pdb=" O LEU L 52 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N TYR L 54 " --> pdb=" O LEU L 38 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N LEU L 38 " --> pdb=" O TYR L 54 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN L 43 " --> pdb=" O VAL L 90 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL L 90 " --> pdb=" O GLN L 43 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 68 through 71 removed outlier: 3.561A pdb=" N SER L 68 " --> pdb=" O ARG L 79 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.542A pdb=" N THR H 119 " --> pdb=" O GLU H 10 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 22 through 23 removed outlier: 3.559A pdb=" N CYS H 22 " --> pdb=" O ALA H 79 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 58 through 60 removed outlier: 6.207A pdb=" N LEU H 45 " --> pdb=" O ARG H 40 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N ARG H 40 " --> pdb=" O LEU H 45 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N TRP H 47 " --> pdb=" O LYS H 38 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LYS H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N TRP H 36 " --> pdb=" O GLY H 49 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN H 39 " --> pdb=" O VAL H 93 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL H 93 " --> pdb=" O GLN H 39 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 58 through 60 removed outlier: 6.207A pdb=" N LEU H 45 " --> pdb=" O ARG H 40 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N ARG H 40 " --> pdb=" O LEU H 45 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N TRP H 47 " --> pdb=" O LYS H 38 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LYS H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N TRP H 36 " --> pdb=" O GLY H 49 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 4 through 6 Processing sheet with id=AB1, first strand: chain 'A' and resid 17 through 19 removed outlier: 3.555A pdb=" N VAL A 18 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 45 through 51 removed outlier: 6.359A pdb=" N TRP A 36 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N TYR A 50 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N MET A 34 " --> pdb=" O TYR A 50 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL A 37 " --> pdb=" O PHE A 95 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 4 through 5 removed outlier: 3.908A pdb=" N VAL C 19 " --> pdb=" O ILE C 75 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE C 75 " --> pdb=" O VAL C 19 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE C 71 " --> pdb=" O CYS C 23 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER C 65 " --> pdb=" O SER C 72 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS C 74 " --> pdb=" O SER C 63 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N SER C 63 " --> pdb=" O LYS C 74 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 45 through 48 removed outlier: 6.028A pdb=" N LEU C 46 " --> pdb=" O GLN C 37 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N GLN C 37 " --> pdb=" O LEU C 46 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TRP C 35 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 4 through 5 removed outlier: 3.609A pdb=" N LYS D 4 " --> pdb=" O PHE D 43 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N PHE D 43 " --> pdb=" O LYS D 4 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 17 through 22 removed outlier: 6.588A pdb=" N ALA D 18 " --> pdb=" O ASN D 147 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N TYR D 149 " --> pdb=" O ALA D 18 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N VAL D 20 " --> pdb=" O TYR D 149 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE D 142 " --> pdb=" O GLN D 133 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ALA D 127 " --> pdb=" O ILE D 148 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ALA D 150 " --> pdb=" O LEU D 125 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LEU D 125 " --> pdb=" O ALA D 150 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP D 54 " --> pdb=" O TYR D 95 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL D 56 " --> pdb=" O VAL D 93 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N VAL D 93 " --> pdb=" O VAL D 56 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 36 through 37 removed outlier: 3.814A pdb=" N VAL D 36 " --> pdb=" O LEU D 107 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 75 through 76 70 hydrogen bonds defined for protein. 171 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: 1.07 Time building geometry restraints manager: 1.15 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: 1474 1.34 - 1.46: 1247 1.46 - 1.58: 2040 1.58 - 1.70: 0 1.70 - 1.82: 25 Bond restraints: 4786 Sorted by residual: bond pdb=" CA ASP C 49 " pdb=" C ASP C 49 " ideal model delta sigma weight residual 1.528 1.488 0.040 1.34e-02 5.57e+03 8.86e+00 bond pdb=" CA ASP L 75 " pdb=" C ASP L 75 " ideal model delta sigma weight residual 1.522 1.496 0.026 1.21e-02 6.83e+03 4.45e+00 bond pdb=" CA ASP D 153 " pdb=" CB ASP D 153 " ideal model delta sigma weight residual 1.525 1.554 -0.029 1.47e-02 4.63e+03 3.95e+00 bond pdb=" N ASP L 75 " pdb=" CA ASP L 75 " ideal model delta sigma weight residual 1.454 1.430 0.025 1.27e-02 6.20e+03 3.78e+00 bond pdb=" N ALA C 9 " pdb=" CA ALA C 9 " ideal model delta sigma weight residual 1.457 1.482 -0.025 1.29e-02 6.01e+03 3.68e+00 ... (remaining 4781 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 6190 1.91 - 3.82: 257 3.82 - 5.73: 42 5.73 - 7.64: 15 7.64 - 9.55: 5 Bond angle restraints: 6509 Sorted by residual: angle pdb=" C GLU L 98 " pdb=" CA GLU L 98 " pdb=" CB GLU L 98 " ideal model delta sigma weight residual 116.34 110.71 5.63 1.40e+00 5.10e-01 1.62e+01 angle pdb=" C LEU D 109 " pdb=" N THR D 110 " pdb=" CA THR D 110 " ideal model delta sigma weight residual 121.61 127.17 -5.56 1.39e+00 5.18e-01 1.60e+01 angle pdb=" N SER C 7 " pdb=" CA SER C 7 " pdb=" C SER C 7 " ideal model delta sigma weight residual 109.81 117.43 -7.62 2.21e+00 2.05e-01 1.19e+01 angle pdb=" CA LEU C 11 " pdb=" C LEU C 11 " pdb=" N SER C 12 " ideal model delta sigma weight residual 119.56 117.61 1.95 5.80e-01 2.97e+00 1.13e+01 angle pdb=" C GLU C 105 " pdb=" N MET C 106 " pdb=" CA MET C 106 " ideal model delta sigma weight residual 121.70 127.61 -5.91 1.80e+00 3.09e-01 1.08e+01 ... (remaining 6504 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.58: 2470 16.58 - 33.17: 246 33.17 - 49.75: 51 49.75 - 66.33: 10 66.33 - 82.92: 4 Dihedral angle restraints: 2781 sinusoidal: 1039 harmonic: 1742 Sorted by residual: dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 93 " pdb=" CB CYS L 93 " ideal model delta sinusoidal sigma weight residual 93.00 137.99 -44.99 1 1.00e+01 1.00e-02 2.81e+01 dihedral pdb=" CA PHE D 84 " pdb=" C PHE D 84 " pdb=" N PRO D 85 " pdb=" CA PRO D 85 " ideal model delta harmonic sigma weight residual 180.00 158.28 21.72 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual 93.00 57.62 35.38 1 1.00e+01 1.00e-02 1.77e+01 ... (remaining 2778 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 516 0.046 - 0.092: 142 0.092 - 0.138: 49 0.138 - 0.184: 7 0.184 - 0.230: 1 Chirality restraints: 715 Sorted by residual: chirality pdb=" CB THR C 52 " pdb=" CA THR C 52 " pdb=" OG1 THR C 52 " pdb=" CG2 THR C 52 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CB THR H 116 " pdb=" CA THR H 116 " pdb=" OG1 THR H 116 " pdb=" CG2 THR H 116 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.16 2.00e-01 2.50e+01 6.77e-01 chirality pdb=" CA THR C 94 " pdb=" N THR C 94 " pdb=" C THR C 94 " pdb=" CB THR C 94 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.16 2.00e-01 2.50e+01 6.14e-01 ... (remaining 712 not shown) Planarity restraints: 830 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN L 11 " 0.063 5.00e-02 4.00e+02 9.59e-02 1.47e+01 pdb=" N PRO L 12 " -0.166 5.00e-02 4.00e+02 pdb=" CA PRO L 12 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO L 12 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 33 " 0.016 2.00e-02 2.50e+03 1.41e-02 4.97e+00 pdb=" CG TRP A 33 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP A 33 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP A 33 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 33 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 33 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 33 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 33 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 33 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 33 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE D 84 " 0.029 5.00e-02 4.00e+02 4.44e-02 3.16e+00 pdb=" N PRO D 85 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO D 85 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 85 " 0.025 5.00e-02 4.00e+02 ... (remaining 827 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 480 2.75 - 3.29: 4131 3.29 - 3.83: 6870 3.83 - 4.36: 7216 4.36 - 4.90: 12932 Nonbonded interactions: 31629 Sorted by model distance: nonbonded pdb=" O ALA H 24 " pdb=" OG SER H 77 " model vdw 2.215 3.040 nonbonded pdb=" O SER D 72 " pdb=" OG1 THR D 110 " model vdw 2.338 3.040 nonbonded pdb=" OG SER D 80 " pdb=" N SER D 81 " model vdw 2.345 3.120 nonbonded pdb=" NZ LYS D 76 " pdb=" OH TYR D 108 " model vdw 2.372 3.120 nonbonded pdb=" OG SER C 14 " pdb=" OE2 GLU C 17 " model vdw 2.373 3.040 ... (remaining 31624 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 group one per residue 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: 1.970 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.060 Process input model: 16.180 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 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 : 0.004 0.045 4786 Z= 0.255 Angle : 0.921 9.551 6509 Z= 0.489 Chirality : 0.049 0.230 715 Planarity : 0.007 0.096 830 Dihedral : 13.893 82.918 1664 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.34 % Allowed : 8.42 % Favored : 91.25 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.32), residues: 594 helix: None (None), residues: 0 sheet: -0.28 (0.39), residues: 193 loop : -2.09 (0.28), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP A 33 HIS 0.005 0.001 HIS C 90 PHE 0.015 0.002 PHE H 76 TYR 0.019 0.002 TYR L 101 ARG 0.011 0.001 ARG A 98 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 53 ILE cc_start: 0.8206 (mm) cc_final: 0.8003 (mm) REVERT: L 86 GLU cc_start: 0.8674 (pm20) cc_final: 0.7587 (pm20) REVERT: C 27 GLU cc_start: 0.8128 (mp0) cc_final: 0.7901 (mp0) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.1370 time to fit residues: 19.7132 Evaluate side-chains 75 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 49 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 23 optimal weight: 0.1980 chunk 46 optimal weight: 0.9980 chunk 17 optimal weight: 9.9990 chunk 28 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 6 GLN ** D 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 GLN ** 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 = 0.3652 r_free = 0.3652 target = 0.123415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.102655 restraints weight = 10652.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.105670 restraints weight = 6381.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.107750 restraints weight = 4429.163| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 4786 Z= 0.288 Angle : 0.647 5.822 6509 Z= 0.339 Chirality : 0.043 0.132 715 Planarity : 0.005 0.062 830 Dihedral : 5.304 23.959 657 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.33), residues: 594 helix: None (None), residues: 0 sheet: -0.05 (0.37), residues: 215 loop : -2.19 (0.28), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 33 HIS 0.007 0.002 HIS C 90 PHE 0.015 0.002 PHE A 104 TYR 0.017 0.002 TYR H 94 ARG 0.005 0.001 ARG L 55 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 54 TYR cc_start: 0.6227 (p90) cc_final: 0.5924 (p90) REVERT: L 86 GLU cc_start: 0.8629 (pm20) cc_final: 0.8273 (pm20) REVERT: C 6 GLN cc_start: 0.8403 (pm20) cc_final: 0.7699 (pm20) REVERT: C 35 TRP cc_start: 0.8169 (m100) cc_final: 0.7735 (m100) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.1332 time to fit residues: 18.6166 Evaluate side-chains 79 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 6 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 54 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 47 optimal weight: 0.7980 chunk 16 optimal weight: 4.9990 chunk 52 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 46 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 = 0.3683 r_free = 0.3683 target = 0.125992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.106208 restraints weight = 10539.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.109125 restraints weight = 6352.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.111217 restraints weight = 4403.721| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4786 Z= 0.179 Angle : 0.604 7.442 6509 Z= 0.307 Chirality : 0.042 0.138 715 Planarity : 0.004 0.040 830 Dihedral : 4.991 20.740 657 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 0.20 % Allowed : 3.54 % Favored : 96.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.33), residues: 594 helix: None (None), residues: 0 sheet: 0.01 (0.36), residues: 222 loop : -2.24 (0.28), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 36 HIS 0.004 0.001 HIS C 90 PHE 0.013 0.001 PHE A 104 TYR 0.014 0.001 TYR C 87 ARG 0.003 0.000 ARG C 24 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 104 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 86 GLU cc_start: 0.8538 (pm20) cc_final: 0.8281 (pm20) REVERT: H 101 TYR cc_start: 0.7692 (t80) cc_final: 0.7374 (t80) REVERT: C 35 TRP cc_start: 0.8056 (m100) cc_final: 0.7766 (m100) outliers start: 1 outliers final: 1 residues processed: 105 average time/residue: 0.1320 time to fit residues: 18.3252 Evaluate side-chains 73 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 72 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 56 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 22 optimal weight: 8.9990 chunk 43 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 76 ASN ** D 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 GLN ** 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 = 0.3667 r_free = 0.3667 target = 0.125189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.105633 restraints weight = 10567.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.108544 restraints weight = 6384.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.110613 restraints weight = 4449.588| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4786 Z= 0.192 Angle : 0.591 5.967 6509 Z= 0.302 Chirality : 0.042 0.129 715 Planarity : 0.004 0.040 830 Dihedral : 4.980 21.031 657 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.33), residues: 594 helix: None (None), residues: 0 sheet: 0.01 (0.36), residues: 224 loop : -2.14 (0.29), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 47 HIS 0.005 0.001 HIS C 90 PHE 0.012 0.001 PHE A 104 TYR 0.013 0.001 TYR L 101 ARG 0.004 0.001 ARG L 55 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 54 TYR cc_start: 0.6105 (p90) cc_final: 0.5810 (p90) REVERT: L 86 GLU cc_start: 0.8518 (pm20) cc_final: 0.8240 (pm20) REVERT: C 35 TRP cc_start: 0.8051 (m100) cc_final: 0.7779 (m100) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.1415 time to fit residues: 18.3592 Evaluate side-chains 71 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 33 optimal weight: 0.7980 chunk 35 optimal weight: 0.4980 chunk 9 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 52 optimal weight: 0.5980 chunk 20 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 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 = 0.3676 r_free = 0.3676 target = 0.125798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.106029 restraints weight = 10729.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.109091 restraints weight = 6311.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.111226 restraints weight = 4336.441| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4786 Z= 0.176 Angle : 0.590 6.263 6509 Z= 0.299 Chirality : 0.041 0.155 715 Planarity : 0.004 0.033 830 Dihedral : 4.841 21.515 657 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.33), residues: 594 helix: None (None), residues: 0 sheet: -0.02 (0.36), residues: 221 loop : -2.13 (0.28), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 35 HIS 0.004 0.001 HIS C 90 PHE 0.013 0.001 PHE L 67 TYR 0.012 0.001 TYR L 101 ARG 0.008 0.001 ARG L 82 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 53 ILE cc_start: 0.8123 (mm) cc_final: 0.7873 (mm) REVERT: L 54 TYR cc_start: 0.6113 (p90) cc_final: 0.5821 (p90) REVERT: L 86 GLU cc_start: 0.8544 (pm20) cc_final: 0.8291 (pm20) REVERT: H 101 TYR cc_start: 0.7771 (t80) cc_final: 0.7522 (t80) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.1534 time to fit residues: 21.0221 Evaluate side-chains 70 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 12 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 chunk 55 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 85 ASN ** D 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 GLN ** 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 = 0.3576 r_free = 0.3576 target = 0.118492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.099292 restraints weight = 10868.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.102011 restraints weight = 6655.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.103859 restraints weight = 4670.412| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 4786 Z= 0.312 Angle : 0.679 6.676 6509 Z= 0.348 Chirality : 0.043 0.141 715 Planarity : 0.005 0.045 830 Dihedral : 5.374 23.768 657 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.44 % Favored : 89.56 % Rotamer: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.32), residues: 594 helix: None (None), residues: 0 sheet: -0.36 (0.35), residues: 226 loop : -2.30 (0.28), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 33 HIS 0.008 0.002 HIS C 90 PHE 0.018 0.002 PHE A 60 TYR 0.019 0.002 TYR L 101 ARG 0.007 0.001 ARG L 82 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 54 TYR cc_start: 0.6189 (p90) cc_final: 0.5715 (p90) REVERT: L 82 ARG cc_start: 0.7575 (mmm160) cc_final: 0.7288 (mmm160) REVERT: L 86 GLU cc_start: 0.8466 (pm20) cc_final: 0.8223 (pm20) REVERT: H 48 ILE cc_start: 0.6909 (mt) cc_final: 0.6658 (mt) REVERT: A 39 GLN cc_start: 0.8796 (tp40) cc_final: 0.8453 (tp40) REVERT: C 27 GLU cc_start: 0.8362 (pm20) cc_final: 0.7389 (pm20) REVERT: C 35 TRP cc_start: 0.8261 (m100) cc_final: 0.7978 (m100) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.1453 time to fit residues: 18.3419 Evaluate side-chains 69 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 35 optimal weight: 0.9980 chunk 8 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 chunk 51 optimal weight: 0.8980 chunk 17 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 23 optimal weight: 0.0870 chunk 9 optimal weight: 4.9990 chunk 36 optimal weight: 0.0770 chunk 20 optimal weight: 4.9990 chunk 3 optimal weight: 0.6980 overall best weight: 0.5516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 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 = 0.3639 r_free = 0.3639 target = 0.123199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.103708 restraints weight = 10594.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.106657 restraints weight = 6364.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.108756 restraints weight = 4378.954| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 4786 Z= 0.165 Angle : 0.606 6.744 6509 Z= 0.304 Chirality : 0.042 0.122 715 Planarity : 0.004 0.040 830 Dihedral : 4.911 19.863 657 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.32), residues: 594 helix: None (None), residues: 0 sheet: -0.28 (0.35), residues: 229 loop : -2.23 (0.28), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 35 HIS 0.003 0.001 HIS C 90 PHE 0.009 0.001 PHE D 84 TYR 0.012 0.001 TYR L 101 ARG 0.005 0.001 ARG L 82 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 54 TYR cc_start: 0.6084 (p90) cc_final: 0.5826 (p90) REVERT: L 86 GLU cc_start: 0.8432 (pm20) cc_final: 0.8184 (pm20) REVERT: A 39 GLN cc_start: 0.8735 (tp40) cc_final: 0.8312 (tp40) REVERT: C 90 HIS cc_start: 0.8881 (p90) cc_final: 0.8679 (p90) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.1329 time to fit residues: 17.5837 Evaluate side-chains 73 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 28 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 26 optimal weight: 0.4980 chunk 17 optimal weight: 7.9990 chunk 8 optimal weight: 6.9990 chunk 49 optimal weight: 0.9990 chunk 12 optimal weight: 0.1980 chunk 25 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN ** D 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 GLN ** 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 = 0.3636 r_free = 0.3636 target = 0.122883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.103572 restraints weight = 10885.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.106451 restraints weight = 6517.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.108603 restraints weight = 4516.325| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4786 Z= 0.167 Angle : 0.610 7.079 6509 Z= 0.306 Chirality : 0.042 0.132 715 Planarity : 0.004 0.035 830 Dihedral : 4.836 20.656 657 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 0.20 % Allowed : 1.38 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.32), residues: 594 helix: None (None), residues: 0 sheet: -0.24 (0.36), residues: 220 loop : -2.19 (0.28), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 35 HIS 0.003 0.001 HIS C 90 PHE 0.009 0.001 PHE D 84 TYR 0.015 0.001 TYR D 64 ARG 0.006 0.001 ARG L 82 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 96 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 54 TYR cc_start: 0.6161 (p90) cc_final: 0.5903 (p90) REVERT: L 86 GLU cc_start: 0.8441 (pm20) cc_final: 0.8172 (pm20) REVERT: H 101 TYR cc_start: 0.7848 (t80) cc_final: 0.7606 (t80) REVERT: C 6 GLN cc_start: 0.8342 (pm20) cc_final: 0.8003 (pm20) REVERT: C 27 GLU cc_start: 0.8303 (pm20) cc_final: 0.7368 (pm20) outliers start: 1 outliers final: 0 residues processed: 97 average time/residue: 0.1394 time to fit residues: 17.9988 Evaluate side-chains 70 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 17 optimal weight: 7.9990 chunk 35 optimal weight: 0.6980 chunk 18 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 38 optimal weight: 0.0670 chunk 23 optimal weight: 0.9980 chunk 4 optimal weight: 0.4980 chunk 56 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 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 = 0.3647 r_free = 0.3647 target = 0.123738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.104117 restraints weight = 10879.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.107066 restraints weight = 6564.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.109156 restraints weight = 4547.407| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4786 Z= 0.173 Angle : 0.612 8.696 6509 Z= 0.305 Chirality : 0.042 0.174 715 Planarity : 0.004 0.043 830 Dihedral : 4.790 20.892 657 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.32), residues: 594 helix: None (None), residues: 0 sheet: -0.21 (0.35), residues: 220 loop : -2.17 (0.28), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 35 HIS 0.004 0.001 HIS C 90 PHE 0.007 0.001 PHE H 95 TYR 0.016 0.001 TYR D 64 ARG 0.012 0.001 ARG L 82 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 54 TYR cc_start: 0.6154 (p90) cc_final: 0.5762 (p90) REVERT: L 86 GLU cc_start: 0.8405 (pm20) cc_final: 0.8159 (pm20) REVERT: C 6 GLN cc_start: 0.8259 (pm20) cc_final: 0.7611 (pm20) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.1383 time to fit residues: 17.6468 Evaluate side-chains 72 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 43 optimal weight: 0.3980 chunk 44 optimal weight: 0.3980 chunk 12 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 26 optimal weight: 0.0670 chunk 39 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 22 optimal weight: 8.9990 chunk 1 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 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 = 0.3652 r_free = 0.3652 target = 0.124051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.104675 restraints weight = 10773.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.107602 restraints weight = 6463.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.109705 restraints weight = 4468.404| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 4786 Z= 0.160 Angle : 0.617 10.636 6509 Z= 0.306 Chirality : 0.042 0.164 715 Planarity : 0.004 0.049 830 Dihedral : 4.666 19.772 657 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.33), residues: 594 helix: None (None), residues: 0 sheet: -0.09 (0.37), residues: 210 loop : -2.04 (0.29), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 35 HIS 0.004 0.001 HIS C 90 PHE 0.007 0.001 PHE L 67 TYR 0.014 0.001 TYR D 64 ARG 0.012 0.001 ARG L 82 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 53 ILE cc_start: 0.7970 (mm) cc_final: 0.7763 (mm) REVERT: L 54 TYR cc_start: 0.6065 (p90) cc_final: 0.5670 (p90) REVERT: L 82 ARG cc_start: 0.7410 (mmm160) cc_final: 0.7191 (mmm160) REVERT: L 86 GLU cc_start: 0.8442 (pm20) cc_final: 0.8174 (pm20) REVERT: H 101 TYR cc_start: 0.7844 (t80) cc_final: 0.7604 (t80) REVERT: C 6 GLN cc_start: 0.8253 (pm20) cc_final: 0.7588 (pm20) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.1606 time to fit residues: 20.3987 Evaluate side-chains 73 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 36 optimal weight: 0.7980 chunk 50 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 4 optimal weight: 0.3980 chunk 44 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 11 optimal weight: 0.0670 chunk 31 optimal weight: 0.5980 chunk 53 optimal weight: 3.9990 chunk 18 optimal weight: 0.1980 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 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 = 0.3669 r_free = 0.3669 target = 0.125185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.105820 restraints weight = 10637.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.108744 restraints weight = 6373.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.110864 restraints weight = 4419.487| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 4786 Z= 0.152 Angle : 0.595 7.118 6509 Z= 0.294 Chirality : 0.041 0.160 715 Planarity : 0.004 0.044 830 Dihedral : 4.550 19.350 657 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.33), residues: 594 helix: None (None), residues: 0 sheet: -0.01 (0.37), residues: 210 loop : -2.02 (0.29), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 35 HIS 0.002 0.001 HIS C 90 PHE 0.007 0.001 PHE L 67 TYR 0.014 0.001 TYR D 64 ARG 0.011 0.001 ARG L 82 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1804.66 seconds wall clock time: 32 minutes 6.99 seconds (1926.99 seconds total)