Starting phenix.real_space_refine on Sun Apr 27 07:19:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pog_17791/04_2025/8pog_17791.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pog_17791/04_2025/8pog_17791.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8pog_17791/04_2025/8pog_17791.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pog_17791/04_2025/8pog_17791.map" model { file = "/net/cci-nas-00/data/ceres_data/8pog_17791/04_2025/8pog_17791.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pog_17791/04_2025/8pog_17791.cif" } resolution = 4.15 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= 0.024 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 24 5.16 5 C 3132 2.51 5 N 880 2.21 5 O 928 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 4964 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1241 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 6, 'TRANS': 149} Chain: "B" Number of atoms: 1241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1241 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 6, 'TRANS': 149} Chain: "C" Number of atoms: 1241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1241 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 6, 'TRANS': 149} Chain: "D" Number of atoms: 1241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1241 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 6, 'TRANS': 149} Time building chain proxies: 3.86, per 1000 atoms: 0.78 Number of scatterers: 4964 At special positions: 0 Unit cell: (75.33, 87.42, 79.05, 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 24 16.00 O 928 8.00 N 880 7.00 C 3132 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.22 Conformation dependent library (CDL) restraints added in 591.7 milliseconds 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1144 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 4 sheets defined 59.0% alpha, 14.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 7 through 19 removed outlier: 3.547A pdb=" N LEU A 11 " --> pdb=" O ASN A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 39 Processing helix chain 'A' and resid 43 through 58 removed outlier: 3.630A pdb=" N TYR A 58 " --> pdb=" O LEU A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 81 Processing helix chain 'A' and resid 106 through 130 removed outlier: 3.503A pdb=" N GLN A 110 " --> pdb=" O VAL A 106 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N SER A 111 " --> pdb=" O GLU A 107 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N ARG A 112 " --> pdb=" O ASP A 108 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY A 123 " --> pdb=" O ALA A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 133 No H-bonds generated for 'chain 'A' and resid 131 through 133' Processing helix chain 'B' and resid 7 through 19 removed outlier: 3.705A pdb=" N LEU B 11 " --> pdb=" O ASN B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 39 Processing helix chain 'B' and resid 43 through 58 removed outlier: 3.528A pdb=" N GLN B 57 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TYR B 58 " --> pdb=" O LEU B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 81 Processing helix chain 'B' and resid 106 through 130 removed outlier: 4.524A pdb=" N SER B 111 " --> pdb=" O GLU B 107 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N ARG B 112 " --> pdb=" O ASP B 108 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY B 123 " --> pdb=" O ALA B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 133 No H-bonds generated for 'chain 'B' and resid 131 through 133' Processing helix chain 'C' and resid 7 through 19 removed outlier: 3.682A pdb=" N LEU C 11 " --> pdb=" O ASN C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 39 Processing helix chain 'C' and resid 43 through 58 removed outlier: 3.511A pdb=" N LEU C 47 " --> pdb=" O SER C 43 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN C 57 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N TYR C 58 " --> pdb=" O LEU C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 81 Processing helix chain 'C' and resid 106 through 130 removed outlier: 4.609A pdb=" N SER C 111 " --> pdb=" O GLU C 107 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N ARG C 112 " --> pdb=" O ASP C 108 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY C 123 " --> pdb=" O ALA C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 133 No H-bonds generated for 'chain 'C' and resid 131 through 133' Processing helix chain 'D' and resid 7 through 19 removed outlier: 3.627A pdb=" N LEU D 11 " --> pdb=" O ASN D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 39 Processing helix chain 'D' and resid 43 through 58 removed outlier: 3.621A pdb=" N GLN D 57 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N TYR D 58 " --> pdb=" O LEU D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 81 Processing helix chain 'D' and resid 106 through 130 removed outlier: 4.572A pdb=" N SER D 111 " --> pdb=" O GLU D 107 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N ARG D 112 " --> pdb=" O ASP D 108 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY D 123 " --> pdb=" O ALA D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 133 No H-bonds generated for 'chain 'D' and resid 131 through 133' Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 89 removed outlier: 3.571A pdb=" N CYS A 84 " --> pdb=" O GLN A 99 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N ASP A 150 " --> pdb=" O LEU A 145 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N LEU A 145 " --> pdb=" O ASP A 150 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N GLN A 152 " --> pdb=" O GLU A 143 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLU A 143 " --> pdb=" O GLN A 152 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER A 141 " --> pdb=" O ARG A 154 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 84 through 89 removed outlier: 3.525A pdb=" N CYS B 84 " --> pdb=" O GLN B 99 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N ASP B 150 " --> pdb=" O LEU B 145 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N LEU B 145 " --> pdb=" O ASP B 150 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N GLN B 152 " --> pdb=" O GLU B 143 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLU B 143 " --> pdb=" O GLN B 152 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER B 141 " --> pdb=" O ARG B 154 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N HIS B 156 " --> pdb=" O THR B 139 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N THR B 139 " --> pdb=" O HIS B 156 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 84 through 89 removed outlier: 3.556A pdb=" N CYS C 84 " --> pdb=" O GLN C 99 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N ASP C 150 " --> pdb=" O LEU C 145 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N LEU C 145 " --> pdb=" O ASP C 150 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N GLN C 152 " --> pdb=" O GLU C 143 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLU C 143 " --> pdb=" O GLN C 152 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N HIS C 156 " --> pdb=" O THR C 139 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N THR C 139 " --> pdb=" O HIS C 156 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 84 through 89 removed outlier: 3.518A pdb=" N CYS D 84 " --> pdb=" O GLN D 99 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N ASP D 150 " --> pdb=" O LEU D 145 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N LEU D 145 " --> pdb=" O ASP D 150 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N GLN D 152 " --> pdb=" O GLU D 143 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLU D 143 " --> pdb=" O GLN D 152 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG D 154 " --> pdb=" O SER D 141 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER D 141 " --> pdb=" O ARG D 154 " (cutoff:3.500A) 299 hydrogen bonds defined for protein. 885 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: 1.19 Time building geometry restraints manager: 1.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1696 1.34 - 1.46: 1031 1.46 - 1.58: 2317 1.58 - 1.69: 0 1.69 - 1.81: 36 Bond restraints: 5080 Sorted by residual: bond pdb=" CB GLN A 132 " pdb=" CG GLN A 132 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.21e+00 bond pdb=" C VAL B 38 " pdb=" O VAL B 38 " ideal model delta sigma weight residual 1.231 1.241 -0.010 1.02e-02 9.61e+03 9.70e-01 bond pdb=" CB GLU C 40 " pdb=" CG GLU C 40 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.84e-01 bond pdb=" C VAL D 38 " pdb=" O VAL D 38 " ideal model delta sigma weight residual 1.231 1.241 -0.010 1.07e-02 8.73e+03 8.43e-01 bond pdb=" C VAL A 38 " pdb=" O VAL A 38 " ideal model delta sigma weight residual 1.231 1.240 -0.009 1.07e-02 8.73e+03 7.60e-01 ... (remaining 5075 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.17: 6559 1.17 - 2.34: 258 2.34 - 3.50: 69 3.50 - 4.67: 6 4.67 - 5.84: 12 Bond angle restraints: 6904 Sorted by residual: angle pdb=" CA GLU C 40 " pdb=" CB GLU C 40 " pdb=" CG GLU C 40 " ideal model delta sigma weight residual 114.10 119.39 -5.29 2.00e+00 2.50e-01 7.01e+00 angle pdb=" CB GLN A 132 " pdb=" CG GLN A 132 " pdb=" CD GLN A 132 " ideal model delta sigma weight residual 112.60 116.58 -3.98 1.70e+00 3.46e-01 5.48e+00 angle pdb=" CA GLN A 132 " pdb=" CB GLN A 132 " pdb=" CG GLN A 132 " ideal model delta sigma weight residual 114.10 118.40 -4.30 2.00e+00 2.50e-01 4.61e+00 angle pdb=" N VAL B 38 " pdb=" CA VAL B 38 " pdb=" C VAL B 38 " ideal model delta sigma weight residual 111.81 113.58 -1.77 8.60e-01 1.35e+00 4.24e+00 angle pdb=" CA GLU B 40 " pdb=" CB GLU B 40 " pdb=" CG GLU B 40 " ideal model delta sigma weight residual 114.10 118.17 -4.07 2.00e+00 2.50e-01 4.14e+00 ... (remaining 6899 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 2639 17.95 - 35.89: 254 35.89 - 53.84: 56 53.84 - 71.79: 13 71.79 - 89.73: 10 Dihedral angle restraints: 2972 sinusoidal: 1196 harmonic: 1776 Sorted by residual: dihedral pdb=" CB GLU D 86 " pdb=" CG GLU D 86 " pdb=" CD GLU D 86 " pdb=" OE1 GLU D 86 " ideal model delta sinusoidal sigma weight residual 0.00 89.73 -89.73 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU C 86 " pdb=" CG GLU C 86 " pdb=" CD GLU C 86 " pdb=" OE1 GLU C 86 " ideal model delta sinusoidal sigma weight residual 0.00 89.73 -89.73 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU B 86 " pdb=" CG GLU B 86 " pdb=" CD GLU B 86 " pdb=" OE1 GLU B 86 " ideal model delta sinusoidal sigma weight residual 0.00 89.63 -89.63 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 2969 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 476 0.026 - 0.051: 173 0.051 - 0.077: 47 0.077 - 0.102: 39 0.102 - 0.128: 13 Chirality restraints: 748 Sorted by residual: chirality pdb=" CA VAL B 151 " pdb=" N VAL B 151 " pdb=" C VAL B 151 " pdb=" CB VAL B 151 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.08e-01 chirality pdb=" CA VAL B 140 " pdb=" N VAL B 140 " pdb=" C VAL B 140 " pdb=" CB VAL B 140 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.45e-01 chirality pdb=" CA VAL D 151 " pdb=" N VAL D 151 " pdb=" C VAL D 151 " pdb=" CB VAL D 151 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.37e-01 ... (remaining 745 not shown) Planarity restraints: 908 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 124 " -0.009 2.00e-02 2.50e+03 1.89e-02 3.59e+00 pdb=" C LEU B 124 " 0.033 2.00e-02 2.50e+03 pdb=" O LEU B 124 " -0.012 2.00e-02 2.50e+03 pdb=" N TYR B 125 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 124 " 0.009 2.00e-02 2.50e+03 1.84e-02 3.37e+00 pdb=" C LEU A 124 " -0.032 2.00e-02 2.50e+03 pdb=" O LEU A 124 " 0.012 2.00e-02 2.50e+03 pdb=" N TYR A 125 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 122 " 0.009 2.00e-02 2.50e+03 1.76e-02 3.08e+00 pdb=" C GLU B 122 " -0.030 2.00e-02 2.50e+03 pdb=" O GLU B 122 " 0.011 2.00e-02 2.50e+03 pdb=" N GLY B 123 " 0.010 2.00e-02 2.50e+03 ... (remaining 905 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 979 2.77 - 3.31: 4882 3.31 - 3.84: 7703 3.84 - 4.37: 8138 4.37 - 4.90: 14428 Nonbonded interactions: 36130 Sorted by model distance: nonbonded pdb=" OG SER B 90 " pdb=" OD1 ASP B 93 " model vdw 2.242 3.040 nonbonded pdb=" OD1 ASP D 56 " pdb=" NH1 ARG D 127 " model vdw 2.258 3.120 nonbonded pdb=" OD2 ASP B 93 " pdb=" NH1 ARG B 154 " model vdw 2.258 3.120 nonbonded pdb=" N GLU A 42 " pdb=" OE1 GLU A 42 " model vdw 2.286 3.120 nonbonded pdb=" OD1 ASP C 56 " pdb=" NH1 ARG C 127 " model vdw 2.307 3.120 ... (remaining 36125 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 1.430 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: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.120 Find NCS groups from input model: 0.170 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: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5080 Z= 0.141 Angle : 0.588 5.841 6904 Z= 0.333 Chirality : 0.037 0.128 748 Planarity : 0.005 0.039 908 Dihedral : 15.834 89.734 1828 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % 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: 0.40 (0.33), residues: 616 helix: 0.73 (0.28), residues: 336 sheet: 0.14 (0.55), residues: 84 loop : -0.26 (0.43), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 13 HIS 0.002 0.000 HIS B 98 PHE 0.008 0.001 PHE C 46 TYR 0.014 0.001 TYR C 58 ARG 0.009 0.001 ARG C 142 Details of bonding type rmsd hydrogen bonds : bond 0.20781 ( 299) hydrogen bonds : angle 7.53111 ( 885) covalent geometry : bond 0.00259 ( 5080) covalent geometry : angle 0.58762 ( 6904) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.592 Fit side-chains revert: symmetry clash REVERT: B 40 GLU cc_start: 0.5649 (pm20) cc_final: 0.5189 (tt0) REVERT: B 64 GLU cc_start: 0.5687 (mm-30) cc_final: 0.5463 (mp0) REVERT: B 72 ASN cc_start: 0.7195 (m110) cc_final: 0.6715 (m110) REVERT: B 148 LEU cc_start: 0.8423 (mt) cc_final: 0.8159 (mt) REVERT: C 72 ASN cc_start: 0.6919 (m110) cc_final: 0.6543 (m110) REVERT: C 142 ARG cc_start: 0.8322 (mtp-110) cc_final: 0.7978 (mtm110) REVERT: C 148 LEU cc_start: 0.8582 (mt) cc_final: 0.8217 (mt) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.1526 time to fit residues: 24.0624 Evaluate side-chains 107 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 0.0670 chunk 45 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 30 optimal weight: 0.0970 chunk 24 optimal weight: 7.9990 chunk 47 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 chunk 35 optimal weight: 0.0570 chunk 54 optimal weight: 6.9990 overall best weight: 0.3234 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 GLN ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 ASN ** B 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 44 GLN ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.186421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.155160 restraints weight = 6902.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.153511 restraints weight = 9263.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.153649 restraints weight = 9757.833| |-----------------------------------------------------------------------------| r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 5080 Z= 0.120 Angle : 0.482 5.452 6904 Z= 0.250 Chirality : 0.038 0.117 748 Planarity : 0.004 0.021 908 Dihedral : 3.546 12.457 676 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % 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 (0.35), residues: 616 helix: 2.62 (0.27), residues: 344 sheet: -0.14 (0.52), residues: 104 loop : -0.42 (0.48), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 128 HIS 0.005 0.001 HIS A 115 PHE 0.008 0.001 PHE D 46 TYR 0.003 0.001 TYR C 125 ARG 0.004 0.001 ARG D 127 Details of bonding type rmsd hydrogen bonds : bond 0.04729 ( 299) hydrogen bonds : angle 4.33176 ( 885) covalent geometry : bond 0.00240 ( 5080) covalent geometry : angle 0.48244 ( 6904) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 GLU cc_start: 0.7132 (tp30) cc_final: 0.6521 (tp30) REVERT: C 17 GLN cc_start: 0.8668 (tm-30) cc_final: 0.8210 (tp40) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.1661 time to fit residues: 27.4037 Evaluate side-chains 105 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 13 optimal weight: 0.0060 chunk 6 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 32 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 43 optimal weight: 0.0060 chunk 8 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 overall best weight: 0.4212 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 ASN ** B 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 152 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.189129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.155173 restraints weight = 7021.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.152869 restraints weight = 7248.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.153174 restraints weight = 7677.105| |-----------------------------------------------------------------------------| r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 5080 Z= 0.106 Angle : 0.465 4.983 6904 Z= 0.236 Chirality : 0.037 0.127 748 Planarity : 0.003 0.024 908 Dihedral : 3.322 12.748 676 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % 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: 2.56 (0.35), residues: 616 helix: 3.16 (0.28), residues: 340 sheet: 0.15 (0.54), residues: 84 loop : -0.33 (0.44), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 113 HIS 0.003 0.001 HIS A 98 PHE 0.008 0.001 PHE B 24 TYR 0.010 0.001 TYR D 58 ARG 0.005 0.001 ARG A 142 Details of bonding type rmsd hydrogen bonds : bond 0.04022 ( 299) hydrogen bonds : angle 3.95244 ( 885) covalent geometry : bond 0.00226 ( 5080) covalent geometry : angle 0.46527 ( 6904) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 GLU cc_start: 0.7306 (tp30) cc_final: 0.6635 (tp30) REVERT: A 17 GLN cc_start: 0.8636 (tm-30) cc_final: 0.8139 (tp40) REVERT: A 52 ILE cc_start: 0.8948 (mm) cc_final: 0.8745 (mm) REVERT: A 122 GLU cc_start: 0.7595 (mm-30) cc_final: 0.7295 (mm-30) REVERT: B 69 LEU cc_start: 0.8574 (tp) cc_final: 0.8157 (tp) REVERT: B 72 ASN cc_start: 0.7176 (m110) cc_final: 0.6949 (m110) REVERT: B 141 SER cc_start: 0.8532 (t) cc_final: 0.8285 (t) REVERT: C 17 GLN cc_start: 0.8599 (tm-30) cc_final: 0.8133 (tp40) REVERT: C 142 ARG cc_start: 0.8230 (mtp-110) cc_final: 0.7961 (mtp85) REVERT: D 17 GLN cc_start: 0.8570 (tm-30) cc_final: 0.8003 (tp40) REVERT: D 148 LEU cc_start: 0.8116 (mt) cc_final: 0.7826 (mt) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.1438 time to fit residues: 23.8377 Evaluate side-chains 105 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 15 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 50 optimal weight: 0.0370 chunk 37 optimal weight: 0.0270 chunk 20 optimal weight: 0.4980 chunk 32 optimal weight: 0.5980 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 ASN B 110 GLN ** B 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 152 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.185855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.153655 restraints weight = 6847.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.152249 restraints weight = 8660.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.151750 restraints weight = 10252.816| |-----------------------------------------------------------------------------| r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 5080 Z= 0.101 Angle : 0.446 4.982 6904 Z= 0.225 Chirality : 0.036 0.121 748 Planarity : 0.003 0.022 908 Dihedral : 3.263 12.539 676 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % 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: 2.50 (0.34), residues: 616 helix: 3.06 (0.27), residues: 344 sheet: 0.10 (0.53), residues: 84 loop : -0.30 (0.44), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 113 HIS 0.003 0.001 HIS A 98 PHE 0.006 0.001 PHE C 14 TYR 0.009 0.001 TYR D 58 ARG 0.005 0.000 ARG A 142 Details of bonding type rmsd hydrogen bonds : bond 0.03680 ( 299) hydrogen bonds : angle 3.79302 ( 885) covalent geometry : bond 0.00219 ( 5080) covalent geometry : angle 0.44649 ( 6904) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 GLU cc_start: 0.7269 (tp30) cc_final: 0.6604 (tp30) REVERT: A 17 GLN cc_start: 0.8633 (tm-30) cc_final: 0.8229 (tp40) REVERT: B 69 LEU cc_start: 0.8580 (tp) cc_final: 0.8126 (tp) REVERT: C 17 GLN cc_start: 0.8591 (tm-30) cc_final: 0.8180 (tp40) REVERT: D 17 GLN cc_start: 0.8528 (tm-30) cc_final: 0.8064 (tp40) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.1305 time to fit residues: 20.9689 Evaluate side-chains 97 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 27 optimal weight: 0.7980 chunk 28 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 54 optimal weight: 6.9990 chunk 12 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 ASN ** B 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 152 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.180333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.144097 restraints weight = 6965.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.144097 restraints weight = 7068.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.144097 restraints weight = 7068.748| |-----------------------------------------------------------------------------| r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5080 Z= 0.150 Angle : 0.497 4.987 6904 Z= 0.256 Chirality : 0.037 0.114 748 Planarity : 0.003 0.023 908 Dihedral : 3.365 12.000 676 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % 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: 2.32 (0.34), residues: 616 helix: 2.95 (0.28), residues: 344 sheet: 0.04 (0.52), residues: 84 loop : -0.48 (0.44), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 128 HIS 0.005 0.001 HIS A 98 PHE 0.011 0.002 PHE D 117 TYR 0.009 0.001 TYR B 58 ARG 0.003 0.000 ARG A 142 Details of bonding type rmsd hydrogen bonds : bond 0.04582 ( 299) hydrogen bonds : angle 4.15200 ( 885) covalent geometry : bond 0.00348 ( 5080) covalent geometry : angle 0.49666 ( 6904) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 GLN cc_start: 0.8572 (tm-30) cc_final: 0.8199 (tp40) REVERT: C 17 GLN cc_start: 0.8575 (tm-30) cc_final: 0.8173 (tp40) REVERT: D 17 GLN cc_start: 0.8584 (tm-30) cc_final: 0.8159 (tp40) REVERT: D 50 MET cc_start: 0.7261 (mmt) cc_final: 0.6920 (tpp) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.1591 time to fit residues: 23.3467 Evaluate side-chains 95 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 24 optimal weight: 5.9990 chunk 55 optimal weight: 0.0070 chunk 12 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 44 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 chunk 2 optimal weight: 0.0980 chunk 28 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 ASN B 115 HIS ** B 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.183790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.149217 restraints weight = 6898.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.149143 restraints weight = 6942.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.149143 restraints weight = 6972.048| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.3235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 5080 Z= 0.106 Angle : 0.478 5.630 6904 Z= 0.237 Chirality : 0.037 0.119 748 Planarity : 0.003 0.025 908 Dihedral : 3.290 12.245 676 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % 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: 2.40 (0.34), residues: 616 helix: 2.98 (0.27), residues: 344 sheet: 0.14 (0.53), residues: 84 loop : -0.42 (0.45), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 113 HIS 0.006 0.001 HIS B 115 PHE 0.009 0.001 PHE D 117 TYR 0.008 0.001 TYR D 58 ARG 0.006 0.001 ARG B 127 Details of bonding type rmsd hydrogen bonds : bond 0.03743 ( 299) hydrogen bonds : angle 3.90243 ( 885) covalent geometry : bond 0.00236 ( 5080) covalent geometry : angle 0.47788 ( 6904) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 1.004 Fit side-chains revert: symmetry clash REVERT: A 17 GLN cc_start: 0.8544 (tm-30) cc_final: 0.8155 (tp40) REVERT: C 17 GLN cc_start: 0.8509 (tm-30) cc_final: 0.8084 (tp40) REVERT: C 148 LEU cc_start: 0.8408 (mt) cc_final: 0.8192 (mt) REVERT: D 17 GLN cc_start: 0.8476 (tm-30) cc_final: 0.8060 (tp40) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.1671 time to fit residues: 26.3751 Evaluate side-chains 96 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 24 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 57 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 3 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 47 optimal weight: 0.5980 chunk 33 optimal weight: 0.0370 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 ASN ** B 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 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 = 0.4053 r_free = 0.4053 target = 0.183114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.147279 restraints weight = 6715.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 13)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.147279 restraints weight = 6552.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.147279 restraints weight = 6551.574| |-----------------------------------------------------------------------------| r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.3402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5080 Z= 0.121 Angle : 0.494 6.193 6904 Z= 0.249 Chirality : 0.037 0.115 748 Planarity : 0.003 0.025 908 Dihedral : 3.268 12.454 676 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % 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: 2.36 (0.34), residues: 616 helix: 2.98 (0.27), residues: 344 sheet: 0.13 (0.53), residues: 84 loop : -0.50 (0.45), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 113 HIS 0.004 0.001 HIS A 98 PHE 0.009 0.001 PHE D 117 TYR 0.011 0.001 TYR D 58 ARG 0.005 0.001 ARG B 127 Details of bonding type rmsd hydrogen bonds : bond 0.03879 ( 299) hydrogen bonds : angle 3.97094 ( 885) covalent geometry : bond 0.00277 ( 5080) covalent geometry : angle 0.49436 ( 6904) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.541 Fit side-chains REVERT: A 17 GLN cc_start: 0.8528 (tm-30) cc_final: 0.8154 (tp40) REVERT: C 17 GLN cc_start: 0.8508 (tm-30) cc_final: 0.8072 (tp40) REVERT: D 17 GLN cc_start: 0.8478 (tm-30) cc_final: 0.8068 (tp40) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.1992 time to fit residues: 29.5468 Evaluate side-chains 94 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 31 optimal weight: 0.4980 chunk 43 optimal weight: 0.0670 chunk 26 optimal weight: 0.9980 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 ASN ** B 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 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 = 0.4034 r_free = 0.4034 target = 0.181157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.146068 restraints weight = 6973.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.146049 restraints weight = 7013.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.146049 restraints weight = 7031.175| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.3552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5080 Z= 0.133 Angle : 0.524 6.420 6904 Z= 0.266 Chirality : 0.037 0.112 748 Planarity : 0.003 0.025 908 Dihedral : 3.333 13.742 676 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % 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: 2.36 (0.34), residues: 616 helix: 2.99 (0.27), residues: 344 sheet: 0.16 (0.54), residues: 84 loop : -0.53 (0.45), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 128 HIS 0.004 0.001 HIS A 98 PHE 0.010 0.002 PHE D 153 TYR 0.011 0.001 TYR D 58 ARG 0.006 0.001 ARG C 127 Details of bonding type rmsd hydrogen bonds : bond 0.04045 ( 299) hydrogen bonds : angle 4.03173 ( 885) covalent geometry : bond 0.00306 ( 5080) covalent geometry : angle 0.52380 ( 6904) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.545 Fit side-chains revert: symmetry clash REVERT: A 6 GLU cc_start: 0.7467 (tp30) cc_final: 0.6870 (tp30) REVERT: A 17 GLN cc_start: 0.8526 (tm-30) cc_final: 0.8160 (tp40) REVERT: C 17 GLN cc_start: 0.8504 (tm-30) cc_final: 0.8076 (tp40) REVERT: D 17 GLN cc_start: 0.8488 (tm-30) cc_final: 0.8088 (tp40) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.1221 time to fit residues: 17.1837 Evaluate side-chains 91 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 47 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 56 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 19 optimal weight: 0.1980 chunk 38 optimal weight: 1.9990 chunk 2 optimal weight: 0.0670 chunk 57 optimal weight: 3.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 ASN ** B 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 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 = 0.4040 r_free = 0.4040 target = 0.182301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.147077 restraints weight = 6800.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.147077 restraints weight = 6812.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.147077 restraints weight = 6812.406| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5080 Z= 0.115 Angle : 0.507 6.986 6904 Z= 0.250 Chirality : 0.037 0.116 748 Planarity : 0.003 0.025 908 Dihedral : 3.250 12.745 676 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % 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: 2.35 (0.34), residues: 616 helix: 2.94 (0.27), residues: 348 sheet: 0.12 (0.53), residues: 84 loop : -0.52 (0.46), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 128 HIS 0.003 0.001 HIS A 98 PHE 0.008 0.001 PHE D 117 TYR 0.005 0.001 TYR D 58 ARG 0.007 0.001 ARG C 127 Details of bonding type rmsd hydrogen bonds : bond 0.03673 ( 299) hydrogen bonds : angle 3.96296 ( 885) covalent geometry : bond 0.00263 ( 5080) covalent geometry : angle 0.50735 ( 6904) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.511 Fit side-chains REVERT: A 6 GLU cc_start: 0.7529 (tp30) cc_final: 0.6895 (tp30) REVERT: A 17 GLN cc_start: 0.8526 (tm-30) cc_final: 0.8108 (tp40) REVERT: B 64 GLU cc_start: 0.5744 (mm-30) cc_final: 0.5437 (mp0) REVERT: C 17 GLN cc_start: 0.8463 (tm-30) cc_final: 0.8058 (tp40) REVERT: D 17 GLN cc_start: 0.8474 (tm-30) cc_final: 0.8033 (tp40) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.1290 time to fit residues: 17.8810 Evaluate side-chains 92 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 16 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 58 optimal weight: 0.0270 chunk 32 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 9 optimal weight: 8.9990 chunk 36 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 overall best weight: 1.3244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 ASN ** B 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 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 = 0.3984 r_free = 0.3984 target = 0.175385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.143171 restraints weight = 7021.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.139594 restraints weight = 7088.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.139427 restraints weight = 8684.701| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.3779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 5080 Z= 0.200 Angle : 0.597 7.899 6904 Z= 0.306 Chirality : 0.039 0.112 748 Planarity : 0.003 0.023 908 Dihedral : 3.504 13.271 676 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % 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: 2.13 (0.35), residues: 616 helix: 2.86 (0.28), residues: 344 sheet: 0.21 (0.54), residues: 84 loop : -0.85 (0.45), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 128 HIS 0.005 0.001 HIS A 98 PHE 0.012 0.002 PHE B 24 TYR 0.014 0.002 TYR D 58 ARG 0.004 0.001 ARG C 127 Details of bonding type rmsd hydrogen bonds : bond 0.05206 ( 299) hydrogen bonds : angle 4.48910 ( 885) covalent geometry : bond 0.00474 ( 5080) covalent geometry : angle 0.59738 ( 6904) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.597 Fit side-chains REVERT: A 6 GLU cc_start: 0.7583 (tp30) cc_final: 0.6999 (tp30) REVERT: A 17 GLN cc_start: 0.8569 (tm-30) cc_final: 0.8207 (tp40) REVERT: C 17 GLN cc_start: 0.8503 (tm-30) cc_final: 0.8132 (tp40) REVERT: D 17 GLN cc_start: 0.8492 (tm-30) cc_final: 0.8148 (tp40) REVERT: D 58 TYR cc_start: 0.8388 (m-10) cc_final: 0.8067 (m-10) REVERT: D 64 GLU cc_start: 0.5324 (mp0) cc_final: 0.5047 (mp0) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.1449 time to fit residues: 20.1596 Evaluate side-chains 89 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 21 optimal weight: 0.8980 chunk 32 optimal weight: 0.5980 chunk 6 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 1 optimal weight: 0.5980 chunk 42 optimal weight: 0.0040 chunk 33 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 35 optimal weight: 0.0010 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 ASN B 74 ASN ** B 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.182809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.147525 restraints weight = 6868.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.147526 restraints weight = 6811.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.147526 restraints weight = 6810.829| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.3929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 5080 Z= 0.111 Angle : 0.522 7.438 6904 Z= 0.257 Chirality : 0.038 0.119 748 Planarity : 0.003 0.026 908 Dihedral : 3.453 12.942 676 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % 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: 2.32 (0.34), residues: 616 helix: 3.04 (0.27), residues: 344 sheet: 0.15 (0.53), residues: 84 loop : -0.75 (0.45), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 128 HIS 0.003 0.000 HIS A 98 PHE 0.010 0.001 PHE B 153 TYR 0.014 0.001 TYR B 58 ARG 0.007 0.001 ARG C 127 Details of bonding type rmsd hydrogen bonds : bond 0.03662 ( 299) hydrogen bonds : angle 4.05396 ( 885) covalent geometry : bond 0.00250 ( 5080) covalent geometry : angle 0.52175 ( 6904) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1849.89 seconds wall clock time: 33 minutes 27.53 seconds (2007.53 seconds total)