Starting phenix.real_space_refine on Thu Nov 14 10:41:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p0a_17331/11_2024/8p0a_17331.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p0a_17331/11_2024/8p0a_17331.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p0a_17331/11_2024/8p0a_17331.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p0a_17331/11_2024/8p0a_17331.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p0a_17331/11_2024/8p0a_17331.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p0a_17331/11_2024/8p0a_17331.cif" } resolution = 3.67 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= 0.023 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 21 5.16 5 C 3656 2.51 5 N 989 2.21 5 O 1090 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 5764 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2805 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 355, 2796 Classifications: {'peptide': 355} Link IDs: {'PTRANS': 14, 'TRANS': 340} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 355, 2796 Classifications: {'peptide': 355} Link IDs: {'PTRANS': 14, 'TRANS': 340} Chain breaks: 1 bond proxies already assigned to first conformer: 2836 Chain: "B" Number of atoms: 2507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2507 Classifications: {'peptide': 314} Link IDs: {'PTRANS': 10, 'TRANS': 303} Chain breaks: 2 Chain: "C" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 388 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AGLN A 137 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN A 137 " occ=0.50 Time building chain proxies: 5.10, per 1000 atoms: 0.88 Number of scatterers: 5764 At special positions: 0 Unit cell: (75.684, 93.704, 99.11, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 21 16.00 P 6 15.00 Mg 2 11.99 O 1090 8.00 N 989 7.00 C 3656 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: 1.54 Conformation dependent library (CDL) restraints added in 1.2 seconds 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1354 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 8 sheets defined 38.4% alpha, 14.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 37 through 48 removed outlier: 3.874A pdb=" N LEU A 41 " --> pdb=" O GLY A 37 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N MET A 42 " --> pdb=" O LYS A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 71 removed outlier: 3.813A pdb=" N VAL A 70 " --> pdb=" O GLY A 67 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY A 71 " --> pdb=" O ALA A 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 67 through 71' Processing helix chain 'A' and resid 113 through 123 Processing helix chain 'A' and resid 138 through 144 removed outlier: 3.717A pdb=" N ALA A 144 " --> pdb=" O VAL A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 159 removed outlier: 4.122A pdb=" N ALA A 153 " --> pdb=" O LYS A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 167 removed outlier: 5.059A pdb=" N GLN A 166 " --> pdb=" O GLU A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 174 removed outlier: 3.795A pdb=" N LYS A 172 " --> pdb=" O TYR A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 1051 through 1057 Processing helix chain 'A' and resid 1059 through 1090 removed outlier: 3.774A pdb=" N LYS A1063 " --> pdb=" O PHE A1059 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N SER A1076 " --> pdb=" O ALA A1072 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASP A1082 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N GLU A1083 " --> pdb=" O THR A1079 " (cutoff:3.500A) Processing helix chain 'A' and resid 1124 through 1128 removed outlier: 3.600A pdb=" N ASN A1127 " --> pdb=" O PRO A1124 " (cutoff:3.500A) Processing helix chain 'A' and resid 1129 through 1142 removed outlier: 3.750A pdb=" N THR A1134 " --> pdb=" O GLY A1130 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL A1135 " --> pdb=" O GLY A1131 " (cutoff:3.500A) Processing helix chain 'A' and resid 1163 through 1178 removed outlier: 4.043A pdb=" N GLY A1168 " --> pdb=" O ASN A1164 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N LYS A1169 " --> pdb=" O THR A1165 " (cutoff:3.500A) Processing helix chain 'A' and resid 1190 through 1196 removed outlier: 3.661A pdb=" N TYR A1194 " --> pdb=" O LYS A1190 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS A1196 " --> pdb=" O GLU A1192 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 46 Processing helix chain 'B' and resid 59 through 64 Processing helix chain 'B' and resid 117 through 120 Processing helix chain 'B' and resid 121 through 128 Processing helix chain 'B' and resid 151 through 162 removed outlier: 3.544A pdb=" N ARG B 155 " --> pdb=" O PRO B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 1033 through 1048 Processing helix chain 'B' and resid 1111 through 1115 Processing helix chain 'B' and resid 1118 through 1135 Processing helix chain 'B' and resid 1150 through 1163 removed outlier: 4.090A pdb=" N MET B1160 " --> pdb=" O ALA B1156 " (cutoff:3.500A) Processing helix chain 'B' and resid 1178 through 1183 removed outlier: 3.873A pdb=" N GLU B1181 " --> pdb=" O GLU B1178 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER B1182 " --> pdb=" O LEU B1179 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA B1183 " --> pdb=" O LEU B1180 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1178 through 1183' Processing helix chain 'B' and resid 1202 through 1212 removed outlier: 4.107A pdb=" N ASP B1212 " --> pdb=" O ASP B1208 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 585 Processing helix chain 'C' and resid 589 through 603 Processing helix chain 'C' and resid 604 through 607 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 10 removed outlier: 5.705A pdb=" N LEU A 4 " --> pdb=" O SER A 85 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N SER A 85 " --> pdb=" O LEU A 4 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N LEU A 6 " --> pdb=" O VAL A 83 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA A 78 " --> pdb=" O ILE A 98 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N TYR A 105 " --> pdb=" O VAL A 112 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 30 removed outlier: 6.235A pdb=" N PHE A1153 " --> pdb=" O ILE A1185 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N ILE A1187 " --> pdb=" O PHE A1153 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N LEU A1155 " --> pdb=" O ILE A1187 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1095 through 1100 Processing sheet with id=AA4, first strand: chain 'A' and resid 1202 through 1206 Processing sheet with id=AA5, first strand: chain 'B' and resid 5 through 9 removed outlier: 3.698A pdb=" N GLN B 5 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL B 78 " --> pdb=" O ARG B 100 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1139 through 1143 removed outlier: 5.999A pdb=" N ASN B 28 " --> pdb=" O THR B1172 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N TYR B1187 " --> pdb=" O HIS B 27 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL B 29 " --> pdb=" O TYR B1187 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N VAL B1189 " --> pdb=" O VAL B 29 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N VAL B 31 " --> pdb=" O VAL B1189 " (cutoff:3.500A) removed outlier: 9.115A pdb=" N PHE B1191 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ARG B1192 " --> pdb=" O VAL B1195 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1054 through 1057 Processing sheet with id=AA8, first strand: chain 'C' and resid 609 through 610 removed outlier: 3.635A pdb=" N THR C 623 " --> pdb=" O GLU C 610 " (cutoff:3.500A) 215 hydrogen bonds defined for protein. 591 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: 1.56 Time building geometry restraints manager: 1.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1881 1.34 - 1.46: 996 1.46 - 1.58: 2944 1.58 - 1.69: 9 1.69 - 1.81: 36 Bond restraints: 5866 Sorted by residual: bond pdb=" CB LYS B 105 " pdb=" CG LYS B 105 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.11e+00 bond pdb=" O3B ATP B2000 " pdb=" PB ATP B2000 " ideal model delta sigma weight residual 1.592 1.564 0.028 3.00e-02 1.11e+03 8.60e-01 bond pdb=" C ALA A 68 " pdb=" N PRO A 69 " ideal model delta sigma weight residual 1.339 1.370 -0.031 3.40e-02 8.65e+02 8.42e-01 bond pdb=" CG LYS B 105 " pdb=" CD LYS B 105 " ideal model delta sigma weight residual 1.520 1.547 -0.027 3.00e-02 1.11e+03 7.88e-01 bond pdb=" CB ASN A1071 " pdb=" CG ASN A1071 " ideal model delta sigma weight residual 1.516 1.495 0.021 2.50e-02 1.60e+03 7.16e-01 ... (remaining 5861 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 7701 1.80 - 3.61: 176 3.61 - 5.41: 18 5.41 - 7.21: 4 7.21 - 9.02: 5 Bond angle restraints: 7904 Sorted by residual: angle pdb=" C LYS A1056 " pdb=" N GLN A1057 " pdb=" CA GLN A1057 " ideal model delta sigma weight residual 121.94 115.15 6.79 2.00e+00 2.50e-01 1.15e+01 angle pdb=" CB LYS B 105 " pdb=" CG LYS B 105 " pdb=" CD LYS B 105 " ideal model delta sigma weight residual 111.30 118.57 -7.27 2.30e+00 1.89e-01 9.98e+00 angle pdb=" CB MET A 145 " pdb=" CG MET A 145 " pdb=" SD MET A 145 " ideal model delta sigma weight residual 112.70 121.72 -9.02 3.00e+00 1.11e-01 9.04e+00 angle pdb=" N PHE B 53 " pdb=" CA PHE B 53 " pdb=" C PHE B 53 " ideal model delta sigma weight residual 114.04 110.40 3.64 1.24e+00 6.50e-01 8.60e+00 angle pdb=" C LYS A 59 " pdb=" N THR A 60 " pdb=" CA THR A 60 " ideal model delta sigma weight residual 121.54 126.73 -5.19 1.91e+00 2.74e-01 7.37e+00 ... (remaining 7899 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 3179 17.72 - 35.44: 346 35.44 - 53.16: 66 53.16 - 70.88: 27 70.88 - 88.60: 8 Dihedral angle restraints: 3626 sinusoidal: 1535 harmonic: 2091 Sorted by residual: dihedral pdb=" CA GLU A 174 " pdb=" C GLU A 174 " pdb=" N MET A 175 " pdb=" CA MET A 175 " ideal model delta harmonic sigma weight residual 180.00 161.63 18.37 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA GLN A1157 " pdb=" C GLN A1157 " pdb=" N ILE A1158 " pdb=" CA ILE A1158 " ideal model delta harmonic sigma weight residual 180.00 161.93 18.07 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA VAL A1186 " pdb=" C VAL A1186 " pdb=" N ILE A1187 " pdb=" CA ILE A1187 " ideal model delta harmonic sigma weight residual 180.00 162.13 17.87 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 3623 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 578 0.041 - 0.083: 199 0.083 - 0.124: 84 0.124 - 0.165: 9 0.165 - 0.206: 2 Chirality restraints: 872 Sorted by residual: chirality pdb=" CB ILE B 138 " pdb=" CA ILE B 138 " pdb=" CG1 ILE B 138 " pdb=" CG2 ILE B 138 " both_signs ideal model delta sigma weight residual False 2.64 2.85 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CB ILE A 126 " pdb=" CA ILE A 126 " pdb=" CG1 ILE A 126 " pdb=" CG2 ILE A 126 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 6.94e-01 chirality pdb=" CA ILE B 138 " pdb=" N ILE B 138 " pdb=" C ILE B 138 " pdb=" CB ILE B 138 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.05e-01 ... (remaining 869 not shown) Planarity restraints: 1015 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 21 " 0.027 5.00e-02 4.00e+02 4.10e-02 2.69e+00 pdb=" N PRO B 22 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO B 22 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 22 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 57 " -0.026 5.00e-02 4.00e+02 3.90e-02 2.43e+00 pdb=" N PRO B 58 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO B 58 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 58 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET A 145 " -0.007 2.00e-02 2.50e+03 1.42e-02 2.00e+00 pdb=" C MET A 145 " 0.024 2.00e-02 2.50e+03 pdb=" O MET A 145 " -0.009 2.00e-02 2.50e+03 pdb=" N LYS A 146 " -0.008 2.00e-02 2.50e+03 ... (remaining 1012 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 103 2.61 - 3.18: 5329 3.18 - 3.75: 9352 3.75 - 4.33: 12558 4.33 - 4.90: 20141 Nonbonded interactions: 47483 Sorted by model distance: nonbonded pdb=" O1G ATP B2000 " pdb="MG MG B2001 " model vdw 2.036 2.170 nonbonded pdb=" O1B ATP A2000 " pdb="MG MG A2001 " model vdw 2.036 2.170 nonbonded pdb=" O3B ATP B2000 " pdb="MG MG B2001 " model vdw 2.078 2.170 nonbonded pdb=" O2B ATP B2000 " pdb="MG MG B2001 " model vdw 2.126 2.170 nonbonded pdb=" OG1 THR A1217 " pdb=" O PRO C 616 " model vdw 2.134 3.040 ... (remaining 47478 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 18.710 Find NCS groups from input model: 0.090 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6824 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 0.032 5866 Z= 0.209 Angle : 0.655 9.018 7904 Z= 0.343 Chirality : 0.048 0.206 872 Planarity : 0.004 0.043 1015 Dihedral : 16.306 88.597 2272 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 19.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.31), residues: 709 helix: -1.39 (0.31), residues: 244 sheet: -0.82 (0.46), residues: 144 loop : -1.32 (0.34), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 66 PHE 0.012 0.002 PHE A1067 TYR 0.016 0.002 TYR A1194 ARG 0.009 0.001 ARG A 160 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.7279 (ptm) cc_final: 0.6985 (ptm) REVERT: A 1217 THR cc_start: 0.8498 (p) cc_final: 0.8261 (p) REVERT: B 1202 THR cc_start: 0.7696 (m) cc_final: 0.7446 (m) REVERT: C 607 GLN cc_start: 0.7137 (pp30) cc_final: 0.6702 (pp30) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.1869 time to fit residues: 29.8919 Evaluate side-chains 99 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 18 optimal weight: 6.9990 chunk 35 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 63 optimal weight: 0.7980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1144 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6901 moved from start: 0.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5866 Z= 0.274 Angle : 0.682 10.671 7904 Z= 0.353 Chirality : 0.050 0.179 872 Planarity : 0.004 0.041 1015 Dihedral : 12.014 89.988 841 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 18.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 1.29 % Allowed : 12.14 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.31), residues: 709 helix: -0.99 (0.32), residues: 238 sheet: -0.80 (0.46), residues: 145 loop : -1.23 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 115 PHE 0.023 0.002 PHE C 600 TYR 0.015 0.002 TYR B 137 ARG 0.006 0.001 ARG A 160 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 105 time to evaluate : 0.582 Fit side-chains revert: symmetry clash REVERT: B 141 GLN cc_start: 0.7878 (OUTLIER) cc_final: 0.7638 (tt0) REVERT: B 1115 LEU cc_start: 0.8161 (mm) cc_final: 0.7889 (mm) REVERT: B 1211 GLU cc_start: 0.7864 (tp30) cc_final: 0.7563 (tp30) REVERT: C 596 LYS cc_start: 0.8383 (ptpp) cc_final: 0.8006 (ptpp) REVERT: C 607 GLN cc_start: 0.7163 (pp30) cc_final: 0.6684 (pp30) outliers start: 8 outliers final: 6 residues processed: 110 average time/residue: 0.1720 time to fit residues: 25.3112 Evaluate side-chains 113 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 106 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ASP Chi-restraints excluded: chain A residue 1165 THR Chi-restraints excluded: chain A residue 1176 GLU Chi-restraints excluded: chain A residue 1203 VAL Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 141 GLN Chi-restraints excluded: chain B residue 1055 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 35 optimal weight: 0.1980 chunk 19 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 chunk 56 optimal weight: 0.5980 chunk 21 optimal weight: 6.9990 chunk 51 optimal weight: 4.9990 chunk 62 optimal weight: 0.3980 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1080 ASN B1119 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6849 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5866 Z= 0.210 Angle : 0.646 10.764 7904 Z= 0.329 Chirality : 0.048 0.176 872 Planarity : 0.004 0.049 1015 Dihedral : 11.350 89.279 841 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 1.46 % Allowed : 15.86 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.31), residues: 709 helix: -1.01 (0.31), residues: 246 sheet: -0.67 (0.46), residues: 143 loop : -1.09 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 115 PHE 0.022 0.002 PHE B 47 TYR 0.017 0.002 TYR A1194 ARG 0.004 0.000 ARG A1066 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 114 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 141 GLN cc_start: 0.7848 (OUTLIER) cc_final: 0.7599 (tt0) REVERT: B 1115 LEU cc_start: 0.8155 (mm) cc_final: 0.7797 (mm) REVERT: B 1119 GLN cc_start: 0.7395 (OUTLIER) cc_final: 0.7153 (mm-40) REVERT: B 1211 GLU cc_start: 0.8169 (tp30) cc_final: 0.7780 (tp30) REVERT: C 607 GLN cc_start: 0.7245 (pp30) cc_final: 0.6736 (pp30) outliers start: 9 outliers final: 6 residues processed: 120 average time/residue: 0.1891 time to fit residues: 29.7264 Evaluate side-chains 108 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 100 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ASP Chi-restraints excluded: chain A residue 1176 GLU Chi-restraints excluded: chain A residue 1217 THR Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 141 GLN Chi-restraints excluded: chain B residue 1055 LEU Chi-restraints excluded: chain B residue 1119 GLN Chi-restraints excluded: chain B residue 1149 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 47 optimal weight: 6.9990 chunk 33 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 38 optimal weight: 0.3980 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1112 ASN B 141 GLN B1193 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6967 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 5866 Z= 0.333 Angle : 0.694 10.375 7904 Z= 0.358 Chirality : 0.050 0.203 872 Planarity : 0.004 0.046 1015 Dihedral : 11.317 87.280 841 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 19.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 2.91 % Allowed : 17.64 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.31), residues: 709 helix: -1.00 (0.32), residues: 239 sheet: -1.03 (0.46), residues: 138 loop : -1.22 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 115 PHE 0.021 0.002 PHE B 47 TYR 0.015 0.002 TYR B 137 ARG 0.004 0.000 ARG A1066 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 102 time to evaluate : 0.580 Fit side-chains revert: symmetry clash REVERT: A 160 ARG cc_start: 0.8169 (mmm-85) cc_final: 0.7791 (mmm160) REVERT: B 1115 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7917 (mt) REVERT: B 1211 GLU cc_start: 0.8260 (tp30) cc_final: 0.7839 (tp30) REVERT: C 607 GLN cc_start: 0.7291 (pp30) cc_final: 0.6714 (pp30) outliers start: 18 outliers final: 13 residues processed: 116 average time/residue: 0.1728 time to fit residues: 26.6125 Evaluate side-chains 116 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 63 ASP Chi-restraints excluded: chain A residue 1159 ASP Chi-restraints excluded: chain A residue 1165 THR Chi-restraints excluded: chain A residue 1176 GLU Chi-restraints excluded: chain A residue 1203 VAL Chi-restraints excluded: chain A residue 1217 THR Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 141 GLN Chi-restraints excluded: chain B residue 1055 LEU Chi-restraints excluded: chain B residue 1115 LEU Chi-restraints excluded: chain B residue 1149 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 0 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 46 optimal weight: 6.9990 chunk 34 optimal weight: 6.9990 chunk 60 optimal weight: 0.7980 chunk 17 optimal weight: 5.9990 chunk 22 optimal weight: 0.0570 chunk 13 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1112 ASN B 17 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6884 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5866 Z= 0.209 Angle : 0.659 12.321 7904 Z= 0.334 Chirality : 0.048 0.187 872 Planarity : 0.004 0.045 1015 Dihedral : 10.916 89.087 841 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 16.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 2.75 % Allowed : 19.42 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.31), residues: 709 helix: -0.91 (0.32), residues: 240 sheet: -0.83 (0.45), residues: 146 loop : -1.15 (0.35), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 115 PHE 0.021 0.001 PHE A1067 TYR 0.019 0.002 TYR A1194 ARG 0.003 0.000 ARG A1066 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.7385 (ptm) cc_final: 0.7044 (ptm) REVERT: B 141 GLN cc_start: 0.7854 (OUTLIER) cc_final: 0.7583 (tt0) REVERT: B 1115 LEU cc_start: 0.8107 (mm) cc_final: 0.7842 (mt) REVERT: B 1178 GLU cc_start: 0.7488 (mm-30) cc_final: 0.7282 (mm-30) REVERT: B 1211 GLU cc_start: 0.8288 (tp30) cc_final: 0.7845 (tp30) REVERT: C 607 GLN cc_start: 0.7212 (pp30) cc_final: 0.6683 (pp30) outliers start: 17 outliers final: 13 residues processed: 116 average time/residue: 0.1642 time to fit residues: 25.6731 Evaluate side-chains 108 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 63 ASP Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 1159 ASP Chi-restraints excluded: chain A residue 1165 THR Chi-restraints excluded: chain A residue 1176 GLU Chi-restraints excluded: chain A residue 1203 VAL Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 141 GLN Chi-restraints excluded: chain B residue 1048 VAL Chi-restraints excluded: chain B residue 1055 LEU Chi-restraints excluded: chain B residue 1149 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 16 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 35 optimal weight: 0.0980 chunk 65 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 38 optimal weight: 0.3980 chunk 49 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1112 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6860 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5866 Z= 0.197 Angle : 0.662 12.924 7904 Z= 0.333 Chirality : 0.048 0.209 872 Planarity : 0.004 0.042 1015 Dihedral : 10.562 86.495 841 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 3.56 % Allowed : 20.23 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.32), residues: 709 helix: -0.76 (0.32), residues: 240 sheet: -0.75 (0.46), residues: 146 loop : -1.16 (0.35), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 115 PHE 0.026 0.001 PHE B 47 TYR 0.019 0.002 TYR A1194 ARG 0.003 0.000 ARG A 171 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.7361 (ptm) cc_final: 0.7049 (ptm) REVERT: A 1057 GLN cc_start: 0.8961 (OUTLIER) cc_final: 0.8671 (pm20) REVERT: B 47 PHE cc_start: 0.7915 (t80) cc_final: 0.7682 (t80) REVERT: B 141 GLN cc_start: 0.7787 (OUTLIER) cc_final: 0.7331 (tt0) REVERT: B 1115 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7868 (mt) REVERT: B 1211 GLU cc_start: 0.8294 (tp30) cc_final: 0.7898 (tp30) REVERT: C 607 GLN cc_start: 0.7239 (pp30) cc_final: 0.6742 (pp30) outliers start: 22 outliers final: 14 residues processed: 118 average time/residue: 0.1822 time to fit residues: 28.3076 Evaluate side-chains 111 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 94 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 63 ASP Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 1057 GLN Chi-restraints excluded: chain A residue 1159 ASP Chi-restraints excluded: chain A residue 1165 THR Chi-restraints excluded: chain A residue 1176 GLU Chi-restraints excluded: chain A residue 1203 VAL Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 141 GLN Chi-restraints excluded: chain B residue 1045 GLN Chi-restraints excluded: chain B residue 1048 VAL Chi-restraints excluded: chain B residue 1055 LEU Chi-restraints excluded: chain B residue 1115 LEU Chi-restraints excluded: chain B residue 1149 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 38 optimal weight: 0.4980 chunk 57 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 41 optimal weight: 8.9990 chunk 31 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 40 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1112 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6869 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5866 Z= 0.209 Angle : 0.662 11.205 7904 Z= 0.337 Chirality : 0.048 0.226 872 Planarity : 0.004 0.041 1015 Dihedral : 10.499 85.717 841 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 3.40 % Allowed : 21.36 % Favored : 75.24 % 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: -1.55 (0.32), residues: 709 helix: -0.89 (0.32), residues: 245 sheet: -0.72 (0.46), residues: 146 loop : -1.15 (0.36), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 115 PHE 0.020 0.002 PHE B 47 TYR 0.018 0.002 TYR A1194 ARG 0.003 0.000 ARG A1066 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 102 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.7327 (ptm) cc_final: 0.7001 (ptm) REVERT: B 93 LYS cc_start: 0.7357 (tptp) cc_final: 0.7154 (tptt) REVERT: B 141 GLN cc_start: 0.7838 (OUTLIER) cc_final: 0.7389 (tt0) REVERT: B 1115 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7883 (mt) REVERT: B 1211 GLU cc_start: 0.8338 (tp30) cc_final: 0.7923 (tp30) REVERT: C 607 GLN cc_start: 0.7282 (pp30) cc_final: 0.6774 (pp30) outliers start: 21 outliers final: 16 residues processed: 117 average time/residue: 0.1846 time to fit residues: 28.2768 Evaluate side-chains 113 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 95 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 63 ASP Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 1057 GLN Chi-restraints excluded: chain A residue 1159 ASP Chi-restraints excluded: chain A residue 1165 THR Chi-restraints excluded: chain A residue 1176 GLU Chi-restraints excluded: chain A residue 1203 VAL Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 141 GLN Chi-restraints excluded: chain B residue 1045 GLN Chi-restraints excluded: chain B residue 1048 VAL Chi-restraints excluded: chain B residue 1055 LEU Chi-restraints excluded: chain B residue 1115 LEU Chi-restraints excluded: chain B residue 1149 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 13 optimal weight: 0.0040 chunk 42 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 58 optimal weight: 0.0670 chunk 62 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.9934 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6907 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5866 Z= 0.247 Angle : 0.681 11.627 7904 Z= 0.348 Chirality : 0.049 0.243 872 Planarity : 0.004 0.040 1015 Dihedral : 10.537 85.779 841 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 16.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 3.40 % Allowed : 21.52 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.32), residues: 709 helix: -0.57 (0.33), residues: 231 sheet: -0.83 (0.45), residues: 146 loop : -1.25 (0.35), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 115 PHE 0.037 0.002 PHE C 600 TYR 0.017 0.002 TYR A1194 ARG 0.003 0.000 ARG B1176 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ASP cc_start: 0.8080 (OUTLIER) cc_final: 0.7578 (t0) REVERT: A 82 MET cc_start: 0.7381 (ptm) cc_final: 0.6991 (ptm) REVERT: B 141 GLN cc_start: 0.7973 (OUTLIER) cc_final: 0.7467 (tt0) REVERT: B 1115 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7830 (mt) REVERT: B 1211 GLU cc_start: 0.8427 (tp30) cc_final: 0.8000 (tp30) REVERT: C 607 GLN cc_start: 0.7294 (pp30) cc_final: 0.6769 (pp30) outliers start: 21 outliers final: 14 residues processed: 113 average time/residue: 0.1778 time to fit residues: 26.6055 Evaluate side-chains 114 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 63 ASP Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 1057 GLN Chi-restraints excluded: chain A residue 1159 ASP Chi-restraints excluded: chain A residue 1165 THR Chi-restraints excluded: chain A residue 1176 GLU Chi-restraints excluded: chain A residue 1203 VAL Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 141 GLN Chi-restraints excluded: chain B residue 1045 GLN Chi-restraints excluded: chain B residue 1048 VAL Chi-restraints excluded: chain B residue 1055 LEU Chi-restraints excluded: chain B residue 1115 LEU Chi-restraints excluded: chain B residue 1149 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 27 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 41 optimal weight: 9.9990 chunk 66 optimal weight: 6.9990 chunk 40 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 5866 Z= 0.302 Angle : 0.725 13.661 7904 Z= 0.369 Chirality : 0.050 0.246 872 Planarity : 0.004 0.040 1015 Dihedral : 10.740 89.069 841 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 19.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 3.40 % Allowed : 22.01 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.32), residues: 709 helix: -0.82 (0.32), residues: 236 sheet: -1.05 (0.44), residues: 146 loop : -1.25 (0.35), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 115 PHE 0.041 0.002 PHE C 600 TYR 0.016 0.002 TYR A1173 ARG 0.004 0.000 ARG A 57 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 103 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ASP cc_start: 0.8158 (OUTLIER) cc_final: 0.7599 (t0) REVERT: B 141 GLN cc_start: 0.7943 (OUTLIER) cc_final: 0.7353 (tt0) REVERT: B 1115 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7896 (mm) REVERT: B 1211 GLU cc_start: 0.8439 (tp30) cc_final: 0.7997 (tp30) REVERT: C 607 GLN cc_start: 0.7312 (pp30) cc_final: 0.6744 (pp30) outliers start: 21 outliers final: 14 residues processed: 119 average time/residue: 0.1691 time to fit residues: 26.7841 Evaluate side-chains 119 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 102 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 63 ASP Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 1057 GLN Chi-restraints excluded: chain A residue 1159 ASP Chi-restraints excluded: chain A residue 1165 THR Chi-restraints excluded: chain A residue 1176 GLU Chi-restraints excluded: chain A residue 1203 VAL Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 141 GLN Chi-restraints excluded: chain B residue 1045 GLN Chi-restraints excluded: chain B residue 1048 VAL Chi-restraints excluded: chain B residue 1055 LEU Chi-restraints excluded: chain B residue 1115 LEU Chi-restraints excluded: chain B residue 1149 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 69 optimal weight: 9.9990 chunk 64 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 17 optimal weight: 8.9990 chunk 51 optimal weight: 0.5980 chunk 8 optimal weight: 5.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 5866 Z= 0.441 Angle : 0.831 14.331 7904 Z= 0.426 Chirality : 0.053 0.257 872 Planarity : 0.005 0.048 1015 Dihedral : 11.119 88.959 841 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 21.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.63 % Favored : 90.37 % Rotamer: Outliers : 3.07 % Allowed : 22.65 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.31), residues: 709 helix: -1.12 (0.32), residues: 230 sheet: -1.45 (0.43), residues: 146 loop : -1.26 (0.35), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS B 27 PHE 0.043 0.003 PHE C 600 TYR 0.016 0.003 TYR A1173 ARG 0.011 0.001 ARG B1176 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 ASP cc_start: 0.8211 (OUTLIER) cc_final: 0.7524 (t0) REVERT: B 141 GLN cc_start: 0.8051 (OUTLIER) cc_final: 0.7603 (tt0) REVERT: B 1115 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.8009 (mm) REVERT: B 1211 GLU cc_start: 0.8462 (tp30) cc_final: 0.8015 (tp30) REVERT: C 607 GLN cc_start: 0.7335 (pp30) cc_final: 0.6739 (pp30) outliers start: 19 outliers final: 14 residues processed: 114 average time/residue: 0.1698 time to fit residues: 25.8940 Evaluate side-chains 111 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 94 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 63 ASP Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 1057 GLN Chi-restraints excluded: chain A residue 1159 ASP Chi-restraints excluded: chain A residue 1165 THR Chi-restraints excluded: chain A residue 1176 GLU Chi-restraints excluded: chain A residue 1203 VAL Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 141 GLN Chi-restraints excluded: chain B residue 1036 VAL Chi-restraints excluded: chain B residue 1048 VAL Chi-restraints excluded: chain B residue 1055 LEU Chi-restraints excluded: chain B residue 1115 LEU Chi-restraints excluded: chain B residue 1149 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 15 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 23 optimal weight: 0.0970 chunk 57 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 48 optimal weight: 0.3980 chunk 3 optimal weight: 0.0010 chunk 40 optimal weight: 0.3980 chunk 63 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 overall best weight: 0.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.200572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.164487 restraints weight = 20937.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.172513 restraints weight = 10358.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.178138 restraints weight = 5274.978| |-----------------------------------------------------------------------------| r_work (final): 0.4187 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4187 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4187 r_free = 0.4187 target_work(ls_wunit_k1) = 0.175 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4188 r_free = 0.4188 target_work(ls_wunit_k1) = 0.175 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4188 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6794 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5866 Z= 0.210 Angle : 0.734 13.840 7904 Z= 0.371 Chirality : 0.049 0.238 872 Planarity : 0.004 0.041 1015 Dihedral : 10.469 85.715 841 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 17.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 2.75 % Allowed : 23.79 % Favored : 73.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.31), residues: 709 helix: -0.83 (0.33), residues: 236 sheet: -1.14 (0.44), residues: 146 loop : -1.29 (0.35), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 27 PHE 0.043 0.002 PHE C 600 TYR 0.020 0.002 TYR A1194 ARG 0.008 0.001 ARG B1176 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1515.03 seconds wall clock time: 28 minutes 19.86 seconds (1699.86 seconds total)