Starting phenix.real_space_refine on Fri Dec 27 11:45:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8byl_16327/12_2024/8byl_16327.cif Found real_map, /net/cci-nas-00/data/ceres_data/8byl_16327/12_2024/8byl_16327.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8byl_16327/12_2024/8byl_16327.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8byl_16327/12_2024/8byl_16327.map" model { file = "/net/cci-nas-00/data/ceres_data/8byl_16327/12_2024/8byl_16327.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8byl_16327/12_2024/8byl_16327.cif" } resolution = 3.5 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= -0.001 sd= 0.028 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 24 5.16 5 C 2775 2.51 5 N 745 2.21 5 O 833 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 4378 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1111 Classifications: {'peptide': 155} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 9, 'TRANS': 145} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 135 Unresolved non-hydrogen angles: 162 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 7, 'ASP:plan': 4, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 67 Chain: "B" Number of atoms: 2585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2585 Classifications: {'peptide': 332} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 14, 'TRANS': 317} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'GLU:plan': 3, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "C" Number of atoms: 584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 584 Classifications: {'peptide': 69} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 63} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 98 Classifications: {'peptide': 15} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 12} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'TPO:plan-1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 3.65, per 1000 atoms: 0.83 Number of scatterers: 4378 At special positions: 0 Unit cell: (80.25, 113.42, 74.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 24 16.00 P 1 15.00 O 833 8.00 N 745 7.00 C 2775 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: 1.10 Conformation dependent library (CDL) restraints added in 618.4 milliseconds 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1092 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 6 sheets defined 41.2% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 1024 through 1032 removed outlier: 3.899A pdb=" N GLU A1032 " --> pdb=" O LYS A1028 " (cutoff:3.500A) Processing helix chain 'A' and resid 1045 through 1057 Processing helix chain 'A' and resid 1069 through 1074 Processing helix chain 'A' and resid 1074 through 1080 Processing helix chain 'A' and resid 1089 through 1094 removed outlier: 4.073A pdb=" N LYS A1094 " --> pdb=" O GLN A1090 " (cutoff:3.500A) Processing helix chain 'A' and resid 1096 through 1111 Processing helix chain 'A' and resid 1112 through 1127 removed outlier: 3.903A pdb=" N CYS A1120 " --> pdb=" O LEU A1116 " (cutoff:3.500A) Processing helix chain 'A' and resid 1131 through 1140 removed outlier: 3.589A pdb=" N ILE A1135 " --> pdb=" O THR A1131 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ARG A1136 " --> pdb=" O PRO A1132 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N LYS A1137 " --> pdb=" O GLU A1133 " (cutoff:3.500A) Processing helix chain 'A' and resid 1148 through 1157 removed outlier: 3.624A pdb=" N VAL A1153 " --> pdb=" O GLU A1149 " (cutoff:3.500A) Processing helix chain 'B' and resid 2101 through 2111 removed outlier: 3.500A pdb=" N GLY B2107 " --> pdb=" O GLU B2103 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N CYS B2111 " --> pdb=" O GLY B2107 " (cutoff:3.500A) Processing helix chain 'B' and resid 2113 through 2118 removed outlier: 3.747A pdb=" N LEU B2118 " --> pdb=" O LEU B2114 " (cutoff:3.500A) Processing helix chain 'B' and resid 2119 through 2123 removed outlier: 3.647A pdb=" N VAL B2123 " --> pdb=" O VAL B2120 " (cutoff:3.500A) Processing helix chain 'B' and resid 2124 through 2132 removed outlier: 3.632A pdb=" N SER B2132 " --> pdb=" O TYR B2128 " (cutoff:3.500A) Processing helix chain 'B' and resid 2148 through 2158 Processing helix chain 'B' and resid 2194 through 2203 Processing helix chain 'B' and resid 2219 through 2226 removed outlier: 3.509A pdb=" N VAL B2223 " --> pdb=" O SER B2219 " (cutoff:3.500A) Processing helix chain 'B' and resid 2227 through 2229 No H-bonds generated for 'chain 'B' and resid 2227 through 2229' Processing helix chain 'B' and resid 2244 through 2255 Processing helix chain 'B' and resid 2270 through 2281 Processing helix chain 'B' and resid 2293 through 2297 Processing helix chain 'B' and resid 2298 through 2309 Processing helix chain 'B' and resid 2324 through 2326 No H-bonds generated for 'chain 'B' and resid 2324 through 2326' Processing helix chain 'B' and resid 2327 through 2334 removed outlier: 3.722A pdb=" N PHE B2331 " --> pdb=" O CYS B2327 " (cutoff:3.500A) Processing helix chain 'B' and resid 2352 through 2357 removed outlier: 4.003A pdb=" N LEU B2356 " --> pdb=" O THR B2352 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY B2357 " --> pdb=" O LEU B2353 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2352 through 2357' Processing helix chain 'B' and resid 2374 through 2382 removed outlier: 3.651A pdb=" N LEU B2378 " --> pdb=" O GLY B2374 " (cutoff:3.500A) Processing helix chain 'C' and resid 3025 through 3030 removed outlier: 4.156A pdb=" N LYS C3030 " --> pdb=" O LYS C3026 " (cutoff:3.500A) Processing helix chain 'C' and resid 3039 through 3044 removed outlier: 3.581A pdb=" N ARG C3044 " --> pdb=" O GLU C3040 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1008 through 1009 removed outlier: 4.317A pdb=" N PHE A1014 " --> pdb=" O SER A1008 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 2185 through 2187 removed outlier: 3.798A pdb=" N ASP B2141 " --> pdb=" O LEU B2416 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 2210 through 2212 removed outlier: 8.026A pdb=" N LEU B2235 " --> pdb=" O ASN B2262 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU B2261 " --> pdb=" O GLN B2287 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 2317 through 2318 removed outlier: 7.304A pdb=" N LEU B2317 " --> pdb=" O SER B2343 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 3007 through 3008 removed outlier: 3.896A pdb=" N TYR C3007 " --> pdb=" O MET C3023 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 3007 through 3008 removed outlier: 3.896A pdb=" N TYR C3007 " --> pdb=" O MET C3023 " (cutoff:3.500A) removed outlier: 8.736A pdb=" N ILE C3066 " --> pdb=" O ILE C3059 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ILE C3059 " --> pdb=" O ILE C3066 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N LEU C3068 " --> pdb=" O TYR C3057 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR C3057 " --> pdb=" O LEU C3068 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL C3055 " --> pdb=" O ARG C3070 " (cutoff:3.500A) 133 hydrogen bonds defined for protein. 378 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: 1.15 Time building geometry restraints manager: 1.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 921 1.33 - 1.45: 962 1.45 - 1.57: 2555 1.57 - 1.69: 1 1.69 - 1.81: 31 Bond restraints: 4470 Sorted by residual: bond pdb=" OG1 TPO D4187 " pdb=" P TPO D4187 " ideal model delta sigma weight residual 1.717 1.604 0.113 2.00e-02 2.50e+03 3.19e+01 bond pdb=" CB TPO D4187 " pdb=" OG1 TPO D4187 " ideal model delta sigma weight residual 1.406 1.464 -0.058 2.00e-02 2.50e+03 8.35e+00 bond pdb=" C PRO A1070 " pdb=" N PRO A1071 " ideal model delta sigma weight residual 1.329 1.363 -0.034 1.18e-02 7.18e+03 8.23e+00 bond pdb=" N LEU B2130 " pdb=" CA LEU B2130 " ideal model delta sigma weight residual 1.456 1.489 -0.032 1.31e-02 5.83e+03 6.03e+00 bond pdb=" C PRO A1132 " pdb=" O PRO A1132 " ideal model delta sigma weight residual 1.238 1.209 0.029 1.37e-02 5.33e+03 4.47e+00 ... (remaining 4465 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 5924 1.72 - 3.44: 135 3.44 - 5.16: 26 5.16 - 6.87: 4 6.87 - 8.59: 3 Bond angle restraints: 6092 Sorted by residual: angle pdb=" N PRO A1072 " pdb=" CA PRO A1072 " pdb=" CB PRO A1072 " ideal model delta sigma weight residual 103.33 109.89 -6.56 1.10e+00 8.26e-01 3.56e+01 angle pdb=" C PRO A1132 " pdb=" CA PRO A1132 " pdb=" CB PRO A1132 " ideal model delta sigma weight residual 111.44 103.18 8.26 1.51e+00 4.39e-01 3.00e+01 angle pdb=" C TYR C3012 " pdb=" N ASP C3013 " pdb=" CA ASP C3013 " ideal model delta sigma weight residual 122.82 114.23 8.59 1.68e+00 3.54e-01 2.62e+01 angle pdb=" C ARG B2294 " pdb=" CA ARG B2294 " pdb=" CB ARG B2294 " ideal model delta sigma weight residual 116.63 111.53 5.10 1.16e+00 7.43e-01 1.94e+01 angle pdb=" N ASP A1084 " pdb=" CA ASP A1084 " pdb=" C ASP A1084 " ideal model delta sigma weight residual 108.31 101.83 6.48 1.52e+00 4.33e-01 1.82e+01 ... (remaining 6087 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 2323 17.64 - 35.29: 291 35.29 - 52.93: 58 52.93 - 70.58: 15 70.58 - 88.22: 7 Dihedral angle restraints: 2694 sinusoidal: 1026 harmonic: 1668 Sorted by residual: dihedral pdb=" CA VAL A1087 " pdb=" C VAL A1087 " pdb=" N TRP A1088 " pdb=" CA TRP A1088 " ideal model delta harmonic sigma weight residual -180.00 -157.98 -22.02 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA PRO B2384 " pdb=" C PRO B2384 " pdb=" N HIS B2385 " pdb=" CA HIS B2385 " ideal model delta harmonic sigma weight residual 180.00 161.49 18.51 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" C PRO A1132 " pdb=" N PRO A1132 " pdb=" CA PRO A1132 " pdb=" CB PRO A1132 " ideal model delta harmonic sigma weight residual -120.70 -111.79 -8.91 0 2.50e+00 1.60e-01 1.27e+01 ... (remaining 2691 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 526 0.046 - 0.092: 138 0.092 - 0.138: 40 0.138 - 0.184: 4 0.184 - 0.230: 4 Chirality restraints: 712 Sorted by residual: chirality pdb=" CA PRO A1072 " pdb=" N PRO A1072 " pdb=" C PRO A1072 " pdb=" CB PRO A1072 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CA LEU B2416 " pdb=" N LEU B2416 " pdb=" C LEU B2416 " pdb=" CB LEU B2416 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CB ILE A1112 " pdb=" CA ILE A1112 " pdb=" CG1 ILE A1112 " pdb=" CG2 ILE A1112 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 709 not shown) Planarity restraints: 785 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B2169 " -0.011 2.00e-02 2.50e+03 2.13e-02 4.55e+00 pdb=" C PHE B2169 " 0.037 2.00e-02 2.50e+03 pdb=" O PHE B2169 " -0.014 2.00e-02 2.50e+03 pdb=" N MET B2170 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A1085 " -0.032 5.00e-02 4.00e+02 4.93e-02 3.88e+00 pdb=" N PRO A1086 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO A1086 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A1086 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A1045 " 0.030 5.00e-02 4.00e+02 4.49e-02 3.23e+00 pdb=" N PRO A1046 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO A1046 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A1046 " 0.025 5.00e-02 4.00e+02 ... (remaining 782 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1342 2.82 - 3.34: 4074 3.34 - 3.86: 6796 3.86 - 4.38: 7721 4.38 - 4.90: 13382 Nonbonded interactions: 33315 Sorted by model distance: nonbonded pdb=" N GLU A1019 " pdb=" OE1 GLU A1019 " model vdw 2.304 3.120 nonbonded pdb=" OD1 ASP B2316 " pdb=" OG SER B2318 " model vdw 2.309 3.040 nonbonded pdb=" O LEU B2118 " pdb=" OG SER B2121 " model vdw 2.318 3.040 nonbonded pdb=" O THR B2139 " pdb=" OG1 THR B2139 " model vdw 2.354 3.040 nonbonded pdb=" NE1 TRP B2265 " pdb=" OG SER C3041 " model vdw 2.355 3.120 ... (remaining 33310 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.580 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.470 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.113 4470 Z= 0.263 Angle : 0.657 8.592 6092 Z= 0.385 Chirality : 0.047 0.230 712 Planarity : 0.004 0.049 785 Dihedral : 16.827 88.221 1602 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.05 % Allowed : 23.16 % Favored : 75.79 % 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: -1.39 (0.36), residues: 558 helix: -0.13 (0.40), residues: 185 sheet: -1.76 (0.77), residues: 48 loop : -1.26 (0.35), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1088 HIS 0.003 0.001 HIS B2339 PHE 0.010 0.001 PHE B2267 TYR 0.008 0.001 TYR A1109 ARG 0.002 0.000 ARG B2294 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 0.557 Fit side-chains revert: symmetry clash REVERT: B 2332 PHE cc_start: 0.8265 (OUTLIER) cc_final: 0.7916 (m-80) outliers start: 5 outliers final: 1 residues processed: 77 average time/residue: 0.1765 time to fit residues: 17.2673 Evaluate side-chains 77 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 75 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2147 LEU Chi-restraints excluded: chain B residue 2332 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 46 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 28 optimal weight: 0.0070 chunk 22 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 32 optimal weight: 0.0970 chunk 49 optimal weight: 0.9980 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C3021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.1031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4470 Z= 0.182 Angle : 0.568 6.467 6092 Z= 0.297 Chirality : 0.044 0.199 712 Planarity : 0.004 0.055 785 Dihedral : 4.937 43.276 601 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.16 % Allowed : 21.68 % Favored : 75.16 % 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: -1.37 (0.36), residues: 558 helix: -0.19 (0.38), residues: 203 sheet: -1.70 (0.75), residues: 53 loop : -1.24 (0.35), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C3043 HIS 0.003 0.001 HIS B2339 PHE 0.006 0.001 PHE B2267 TYR 0.012 0.001 TYR C3012 ARG 0.003 0.000 ARG B2308 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 0.523 Fit side-chains revert: symmetry clash REVERT: A 1014 PHE cc_start: 0.7746 (t80) cc_final: 0.7471 (t80) REVERT: C 3012 TYR cc_start: 0.7330 (OUTLIER) cc_final: 0.5958 (p90) REVERT: C 3021 HIS cc_start: 0.8350 (p90) cc_final: 0.8074 (p90) outliers start: 15 outliers final: 9 residues processed: 87 average time/residue: 0.1593 time to fit residues: 17.9275 Evaluate side-chains 83 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1059 ILE Chi-restraints excluded: chain A residue 1088 TRP Chi-restraints excluded: chain A residue 1141 ILE Chi-restraints excluded: chain A residue 1144 ASP Chi-restraints excluded: chain B residue 2168 SER Chi-restraints excluded: chain B residue 2216 LEU Chi-restraints excluded: chain B residue 2394 THR Chi-restraints excluded: chain C residue 3012 TYR Chi-restraints excluded: chain C residue 3050 GLN Chi-restraints excluded: chain C residue 3059 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 27 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 50 optimal weight: 0.2980 chunk 54 optimal weight: 0.3980 chunk 44 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C3021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.1198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4470 Z= 0.212 Angle : 0.585 7.635 6092 Z= 0.303 Chirality : 0.044 0.182 712 Planarity : 0.004 0.053 785 Dihedral : 4.428 17.490 597 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 4.42 % Allowed : 21.68 % Favored : 73.89 % 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: -1.30 (0.36), residues: 558 helix: -0.08 (0.38), residues: 202 sheet: -1.71 (0.74), residues: 53 loop : -1.23 (0.35), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C3043 HIS 0.003 0.001 HIS B2339 PHE 0.007 0.001 PHE B2246 TYR 0.011 0.001 TYR C3012 ARG 0.002 0.000 ARG B2308 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 78 time to evaluate : 0.509 Fit side-chains REVERT: A 1014 PHE cc_start: 0.7727 (t80) cc_final: 0.7368 (t80) REVERT: A 1102 GLU cc_start: 0.7309 (OUTLIER) cc_final: 0.6684 (mp0) REVERT: B 2169 PHE cc_start: 0.8382 (t80) cc_final: 0.8165 (t80) REVERT: B 2269 PHE cc_start: 0.8691 (OUTLIER) cc_final: 0.8123 (m-10) REVERT: C 3012 TYR cc_start: 0.7630 (OUTLIER) cc_final: 0.5819 (p90) REVERT: C 3021 HIS cc_start: 0.8370 (p90) cc_final: 0.7987 (p90) outliers start: 21 outliers final: 11 residues processed: 90 average time/residue: 0.1536 time to fit residues: 17.9197 Evaluate side-chains 87 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1059 ILE Chi-restraints excluded: chain A residue 1088 TRP Chi-restraints excluded: chain A residue 1102 GLU Chi-restraints excluded: chain A residue 1116 LEU Chi-restraints excluded: chain A residue 1141 ILE Chi-restraints excluded: chain A residue 1144 ASP Chi-restraints excluded: chain B residue 2168 SER Chi-restraints excluded: chain B residue 2216 LEU Chi-restraints excluded: chain B residue 2269 PHE Chi-restraints excluded: chain B residue 2394 THR Chi-restraints excluded: chain C residue 3012 TYR Chi-restraints excluded: chain C residue 3050 GLN Chi-restraints excluded: chain C residue 3059 ILE Chi-restraints excluded: chain C residue 3066 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 49 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 5 optimal weight: 4.9990 chunk 23 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 50 optimal weight: 0.0030 chunk 53 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 14 optimal weight: 5.9990 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B2273 HIS ** C3021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4470 Z= 0.203 Angle : 0.574 6.438 6092 Z= 0.298 Chirality : 0.045 0.168 712 Planarity : 0.004 0.052 785 Dihedral : 4.408 17.533 597 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 4.63 % Allowed : 21.89 % Favored : 73.47 % 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: -1.33 (0.36), residues: 558 helix: -0.04 (0.38), residues: 203 sheet: -2.21 (0.66), residues: 65 loop : -1.11 (0.36), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C3043 HIS 0.003 0.001 HIS B2339 PHE 0.007 0.001 PHE B2393 TYR 0.018 0.002 TYR A1109 ARG 0.001 0.000 ARG B2308 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 83 time to evaluate : 0.564 Fit side-chains revert: symmetry clash REVERT: B 2169 PHE cc_start: 0.8384 (t80) cc_final: 0.8180 (t80) REVERT: B 2269 PHE cc_start: 0.8683 (OUTLIER) cc_final: 0.8144 (m-10) REVERT: C 3012 TYR cc_start: 0.7794 (OUTLIER) cc_final: 0.6037 (p90) REVERT: C 3021 HIS cc_start: 0.8353 (p90) cc_final: 0.7989 (p90) outliers start: 22 outliers final: 14 residues processed: 97 average time/residue: 0.1544 time to fit residues: 19.3508 Evaluate side-chains 93 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1059 ILE Chi-restraints excluded: chain A residue 1088 TRP Chi-restraints excluded: chain A residue 1102 GLU Chi-restraints excluded: chain A residue 1116 LEU Chi-restraints excluded: chain A residue 1141 ILE Chi-restraints excluded: chain A residue 1144 ASP Chi-restraints excluded: chain B residue 2168 SER Chi-restraints excluded: chain B residue 2202 LEU Chi-restraints excluded: chain B residue 2216 LEU Chi-restraints excluded: chain B residue 2269 PHE Chi-restraints excluded: chain B residue 2345 CYS Chi-restraints excluded: chain B residue 2394 THR Chi-restraints excluded: chain C residue 3012 TYR Chi-restraints excluded: chain C residue 3050 GLN Chi-restraints excluded: chain C residue 3059 ILE Chi-restraints excluded: chain C residue 3066 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 44 optimal weight: 0.2980 chunk 30 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 39 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 45 optimal weight: 0.2980 chunk 36 optimal weight: 0.1980 chunk 27 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B2273 HIS ** C3021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4470 Z= 0.185 Angle : 0.578 7.681 6092 Z= 0.300 Chirality : 0.045 0.165 712 Planarity : 0.004 0.051 785 Dihedral : 4.323 17.580 597 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 4.42 % Allowed : 22.74 % Favored : 72.84 % 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: -1.27 (0.36), residues: 558 helix: -0.02 (0.38), residues: 204 sheet: -2.16 (0.66), residues: 65 loop : -1.06 (0.37), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C3043 HIS 0.003 0.001 HIS B2339 PHE 0.008 0.001 PHE A1014 TYR 0.019 0.001 TYR A1109 ARG 0.001 0.000 ARG B2308 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 77 time to evaluate : 0.544 Fit side-chains revert: symmetry clash REVERT: B 2169 PHE cc_start: 0.8266 (t80) cc_final: 0.8048 (t80) REVERT: B 2269 PHE cc_start: 0.8663 (OUTLIER) cc_final: 0.8152 (m-10) REVERT: C 3012 TYR cc_start: 0.7797 (OUTLIER) cc_final: 0.6154 (p90) REVERT: C 3021 HIS cc_start: 0.8348 (p90) cc_final: 0.8012 (p90) outliers start: 21 outliers final: 12 residues processed: 89 average time/residue: 0.1714 time to fit residues: 19.4976 Evaluate side-chains 99 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1059 ILE Chi-restraints excluded: chain A residue 1088 TRP Chi-restraints excluded: chain A residue 1102 GLU Chi-restraints excluded: chain A residue 1116 LEU Chi-restraints excluded: chain A residue 1141 ILE Chi-restraints excluded: chain A residue 1144 ASP Chi-restraints excluded: chain B residue 2147 LEU Chi-restraints excluded: chain B residue 2168 SER Chi-restraints excluded: chain B residue 2202 LEU Chi-restraints excluded: chain B residue 2269 PHE Chi-restraints excluded: chain B residue 2394 THR Chi-restraints excluded: chain C residue 3012 TYR Chi-restraints excluded: chain C residue 3050 GLN Chi-restraints excluded: chain C residue 3059 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 47 optimal weight: 0.4980 chunk 10 optimal weight: 0.0970 chunk 31 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B2224 ASN B2273 HIS ** C3021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4470 Z= 0.197 Angle : 0.578 6.401 6092 Z= 0.300 Chirality : 0.044 0.149 712 Planarity : 0.004 0.051 785 Dihedral : 4.320 17.779 597 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 5.05 % Allowed : 22.53 % Favored : 72.42 % 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: -1.36 (0.36), residues: 558 helix: -0.16 (0.37), residues: 210 sheet: -2.17 (0.66), residues: 65 loop : -1.09 (0.37), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C3043 HIS 0.003 0.001 HIS B2339 PHE 0.007 0.001 PHE B2393 TYR 0.021 0.002 TYR A1109 ARG 0.001 0.000 ARG C3020 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 86 time to evaluate : 0.523 Fit side-chains revert: symmetry clash REVERT: A 1150 GLU cc_start: 0.7042 (tt0) cc_final: 0.6075 (tp30) REVERT: B 2169 PHE cc_start: 0.8226 (t80) cc_final: 0.7965 (t80) REVERT: B 2269 PHE cc_start: 0.8666 (OUTLIER) cc_final: 0.8046 (m-10) REVERT: C 3012 TYR cc_start: 0.7850 (OUTLIER) cc_final: 0.6150 (p90) REVERT: C 3021 HIS cc_start: 0.8320 (p90) cc_final: 0.7978 (p90) outliers start: 24 outliers final: 17 residues processed: 101 average time/residue: 0.1586 time to fit residues: 20.6627 Evaluate side-chains 96 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 77 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1059 ILE Chi-restraints excluded: chain A residue 1088 TRP Chi-restraints excluded: chain A residue 1102 GLU Chi-restraints excluded: chain A residue 1116 LEU Chi-restraints excluded: chain A residue 1141 ILE Chi-restraints excluded: chain A residue 1144 ASP Chi-restraints excluded: chain B residue 2147 LEU Chi-restraints excluded: chain B residue 2161 ILE Chi-restraints excluded: chain B residue 2168 SER Chi-restraints excluded: chain B residue 2202 LEU Chi-restraints excluded: chain B residue 2216 LEU Chi-restraints excluded: chain B residue 2269 PHE Chi-restraints excluded: chain B residue 2323 LEU Chi-restraints excluded: chain B residue 2345 CYS Chi-restraints excluded: chain B residue 2394 THR Chi-restraints excluded: chain C residue 3012 TYR Chi-restraints excluded: chain C residue 3048 VAL Chi-restraints excluded: chain C residue 3050 GLN Chi-restraints excluded: chain C residue 3066 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 5 optimal weight: 0.0570 chunk 30 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 44 optimal weight: 0.4980 chunk 29 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B2273 HIS ** C3021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4470 Z= 0.206 Angle : 0.593 6.393 6092 Z= 0.310 Chirality : 0.044 0.145 712 Planarity : 0.004 0.051 785 Dihedral : 4.306 17.819 597 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 5.26 % Allowed : 22.74 % Favored : 72.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.36), residues: 558 helix: -0.07 (0.38), residues: 208 sheet: -2.03 (0.76), residues: 48 loop : -1.24 (0.36), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C3043 HIS 0.003 0.001 HIS B2339 PHE 0.007 0.001 PHE B2393 TYR 0.021 0.002 TYR A1109 ARG 0.007 0.000 ARG B2257 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 77 time to evaluate : 0.565 Fit side-chains revert: symmetry clash REVERT: A 1150 GLU cc_start: 0.7011 (tt0) cc_final: 0.6021 (tp30) REVERT: B 2269 PHE cc_start: 0.8646 (OUTLIER) cc_final: 0.8017 (m-10) REVERT: C 3012 TYR cc_start: 0.7887 (OUTLIER) cc_final: 0.6173 (p90) REVERT: C 3021 HIS cc_start: 0.8330 (p90) cc_final: 0.7944 (p90) outliers start: 25 outliers final: 18 residues processed: 94 average time/residue: 0.1597 time to fit residues: 19.5674 Evaluate side-chains 94 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 74 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1059 ILE Chi-restraints excluded: chain A residue 1088 TRP Chi-restraints excluded: chain A residue 1102 GLU Chi-restraints excluded: chain A residue 1116 LEU Chi-restraints excluded: chain A residue 1141 ILE Chi-restraints excluded: chain A residue 1144 ASP Chi-restraints excluded: chain B residue 2161 ILE Chi-restraints excluded: chain B residue 2168 SER Chi-restraints excluded: chain B residue 2202 LEU Chi-restraints excluded: chain B residue 2216 LEU Chi-restraints excluded: chain B residue 2269 PHE Chi-restraints excluded: chain B residue 2323 LEU Chi-restraints excluded: chain B residue 2345 CYS Chi-restraints excluded: chain B residue 2394 THR Chi-restraints excluded: chain C residue 3009 SER Chi-restraints excluded: chain C residue 3012 TYR Chi-restraints excluded: chain C residue 3048 VAL Chi-restraints excluded: chain C residue 3050 GLN Chi-restraints excluded: chain C residue 3059 ILE Chi-restraints excluded: chain C residue 3066 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 15 optimal weight: 0.0070 chunk 10 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 50 optimal weight: 0.0470 chunk 46 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 overall best weight: 0.4696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B2273 HIS C3021 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4470 Z= 0.188 Angle : 0.576 6.363 6092 Z= 0.300 Chirality : 0.044 0.146 712 Planarity : 0.004 0.052 785 Dihedral : 4.235 17.920 597 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 4.21 % Allowed : 23.58 % Favored : 72.21 % 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: -1.26 (0.36), residues: 558 helix: -0.01 (0.38), residues: 208 sheet: -2.02 (0.76), residues: 48 loop : -1.20 (0.36), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C3043 HIS 0.003 0.001 HIS B2339 PHE 0.007 0.001 PHE A1014 TYR 0.020 0.002 TYR A1109 ARG 0.008 0.000 ARG B2257 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 75 time to evaluate : 0.532 Fit side-chains revert: symmetry clash REVERT: A 1150 GLU cc_start: 0.6923 (tt0) cc_final: 0.5971 (tp30) REVERT: B 2269 PHE cc_start: 0.8623 (OUTLIER) cc_final: 0.8042 (m-10) REVERT: C 3012 TYR cc_start: 0.7790 (OUTLIER) cc_final: 0.6291 (p90) outliers start: 20 outliers final: 16 residues processed: 87 average time/residue: 0.1630 time to fit residues: 18.3937 Evaluate side-chains 90 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 72 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1059 ILE Chi-restraints excluded: chain A residue 1088 TRP Chi-restraints excluded: chain A residue 1102 GLU Chi-restraints excluded: chain A residue 1116 LEU Chi-restraints excluded: chain A residue 1141 ILE Chi-restraints excluded: chain A residue 1144 ASP Chi-restraints excluded: chain B residue 2161 ILE Chi-restraints excluded: chain B residue 2168 SER Chi-restraints excluded: chain B residue 2202 LEU Chi-restraints excluded: chain B residue 2216 LEU Chi-restraints excluded: chain B residue 2269 PHE Chi-restraints excluded: chain B residue 2323 LEU Chi-restraints excluded: chain C residue 3009 SER Chi-restraints excluded: chain C residue 3012 TYR Chi-restraints excluded: chain C residue 3048 VAL Chi-restraints excluded: chain C residue 3050 GLN Chi-restraints excluded: chain C residue 3059 ILE Chi-restraints excluded: chain C residue 3066 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 50 optimal weight: 0.3980 chunk 29 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 15 optimal weight: 0.0050 chunk 44 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B2273 HIS ** C3021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4470 Z= 0.202 Angle : 0.598 6.365 6092 Z= 0.313 Chirality : 0.044 0.141 712 Planarity : 0.004 0.052 785 Dihedral : 4.236 17.714 597 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 5.05 % Allowed : 22.53 % Favored : 72.42 % 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: -1.26 (0.36), residues: 558 helix: 0.03 (0.38), residues: 208 sheet: -2.01 (0.76), residues: 48 loop : -1.23 (0.36), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C3043 HIS 0.003 0.001 HIS B2339 PHE 0.008 0.001 PHE B2393 TYR 0.021 0.001 TYR A1109 ARG 0.007 0.000 ARG B2257 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 76 time to evaluate : 0.543 Fit side-chains revert: symmetry clash REVERT: A 1133 GLU cc_start: 0.8642 (tp30) cc_final: 0.8393 (tp30) REVERT: A 1150 GLU cc_start: 0.6954 (tt0) cc_final: 0.5975 (tp30) REVERT: B 2269 PHE cc_start: 0.8645 (OUTLIER) cc_final: 0.8110 (m-10) REVERT: C 3012 TYR cc_start: 0.7851 (OUTLIER) cc_final: 0.6295 (p90) outliers start: 24 outliers final: 19 residues processed: 91 average time/residue: 0.1708 time to fit residues: 20.0644 Evaluate side-chains 94 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 73 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1059 ILE Chi-restraints excluded: chain A residue 1087 VAL Chi-restraints excluded: chain A residue 1088 TRP Chi-restraints excluded: chain A residue 1102 GLU Chi-restraints excluded: chain A residue 1116 LEU Chi-restraints excluded: chain A residue 1141 ILE Chi-restraints excluded: chain A residue 1144 ASP Chi-restraints excluded: chain B residue 2161 ILE Chi-restraints excluded: chain B residue 2168 SER Chi-restraints excluded: chain B residue 2202 LEU Chi-restraints excluded: chain B residue 2216 LEU Chi-restraints excluded: chain B residue 2269 PHE Chi-restraints excluded: chain B residue 2297 LEU Chi-restraints excluded: chain B residue 2323 LEU Chi-restraints excluded: chain B residue 2345 CYS Chi-restraints excluded: chain C residue 3009 SER Chi-restraints excluded: chain C residue 3012 TYR Chi-restraints excluded: chain C residue 3048 VAL Chi-restraints excluded: chain C residue 3050 GLN Chi-restraints excluded: chain C residue 3059 ILE Chi-restraints excluded: chain C residue 3066 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 24 optimal weight: 1.9990 chunk 36 optimal weight: 0.0670 chunk 54 optimal weight: 2.9990 chunk 50 optimal weight: 0.0770 chunk 43 optimal weight: 0.1980 chunk 4 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 overall best weight: 0.3876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B2273 HIS ** C3021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4470 Z= 0.178 Angle : 0.578 6.339 6092 Z= 0.301 Chirality : 0.043 0.140 712 Planarity : 0.004 0.051 785 Dihedral : 4.115 17.994 597 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 4.84 % Allowed : 22.53 % Favored : 72.63 % 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: -1.21 (0.36), residues: 558 helix: 0.09 (0.38), residues: 208 sheet: -1.96 (0.76), residues: 48 loop : -1.22 (0.36), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C3043 HIS 0.003 0.001 HIS B2339 PHE 0.009 0.001 PHE A1014 TYR 0.020 0.002 TYR A1109 ARG 0.008 0.000 ARG B2257 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 78 time to evaluate : 0.526 Fit side-chains revert: symmetry clash REVERT: A 1150 GLU cc_start: 0.6894 (tt0) cc_final: 0.5967 (tp30) REVERT: B 2269 PHE cc_start: 0.8597 (OUTLIER) cc_final: 0.8070 (m-10) REVERT: C 3012 TYR cc_start: 0.7742 (OUTLIER) cc_final: 0.6507 (p90) outliers start: 23 outliers final: 18 residues processed: 91 average time/residue: 0.1831 time to fit residues: 21.3347 Evaluate side-chains 102 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 82 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1059 ILE Chi-restraints excluded: chain A residue 1088 TRP Chi-restraints excluded: chain A residue 1102 GLU Chi-restraints excluded: chain A residue 1116 LEU Chi-restraints excluded: chain A residue 1141 ILE Chi-restraints excluded: chain A residue 1144 ASP Chi-restraints excluded: chain B residue 2161 ILE Chi-restraints excluded: chain B residue 2168 SER Chi-restraints excluded: chain B residue 2202 LEU Chi-restraints excluded: chain B residue 2269 PHE Chi-restraints excluded: chain B residue 2297 LEU Chi-restraints excluded: chain B residue 2323 LEU Chi-restraints excluded: chain B residue 2345 CYS Chi-restraints excluded: chain B residue 2354 LEU Chi-restraints excluded: chain C residue 3009 SER Chi-restraints excluded: chain C residue 3012 TYR Chi-restraints excluded: chain C residue 3048 VAL Chi-restraints excluded: chain C residue 3050 GLN Chi-restraints excluded: chain C residue 3059 ILE Chi-restraints excluded: chain C residue 3066 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 40 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 chunk 12 optimal weight: 0.0030 chunk 43 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 5 optimal weight: 6.9990 chunk 8 optimal weight: 0.0000 chunk 38 optimal weight: 0.8980 chunk 2 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B2273 HIS ** C3021 HIS ** 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 = 0.4330 r_free = 0.4330 target = 0.204987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.161513 restraints weight = 5146.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.161420 restraints weight = 3191.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.162897 restraints weight = 2449.834| |-----------------------------------------------------------------------------| r_work (final): 0.3912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4470 Z= 0.195 Angle : 0.593 6.351 6092 Z= 0.310 Chirality : 0.044 0.141 712 Planarity : 0.004 0.051 785 Dihedral : 4.149 17.659 597 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 4.63 % Allowed : 22.95 % Favored : 72.42 % 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: -1.21 (0.36), residues: 558 helix: 0.09 (0.38), residues: 208 sheet: -1.93 (0.76), residues: 48 loop : -1.24 (0.36), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C3043 HIS 0.003 0.001 HIS B2339 PHE 0.010 0.001 PHE A1014 TYR 0.021 0.001 TYR A1109 ARG 0.007 0.000 ARG B2257 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1345.41 seconds wall clock time: 25 minutes 17.62 seconds (1517.62 seconds total)