Starting phenix.real_space_refine on Tue Feb 11 07:40:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d6f_46596/02_2025/9d6f_46596.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d6f_46596/02_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_46596/02_2025/9d6f_46596.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d6f_46596/02_2025/9d6f_46596.map" model { file = "/net/cci-nas-00/data/ceres_data/9d6f_46596/02_2025/9d6f_46596.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d6f_46596/02_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-5592/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: 4.00, per 1000 atoms: 0.86 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: 1.04 Conformation dependent library (CDL) restraints added in 586.9 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: 0.66 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: 1.00 Time building geometry restraints manager: 1.24 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: 2.280 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.370 Find NCS groups from input model: 0.060 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.820 ------------------------------------------------------------------------------- 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 : 0.535 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: 0.1355 time to fit residues: 19.6202 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 : 0.541 ------------------------------------------------------------------------------- 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: 2.9990 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: 1.9786 ------------------------------------------------------------------------------- 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** D 135 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.119997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.099313 restraints weight = 10862.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.102154 restraints weight = 6554.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.104229 restraints weight = 4595.306| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 4786 Z= 0.376 Angle : 0.708 5.987 6509 Z= 0.373 Chirality : 0.044 0.132 715 Planarity : 0.006 0.063 830 Dihedral : 5.644 26.509 657 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % 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: -2.02 (0.32), residues: 594 helix: None (None), residues: 0 sheet: -0.08 (0.37), residues: 212 loop : -2.24 (0.28), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP A 33 HIS 0.011 0.002 HIS C 90 PHE 0.019 0.002 PHE A 60 TYR 0.021 0.002 TYR L 101 ARG 0.008 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 98 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 86 GLU cc_start: 0.8606 (pm20) cc_final: 0.8253 (pm20) REVERT: H 101 TYR cc_start: 0.8029 (t80) cc_final: 0.7770 (t80) REVERT: C 6 GLN cc_start: 0.8404 (pm20) cc_final: 0.7715 (pm20) REVERT: D 153 ASP cc_start: 0.8842 (t0) cc_final: 0.8593 (t0) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.1236 time to fit residues: 16.4661 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 6 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 52 optimal weight: 0.7980 chunk 8 optimal weight: 0.0470 overall best weight: 0.7680 ------------------------------------------------------------------------------- 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** D 135 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.124942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.105267 restraints weight = 10502.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.108194 restraints weight = 6299.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.110233 restraints weight = 4364.771| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.1986 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= 0.184 Angle : 0.614 7.356 6509 Z= 0.312 Chirality : 0.042 0.135 715 Planarity : 0.004 0.040 830 Dihedral : 5.159 23.395 657 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.64 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: -1.96 (0.33), residues: 594 helix: None (None), residues: 0 sheet: -0.09 (0.36), residues: 220 loop : -2.21 (0.28), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 35 HIS 0.003 0.001 HIS C 90 PHE 0.012 0.001 PHE C 71 TYR 0.014 0.001 TYR L 101 ARG 0.003 0.000 ARG L 55 *********************** 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 102 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 101 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 86 GLU cc_start: 0.8512 (pm20) cc_final: 0.8267 (pm20) REVERT: C 35 TRP cc_start: 0.8105 (m100) cc_final: 0.7839 (m100) outliers start: 1 outliers final: 1 residues processed: 102 average time/residue: 0.1345 time to fit residues: 18.4115 Evaluate side-chains 72 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 71 time to evaluate : 0.511 ------------------------------------------------------------------------------- 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: 4.9990 chunk 37 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 2 optimal weight: 8.9990 chunk 22 optimal weight: 8.9990 chunk 43 optimal weight: 0.5980 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.3640 r_free = 0.3640 target = 0.123040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.103500 restraints weight = 10602.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.106294 restraints weight = 6421.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.108323 restraints weight = 4489.149| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.2380 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= 0.221 Angle : 0.622 5.865 6509 Z= 0.317 Chirality : 0.042 0.130 715 Planarity : 0.004 0.041 830 Dihedral : 5.188 22.202 657 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.60 % Favored : 90.40 % Rotamer: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % 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: -2.03 (0.32), residues: 594 helix: None (None), residues: 0 sheet: -0.16 (0.35), residues: 227 loop : -2.27 (0.28), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 36 HIS 0.006 0.002 HIS C 90 PHE 0.014 0.002 PHE A 104 TYR 0.014 0.001 TYR L 101 ARG 0.004 0.001 ARG C 24 *********************** 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 102 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 86 GLU cc_start: 0.8510 (pm20) cc_final: 0.8238 (pm20) REVERT: H 59 TYR cc_start: 0.6592 (m-10) cc_final: 0.6380 (m-10) REVERT: C 35 TRP cc_start: 0.8121 (m100) cc_final: 0.7903 (m100) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.1488 time to fit residues: 19.8536 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 : 0.517 ------------------------------------------------------------------------------- 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: 4.9990 chunk 35 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3634 r_free = 0.3634 target = 0.122595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.103142 restraints weight = 10831.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.106064 restraints weight = 6454.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.108046 restraints weight = 4442.416| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.2552 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= 0.198 Angle : 0.601 6.223 6509 Z= 0.306 Chirality : 0.042 0.156 715 Planarity : 0.004 0.039 830 Dihedral : 5.026 20.971 657 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % 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: -2.06 (0.32), residues: 594 helix: None (None), residues: 0 sheet: -0.26 (0.35), residues: 227 loop : -2.23 (0.28), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 35 HIS 0.005 0.001 HIS C 90 PHE 0.011 0.001 PHE A 104 TYR 0.013 0.001 TYR L 101 ARG 0.010 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 104 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 54 TYR cc_start: 0.6185 (p90) cc_final: 0.5954 (p90) REVERT: L 56 MET cc_start: 0.8795 (tpt) cc_final: 0.8587 (tpt) REVERT: L 86 GLU cc_start: 0.8468 (pm20) cc_final: 0.8241 (pm20) REVERT: A 39 GLN cc_start: 0.8779 (tp40) cc_final: 0.8497 (tp40) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.1533 time to fit residues: 20.6255 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 : 0.537 ------------------------------------------------------------------------------- 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: 1.9990 chunk 51 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 29 optimal weight: 7.9990 chunk 55 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 57 optimal weight: 0.7980 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 = 0.3582 r_free = 0.3582 target = 0.119113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.099915 restraints weight = 10741.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.102627 restraints weight = 6578.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.104583 restraints weight = 4602.055| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4786 Z= 0.280 Angle : 0.650 6.264 6509 Z= 0.333 Chirality : 0.043 0.133 715 Planarity : 0.004 0.038 830 Dihedral : 5.233 22.818 657 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.61 % Favored : 89.39 % 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: -2.22 (0.32), residues: 594 helix: None (None), residues: 0 sheet: -0.44 (0.35), residues: 227 loop : -2.28 (0.28), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 35 HIS 0.007 0.001 HIS C 90 PHE 0.015 0.002 PHE A 60 TYR 0.017 0.002 TYR L 101 ARG 0.008 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 95 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 82 ARG cc_start: 0.7632 (mmm160) cc_final: 0.7274 (mmm160) REVERT: L 86 GLU cc_start: 0.8454 (pm20) cc_final: 0.8201 (pm20) REVERT: H 48 ILE cc_start: 0.6877 (mt) cc_final: 0.6573 (mt) REVERT: H 110 ASP cc_start: 0.8413 (p0) cc_final: 0.8211 (p0) REVERT: A 39 GLN cc_start: 0.8753 (tp40) cc_final: 0.8430 (tp40) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.1625 time to fit residues: 19.7687 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 : 0.518 ------------------------------------------------------------------------------- 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: 2.9990 chunk 8 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 51 optimal weight: 0.6980 chunk 17 optimal weight: 5.9990 chunk 55 optimal weight: 0.0370 chunk 23 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 overall best weight: 0.6658 ------------------------------------------------------------------------------- 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 = 0.3632 r_free = 0.3632 target = 0.122385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.102895 restraints weight = 10892.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.105677 restraints weight = 6683.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.107705 restraints weight = 4702.767| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.2919 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= 0.177 Angle : 0.616 6.539 6509 Z= 0.312 Chirality : 0.043 0.173 715 Planarity : 0.004 0.038 830 Dihedral : 5.033 23.201 657 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % 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: -2.11 (0.32), residues: 594 helix: None (None), residues: 0 sheet: -0.33 (0.34), residues: 229 loop : -2.24 (0.28), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 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 0.006 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 101 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 53 ILE cc_start: 0.7973 (mm) cc_final: 0.7729 (mm) REVERT: L 54 TYR cc_start: 0.6117 (p90) cc_final: 0.5855 (p90) REVERT: L 82 ARG cc_start: 0.7627 (mmm160) cc_final: 0.7393 (mmm160) REVERT: L 86 GLU cc_start: 0.8407 (pm20) cc_final: 0.8164 (pm20) REVERT: C 90 HIS cc_start: 0.8839 (p90) cc_final: 0.8604 (p90) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.1411 time to fit residues: 18.8245 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 : 0.508 ------------------------------------------------------------------------------- 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: 9.9990 chunk 39 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 26 optimal weight: 0.0980 chunk 17 optimal weight: 8.9990 chunk 8 optimal weight: 0.0770 chunk 49 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 25 optimal weight: 0.3980 chunk 40 optimal weight: 0.9990 overall best weight: 0.3938 ------------------------------------------------------------------------------- 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 = 0.3651 r_free = 0.3651 target = 0.124249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.104757 restraints weight = 10645.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.107686 restraints weight = 6386.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.109737 restraints weight = 4414.378| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.2954 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= 0.150 Angle : 0.602 7.437 6509 Z= 0.298 Chirality : 0.041 0.124 715 Planarity : 0.004 0.036 830 Dihedral : 4.726 20.088 657 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % 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: -1.88 (0.33), residues: 594 helix: None (None), residues: 0 sheet: -0.15 (0.35), residues: 220 loop : -2.06 (0.29), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP C 35 HIS 0.002 0.000 HIS C 90 PHE 0.008 0.001 PHE L 67 TYR 0.015 0.001 TYR D 64 ARG 0.005 0.001 ARG C 24 *********************** 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 99 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 54 TYR cc_start: 0.5991 (p90) cc_final: 0.5699 (p90) REVERT: L 86 GLU cc_start: 0.8380 (pm20) cc_final: 0.8151 (pm20) REVERT: H 70 LEU cc_start: 0.6905 (mt) cc_final: 0.6414 (mt) REVERT: H 101 TYR cc_start: 0.7684 (t80) cc_final: 0.7365 (t80) REVERT: C 6 GLN cc_start: 0.8149 (pm20) cc_final: 0.7943 (pm20) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.1491 time to fit residues: 19.2121 Evaluate side-chains 77 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.532 ------------------------------------------------------------------------------- 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: 3.9990 chunk 35 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 38 optimal weight: 0.0470 chunk 23 optimal weight: 0.0270 chunk 4 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 overall best weight: 0.7338 ------------------------------------------------------------------------------- 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 = 0.3635 r_free = 0.3635 target = 0.122740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.103069 restraints weight = 10911.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.105989 restraints weight = 6601.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.108076 restraints weight = 4581.142| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4786 Z= 0.179 Angle : 0.622 8.927 6509 Z= 0.311 Chirality : 0.042 0.182 715 Planarity : 0.004 0.037 830 Dihedral : 4.793 19.951 657 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 0.20 % Allowed : 0.59 % Favored : 99.21 % 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 (0.32), residues: 594 helix: None (None), residues: 0 sheet: -0.20 (0.34), residues: 229 loop : -2.15 (0.29), residues: 365 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 0.008 0.001 PHE H 95 TYR 0.015 0.001 TYR D 64 ARG 0.007 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 95 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 94 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 54 TYR cc_start: 0.6018 (p90) cc_final: 0.5752 (p90) REVERT: L 86 GLU cc_start: 0.8402 (pm20) cc_final: 0.8162 (pm20) REVERT: H 70 LEU cc_start: 0.6880 (mt) cc_final: 0.6370 (mt) REVERT: H 110 ASP cc_start: 0.8405 (p0) cc_final: 0.8188 (p0) REVERT: C 6 GLN cc_start: 0.8207 (pm20) cc_final: 0.7968 (pm20) outliers start: 1 outliers final: 0 residues processed: 95 average time/residue: 0.1446 time to fit residues: 18.0332 Evaluate side-chains 74 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.501 ------------------------------------------------------------------------------- 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: 1.9990 chunk 44 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 39 optimal weight: 0.1980 chunk 48 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 22 optimal weight: 8.9990 chunk 1 optimal weight: 5.9990 chunk 14 optimal weight: 0.2980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3633 r_free = 0.3633 target = 0.122990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.103057 restraints weight = 10787.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.106032 restraints weight = 6468.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.108199 restraints weight = 4475.624| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4786 Z= 0.172 Angle : 0.625 9.806 6509 Z= 0.309 Chirality : 0.042 0.172 715 Planarity : 0.004 0.047 830 Dihedral : 4.720 19.676 657 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -1.94 (0.32), residues: 594 helix: None (None), residues: 0 sheet: -0.18 (0.34), residues: 227 loop : -2.15 (0.29), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP C 35 HIS 0.002 0.001 HIS C 90 PHE 0.008 0.001 PHE H 76 TYR 0.015 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 97 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 86 GLU cc_start: 0.8419 (pm20) cc_final: 0.8180 (pm20) REVERT: H 70 LEU cc_start: 0.6858 (mt) cc_final: 0.6348 (mt) REVERT: H 101 TYR cc_start: 0.7764 (t80) cc_final: 0.7442 (t80) REVERT: H 110 ASP cc_start: 0.8411 (p0) cc_final: 0.8206 (p0) REVERT: C 6 GLN cc_start: 0.8133 (pm20) cc_final: 0.7925 (pm20) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.1589 time to fit residues: 20.0490 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 : 0.559 ------------------------------------------------------------------------------- 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: 0.4980 chunk 50 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 4 optimal weight: 0.3980 chunk 44 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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 = 0.3601 r_free = 0.3601 target = 0.120271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.100442 restraints weight = 10853.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.103258 restraints weight = 6568.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.105344 restraints weight = 4588.315| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.3137 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= 0.230 Angle : 0.651 11.670 6509 Z= 0.325 Chirality : 0.042 0.182 715 Planarity : 0.004 0.036 830 Dihedral : 4.946 21.723 657 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.76 % Favored : 90.24 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % 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: -0.26 (0.34), residues: 226 loop : -2.20 (0.29), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 36 HIS 0.005 0.001 HIS C 90 PHE 0.012 0.001 PHE H 95 TYR 0.014 0.001 TYR L 101 ARG 0.009 0.001 ARG L 82 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1729.63 seconds wall clock time: 31 minutes 45.31 seconds (1905.31 seconds total)