Starting phenix.real_space_refine on Fri Dec 27 13:06:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pog_17791/12_2024/8pog_17791.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pog_17791/12_2024/8pog_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_17791/12_2024/8pog_17791.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pog_17791/12_2024/8pog_17791.map" model { file = "/net/cci-nas-00/data/ceres_data/8pog_17791/12_2024/8pog_17791.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pog_17791/12_2024/8pog_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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 3.69, per 1000 atoms: 0.74 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: 1.20 Conformation dependent library (CDL) restraints added in 547.4 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: 0.47 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: 1.25 Time building geometry restraints manager: 1.40 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: 0.00 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: 3.350 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: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 15.010 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.190 ------------------------------------------------------------------------------- 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= 0.171 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 *********************** 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 : 0.566 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: 0.1485 time to fit residues: 23.5045 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 : 0.545 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 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= 0.159 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 *********************** 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 : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 GLU cc_start: 0.7364 (tp30) cc_final: 0.6689 (tp30) REVERT: C 17 GLN cc_start: 0.8665 (tm-30) cc_final: 0.8116 (tp40) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.1654 time to fit residues: 27.2061 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 : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5080 Z= 0.215 Angle : 0.494 5.069 6904 Z= 0.258 Chirality : 0.038 0.123 748 Planarity : 0.003 0.026 908 Dihedral : 3.423 13.267 676 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % 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: 2.38 (0.35), residues: 616 helix: 3.03 (0.28), residues: 340 sheet: 0.14 (0.54), residues: 84 loop : -0.48 (0.43), residues: 192 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 0.011 0.002 PHE A 14 TYR 0.010 0.001 TYR D 58 ARG 0.005 0.001 ARG C 142 *********************** 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 121 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.573 Fit side-chains revert: symmetry clash REVERT: A 6 GLU cc_start: 0.7482 (tp30) cc_final: 0.6780 (tp30) REVERT: A 17 GLN cc_start: 0.8623 (tm-30) cc_final: 0.8119 (tp40) REVERT: A 122 GLU cc_start: 0.7457 (mm-30) cc_final: 0.7225 (mm-30) REVERT: B 72 ASN cc_start: 0.7263 (m110) cc_final: 0.7000 (m110) REVERT: B 141 SER cc_start: 0.8537 (t) cc_final: 0.8294 (t) REVERT: C 17 GLN cc_start: 0.8544 (tm-30) cc_final: 0.8073 (tp40) REVERT: D 17 GLN cc_start: 0.8555 (tm-30) cc_final: 0.8184 (tp40) REVERT: D 148 LEU cc_start: 0.8207 (mt) cc_final: 0.7958 (mt) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.1505 time to fit residues: 23.9734 Evaluate side-chains 103 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 0.7980 chunk 28 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 57 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 48 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 ** 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 152 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5080 Z= 0.202 Angle : 0.477 4.991 6904 Z= 0.246 Chirality : 0.037 0.119 748 Planarity : 0.003 0.023 908 Dihedral : 3.451 12.691 676 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % 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: 2.93 (0.28), residues: 344 sheet: 0.13 (0.53), residues: 84 loop : -0.41 (0.45), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 113 HIS 0.004 0.001 HIS A 98 PHE 0.009 0.002 PHE D 117 TYR 0.010 0.001 TYR D 58 ARG 0.006 0.001 ARG C 127 *********************** 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 116 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 GLU cc_start: 0.7535 (tp30) cc_final: 0.6828 (tp30) REVERT: A 17 GLN cc_start: 0.8589 (tm-30) cc_final: 0.8132 (tp40) REVERT: A 52 ILE cc_start: 0.8845 (mm) cc_final: 0.8624 (mm) REVERT: B 93 ASP cc_start: 0.7248 (m-30) cc_final: 0.6988 (p0) REVERT: C 17 GLN cc_start: 0.8538 (tm-30) cc_final: 0.8054 (tp40) REVERT: C 142 ARG cc_start: 0.8308 (mtp-110) cc_final: 0.8025 (mtp85) REVERT: D 17 GLN cc_start: 0.8532 (tm-30) cc_final: 0.8167 (tp40) REVERT: D 148 LEU cc_start: 0.8222 (mt) cc_final: 0.8021 (mt) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.1713 time to fit residues: 25.7913 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 : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 23 optimal weight: 0.4980 chunk 49 optimal weight: 1.9990 chunk 40 optimal weight: 0.0470 chunk 29 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 overall best weight: 0.5278 ------------------------------------------------------------------------------- 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** D 152 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 5080 Z= 0.166 Angle : 0.463 4.986 6904 Z= 0.235 Chirality : 0.037 0.118 748 Planarity : 0.003 0.024 908 Dihedral : 3.331 12.271 676 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % 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: 2.44 (0.34), residues: 616 helix: 3.00 (0.27), residues: 344 sheet: 0.24 (0.53), residues: 84 loop : -0.39 (0.45), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 113 HIS 0.004 0.001 HIS B 115 PHE 0.007 0.001 PHE D 117 TYR 0.003 0.001 TYR B 125 ARG 0.006 0.001 ARG A 127 *********************** 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 119 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.544 Fit side-chains revert: symmetry clash REVERT: A 17 GLN cc_start: 0.8561 (tm-30) cc_final: 0.8121 (tp40) REVERT: A 127 ARG cc_start: 0.8123 (tpp80) cc_final: 0.7867 (tpp80) REVERT: A 141 SER cc_start: 0.7946 (t) cc_final: 0.7734 (t) REVERT: C 17 GLN cc_start: 0.8516 (tm-30) cc_final: 0.8036 (tp40) REVERT: D 17 GLN cc_start: 0.8496 (tm-30) cc_final: 0.8115 (tp40) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.1861 time to fit residues: 28.2415 Evaluate side-chains 102 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 0.4980 chunk 58 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 0.0770 chunk 55 optimal weight: 2.9990 chunk 6 optimal weight: 0.4980 chunk 33 optimal weight: 0.4980 chunk 42 optimal weight: 0.6980 overall best weight: 0.4538 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5080 Z= 0.158 Angle : 0.483 5.395 6904 Z= 0.240 Chirality : 0.037 0.127 748 Planarity : 0.003 0.025 908 Dihedral : 3.311 13.794 676 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % 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: 2.39 (0.34), residues: 616 helix: 2.97 (0.27), residues: 344 sheet: 0.19 (0.54), residues: 84 loop : -0.45 (0.45), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 113 HIS 0.003 0.001 HIS A 98 PHE 0.012 0.001 PHE B 153 TYR 0.004 0.001 TYR D 125 ARG 0.007 0.001 ARG C 142 *********************** 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 116 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.595 Fit side-chains revert: symmetry clash REVERT: A 17 GLN cc_start: 0.8532 (tm-30) cc_final: 0.8124 (tp40) REVERT: C 17 GLN cc_start: 0.8478 (tm-30) cc_final: 0.8004 (tp40) REVERT: D 17 GLN cc_start: 0.8460 (tm-30) cc_final: 0.8097 (tp40) REVERT: D 148 LEU cc_start: 0.8318 (mt) cc_final: 0.8104 (mt) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.1647 time to fit residues: 24.7093 Evaluate side-chains 100 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 35 optimal weight: 0.2980 chunk 26 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 17 optimal weight: 0.0010 chunk 11 optimal weight: 0.7980 chunk 39 optimal weight: 5.9990 overall best weight: 0.5386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5080 Z= 0.174 Angle : 0.493 6.184 6904 Z= 0.247 Chirality : 0.037 0.118 748 Planarity : 0.003 0.030 908 Dihedral : 3.284 13.868 676 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % 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: 2.28 (0.34), residues: 616 helix: 2.85 (0.27), residues: 348 sheet: 0.20 (0.54), residues: 84 loop : -0.52 (0.46), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 113 HIS 0.003 0.001 HIS A 98 PHE 0.007 0.001 PHE D 117 TYR 0.004 0.001 TYR A 58 ARG 0.008 0.001 ARG A 142 *********************** 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 : 0.520 Fit side-chains REVERT: A 17 GLN cc_start: 0.8524 (tm-30) cc_final: 0.8101 (tp40) REVERT: C 17 GLN cc_start: 0.8496 (tm-30) cc_final: 0.8027 (tp40) REVERT: D 17 GLN cc_start: 0.8484 (tm-30) cc_final: 0.8117 (tp40) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.1232 time to fit residues: 18.7102 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 : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 0.0370 chunk 5 optimal weight: 1.9990 chunk 45 optimal weight: 0.0570 chunk 52 optimal weight: 0.7980 chunk 55 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 overall best weight: 0.5376 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5080 Z= 0.182 Angle : 0.523 7.238 6904 Z= 0.258 Chirality : 0.037 0.116 748 Planarity : 0.003 0.033 908 Dihedral : 3.232 12.672 676 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % 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: 2.34 (0.34), residues: 616 helix: 2.99 (0.27), residues: 344 sheet: 0.18 (0.55), residues: 84 loop : -0.58 (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 0.010 0.001 PHE B 153 TYR 0.007 0.001 TYR D 58 ARG 0.009 0.001 ARG A 142 *********************** 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 107 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.533 Fit side-chains REVERT: A 6 GLU cc_start: 0.7650 (tp30) cc_final: 0.6928 (tp30) REVERT: A 17 GLN cc_start: 0.8518 (tm-30) cc_final: 0.8082 (tp40) REVERT: A 64 GLU cc_start: 0.5567 (mp0) cc_final: 0.5367 (mp0) REVERT: C 17 GLN cc_start: 0.8470 (tm-30) cc_final: 0.8025 (tp40) REVERT: D 17 GLN cc_start: 0.8468 (tm-30) cc_final: 0.8101 (tp40) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.1290 time to fit residues: 19.0432 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 : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 35 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 39 optimal weight: 5.9990 chunk 59 optimal weight: 0.0070 chunk 55 optimal weight: 0.5980 chunk 47 optimal weight: 0.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.3579 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= 0.189 Angle : 0.521 7.236 6904 Z= 0.257 Chirality : 0.037 0.114 748 Planarity : 0.003 0.039 908 Dihedral : 3.242 12.264 676 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % 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: 2.33 (0.34), residues: 616 helix: 3.00 (0.27), residues: 344 sheet: 0.07 (0.54), residues: 84 loop : -0.60 (0.45), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 113 HIS 0.004 0.001 HIS A 98 PHE 0.007 0.001 PHE D 117 TYR 0.011 0.001 TYR D 58 ARG 0.008 0.001 ARG A 142 *********************** 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 106 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.573 Fit side-chains revert: symmetry clash REVERT: A 6 GLU cc_start: 0.7643 (tp30) cc_final: 0.6982 (tp30) REVERT: A 17 GLN cc_start: 0.8515 (tm-30) cc_final: 0.8087 (tp40) REVERT: B 64 GLU cc_start: 0.5810 (mm-30) cc_final: 0.5539 (mp0) REVERT: C 17 GLN cc_start: 0.8492 (tm-30) cc_final: 0.8030 (tp40) REVERT: D 17 GLN cc_start: 0.8473 (tm-30) cc_final: 0.8114 (tp40) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.1296 time to fit residues: 19.0086 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 : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 7 optimal weight: 0.2980 chunk 13 optimal weight: 0.6980 chunk 47 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.3646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5080 Z= 0.202 Angle : 0.527 7.620 6904 Z= 0.263 Chirality : 0.037 0.116 748 Planarity : 0.003 0.037 908 Dihedral : 3.224 11.770 676 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % 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: 2.31 (0.34), residues: 616 helix: 3.01 (0.27), residues: 344 sheet: 0.12 (0.54), residues: 84 loop : -0.68 (0.45), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 113 HIS 0.004 0.001 HIS A 98 PHE 0.010 0.002 PHE D 153 TYR 0.009 0.001 TYR D 58 ARG 0.009 0.001 ARG A 142 ********************** 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 102 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.570 Fit side-chains REVERT: A 6 GLU cc_start: 0.7689 (tp30) cc_final: 0.7039 (tp30) REVERT: A 17 GLN cc_start: 0.8527 (tm-30) cc_final: 0.8128 (tp40) REVERT: B 64 GLU cc_start: 0.5744 (mm-30) cc_final: 0.5538 (mp0) REVERT: C 17 GLN cc_start: 0.8479 (tm-30) cc_final: 0.8000 (tp40) REVERT: C 72 ASN cc_start: 0.6920 (m110) cc_final: 0.6586 (m110) REVERT: D 17 GLN cc_start: 0.8470 (tm-30) cc_final: 0.8116 (tp40) REVERT: D 72 ASN cc_start: 0.6694 (m110) cc_final: 0.6437 (m110) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.1268 time to fit residues: 18.2056 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 : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 1.9990 chunk 6 optimal weight: 0.4980 chunk 8 optimal weight: 0.9980 chunk 41 optimal weight: 0.5980 chunk 2 optimal weight: 0.0770 chunk 34 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 overall best weight: 0.5738 ------------------------------------------------------------------------------- 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 = 0.4029 r_free = 0.4029 target = 0.180174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.145751 restraints weight = 6815.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.145749 restraints weight = 6840.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.145747 restraints weight = 6840.689| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.3772 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= 0.183 Angle : 0.515 7.500 6904 Z= 0.254 Chirality : 0.037 0.116 748 Planarity : 0.003 0.036 908 Dihedral : 3.172 12.753 676 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % 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: 2.26 (0.34), residues: 616 helix: 3.00 (0.27), residues: 344 sheet: 0.07 (0.54), residues: 84 loop : -0.76 (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 0.007 0.001 PHE A 14 TYR 0.008 0.001 TYR D 58 ARG 0.008 0.001 ARG A 142 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1348.77 seconds wall clock time: 25 minutes 20.18 seconds (1520.18 seconds total)