Starting phenix.real_space_refine on Thu Nov 14 11:59:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h8f_34545/11_2024/8h8f_34545.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h8f_34545/11_2024/8h8f_34545.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h8f_34545/11_2024/8h8f_34545.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h8f_34545/11_2024/8h8f_34545.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h8f_34545/11_2024/8h8f_34545.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h8f_34545/11_2024/8h8f_34545.cif" } resolution = 3.48 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= -0.002 sd= 0.081 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 33 5.16 5 C 3990 2.51 5 N 1011 2.21 5 O 1134 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 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: 6168 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 2056 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 12, 'TRANS': 238} Chain: "B" Number of atoms: 2056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 2056 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 12, 'TRANS': 238} Chain: "C" Number of atoms: 2056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 2056 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 12, 'TRANS': 238} Time building chain proxies: 4.56, per 1000 atoms: 0.74 Number of scatterers: 6168 At special positions: 0 Unit cell: (84.786, 84.786, 122.831, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 33 16.00 O 1134 8.00 N 1011 7.00 C 3990 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 147 " - pdb=" SG CYS A 169 " distance=2.03 Simple disulfide: pdb=" SG CYS B 147 " - pdb=" SG CYS B 169 " distance=2.04 Simple disulfide: pdb=" SG CYS C 147 " - pdb=" SG CYS C 169 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.43 Conformation dependent library (CDL) restraints added in 887.7 milliseconds 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1446 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 12 sheets defined 25.6% alpha, 35.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 97 through 117 removed outlier: 3.924A pdb=" N HIS A 117 " --> pdb=" O ASP A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 232 Processing helix chain 'A' and resid 236 through 247 removed outlier: 3.678A pdb=" N GLN A 241 " --> pdb=" O VAL A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 347 removed outlier: 3.733A pdb=" N MET A 326 " --> pdb=" O ASN A 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 117 removed outlier: 3.785A pdb=" N HIS B 117 " --> pdb=" O ASP B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 232 Processing helix chain 'B' and resid 236 through 247 removed outlier: 3.653A pdb=" N GLN B 241 " --> pdb=" O VAL B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 347 removed outlier: 3.751A pdb=" N MET B 326 " --> pdb=" O ASN B 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 117 removed outlier: 3.998A pdb=" N HIS C 117 " --> pdb=" O ASP C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 232 Processing helix chain 'C' and resid 236 through 247 removed outlier: 3.785A pdb=" N GLN C 241 " --> pdb=" O VAL C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 347 removed outlier: 3.864A pdb=" N MET C 326 " --> pdb=" O ASN C 322 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 119 through 125 removed outlier: 4.364A pdb=" N ASP A 317 " --> pdb=" O LYS A 268 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL A 304 " --> pdb=" O THR A 258 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER A 146 " --> pdb=" O GLN A 206 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N HIS A 208 " --> pdb=" O LEU A 144 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N LEU A 144 " --> pdb=" O HIS A 208 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 119 through 125 removed outlier: 4.364A pdb=" N ASP A 317 " --> pdb=" O LYS A 268 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 171 through 172 removed outlier: 3.581A pdb=" N GLY A 134 " --> pdb=" O PHE A 224 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 218 through 219 removed outlier: 3.610A pdb=" N ILE A 219 " --> pdb=" O PHE A 252 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 119 through 125 removed outlier: 3.882A pdb=" N GLN B 313 " --> pdb=" O LEU B 264 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASP B 317 " --> pdb=" O LYS B 268 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL B 304 " --> pdb=" O THR B 258 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN B 299 " --> pdb=" O LEU B 209 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 143 through 144 removed outlier: 3.532A pdb=" N HIS B 208 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN B 299 " --> pdb=" O LEU B 209 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL B 304 " --> pdb=" O THR B 258 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 171 through 175 removed outlier: 3.703A pdb=" N ILE B 174 " --> pdb=" O ALA B 188 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA B 188 " --> pdb=" O ILE B 174 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLY B 134 " --> pdb=" O PHE B 224 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 218 through 219 Processing sheet with id=AA9, first strand: chain 'C' and resid 119 through 123 removed outlier: 3.752A pdb=" N GLN C 313 " --> pdb=" O LEU C 264 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ASP C 317 " --> pdb=" O LYS C 268 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL C 304 " --> pdb=" O THR C 258 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER C 146 " --> pdb=" O GLN C 206 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N HIS C 208 " --> pdb=" O LEU C 144 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N LEU C 144 " --> pdb=" O HIS C 208 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 119 through 123 removed outlier: 3.752A pdb=" N GLN C 313 " --> pdb=" O LEU C 264 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ASP C 317 " --> pdb=" O LYS C 268 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 171 through 175 Processing sheet with id=AB3, first strand: chain 'C' and resid 218 through 219 319 hydrogen bonds defined for protein. 882 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: 1.81 Time building geometry restraints manager: 1.68 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: 1218 1.33 - 1.45: 1612 1.45 - 1.57: 3455 1.57 - 1.70: 0 1.70 - 1.82: 54 Bond restraints: 6339 Sorted by residual: bond pdb=" CE1 HIS B 154 " pdb=" NE2 HIS B 154 " ideal model delta sigma weight residual 1.321 1.361 -0.040 1.00e-02 1.00e+04 1.62e+01 bond pdb=" C PRO B 156 " pdb=" O PRO B 156 " ideal model delta sigma weight residual 1.240 1.205 0.035 1.12e-02 7.97e+03 9.94e+00 bond pdb=" N ILE B 155 " pdb=" CA ILE B 155 " ideal model delta sigma weight residual 1.457 1.484 -0.027 9.00e-03 1.23e+04 9.11e+00 bond pdb=" N LEU A 144 " pdb=" CA LEU A 144 " ideal model delta sigma weight residual 1.455 1.493 -0.038 1.27e-02 6.20e+03 9.09e+00 bond pdb=" N PRO A 139 " pdb=" CA PRO A 139 " ideal model delta sigma weight residual 1.472 1.433 0.039 1.32e-02 5.74e+03 8.70e+00 ... (remaining 6334 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 8243 1.47 - 2.94: 251 2.94 - 4.42: 55 4.42 - 5.89: 22 5.89 - 7.36: 12 Bond angle restraints: 8583 Sorted by residual: angle pdb=" C HIS B 154 " pdb=" N ILE B 155 " pdb=" CA ILE B 155 " ideal model delta sigma weight residual 123.33 117.54 5.79 8.70e-01 1.32e+00 4.43e+01 angle pdb=" C TYR B 152 " pdb=" N ASP B 153 " pdb=" CA ASP B 153 " ideal model delta sigma weight residual 120.82 113.46 7.36 1.41e+00 5.03e-01 2.73e+01 angle pdb=" N ILE B 155 " pdb=" CA ILE B 155 " pdb=" C ILE B 155 " ideal model delta sigma weight residual 107.61 113.28 -5.67 1.19e+00 7.06e-01 2.27e+01 angle pdb=" C ASP B 153 " pdb=" CA ASP B 153 " pdb=" CB ASP B 153 " ideal model delta sigma weight residual 109.90 117.21 -7.31 1.56e+00 4.11e-01 2.20e+01 angle pdb=" N PRO B 157 " pdb=" CA PRO B 157 " pdb=" C PRO B 157 " ideal model delta sigma weight residual 111.41 104.62 6.79 1.50e+00 4.44e-01 2.05e+01 ... (remaining 8578 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 3210 17.69 - 35.39: 431 35.39 - 53.08: 110 53.08 - 70.77: 19 70.77 - 88.47: 7 Dihedral angle restraints: 3777 sinusoidal: 1551 harmonic: 2226 Sorted by residual: dihedral pdb=" CB CYS B 147 " pdb=" SG CYS B 147 " pdb=" SG CYS B 169 " pdb=" CB CYS B 169 " ideal model delta sinusoidal sigma weight residual 93.00 19.05 73.95 1 1.00e+01 1.00e-02 6.95e+01 dihedral pdb=" CB CYS A 147 " pdb=" SG CYS A 147 " pdb=" SG CYS A 169 " pdb=" CB CYS A 169 " ideal model delta sinusoidal sigma weight residual 93.00 20.51 72.49 1 1.00e+01 1.00e-02 6.71e+01 dihedral pdb=" CB CYS C 147 " pdb=" SG CYS C 147 " pdb=" SG CYS C 169 " pdb=" CB CYS C 169 " ideal model delta sinusoidal sigma weight residual 93.00 20.65 72.35 1 1.00e+01 1.00e-02 6.69e+01 ... (remaining 3774 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 784 0.062 - 0.124: 120 0.124 - 0.186: 10 0.186 - 0.247: 2 0.247 - 0.309: 2 Chirality restraints: 918 Sorted by residual: chirality pdb=" CA ILE A 135 " pdb=" N ILE A 135 " pdb=" C ILE A 135 " pdb=" CB ILE A 135 " both_signs ideal model delta sigma weight residual False 2.43 2.74 -0.31 2.00e-01 2.50e+01 2.39e+00 chirality pdb=" CA ARG A 143 " pdb=" N ARG A 143 " pdb=" C ARG A 143 " pdb=" CB ARG A 143 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA LYS B 159 " pdb=" N LYS B 159 " pdb=" C LYS B 159 " pdb=" CB LYS B 159 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 915 not shown) Planarity restraints: 1095 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 143 " 0.494 9.50e-02 1.11e+02 2.22e-01 3.00e+01 pdb=" NE ARG A 143 " -0.029 2.00e-02 2.50e+03 pdb=" CZ ARG A 143 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A 143 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 143 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 309 " 0.045 5.00e-02 4.00e+02 6.94e-02 7.71e+00 pdb=" N PRO A 310 " -0.120 5.00e-02 4.00e+02 pdb=" CA PRO A 310 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 310 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 133 " -0.013 2.00e-02 2.50e+03 2.55e-02 6.49e+00 pdb=" C PRO A 133 " 0.044 2.00e-02 2.50e+03 pdb=" O PRO A 133 " -0.017 2.00e-02 2.50e+03 pdb=" N GLY A 134 " -0.015 2.00e-02 2.50e+03 ... (remaining 1092 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 131 2.69 - 3.24: 5918 3.24 - 3.80: 9442 3.80 - 4.35: 11444 4.35 - 4.90: 19636 Nonbonded interactions: 46571 Sorted by model distance: nonbonded pdb=" N GLU C 281 " pdb=" OE1 GLU C 281 " model vdw 2.140 3.120 nonbonded pdb=" OE1 GLU B 126 " pdb=" NH2 ARG B 198 " model vdw 2.274 3.120 nonbonded pdb=" O ALA B 229 " pdb=" OG SER B 233 " model vdw 2.275 3.040 nonbonded pdb=" NZ LYS C 186 " pdb=" OE1 GLU C 244 " model vdw 2.278 3.120 nonbonded pdb=" OG1 THR A 181 " pdb=" OG1 THR A 184 " model vdw 2.284 3.040 ... (remaining 46566 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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 individual isotropic 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: 1.570 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: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.160 Find NCS groups from input model: 0.180 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6569 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 0.040 6339 Z= 0.222 Angle : 0.692 7.362 8583 Z= 0.410 Chirality : 0.047 0.309 918 Planarity : 0.008 0.222 1095 Dihedral : 17.028 88.468 2322 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.02 % Allowed : 23.00 % Favored : 75.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.30), residues: 747 helix: 1.64 (0.39), residues: 174 sheet: 0.36 (0.33), residues: 267 loop : -1.68 (0.29), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 250 HIS 0.004 0.001 HIS B 117 PHE 0.013 0.002 PHE A 287 TYR 0.022 0.001 TYR B 176 ARG 0.006 0.000 ARG A 112 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 82 time to evaluate : 0.727 Fit side-chains REVERT: A 143 ARG cc_start: 0.6143 (OUTLIER) cc_final: 0.5743 (ptt180) outliers start: 7 outliers final: 3 residues processed: 88 average time/residue: 0.1846 time to fit residues: 21.7232 Evaluate side-chains 85 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 81 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain B residue 154 HIS Chi-restraints excluded: chain B residue 289 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 63 optimal weight: 0.9980 chunk 56 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 19 optimal weight: 0.0070 chunk 38 optimal weight: 0.9980 chunk 30 optimal weight: 7.9990 chunk 58 optimal weight: 0.1980 chunk 22 optimal weight: 9.9990 chunk 35 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 overall best weight: 1.0400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6595 moved from start: 0.0913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6339 Z= 0.215 Angle : 0.610 6.696 8583 Z= 0.319 Chirality : 0.045 0.152 918 Planarity : 0.005 0.057 1095 Dihedral : 5.322 42.975 822 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.33 % Allowed : 24.02 % Favored : 73.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.30), residues: 747 helix: 1.37 (0.39), residues: 177 sheet: 0.59 (0.34), residues: 246 loop : -1.78 (0.29), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 259 HIS 0.004 0.001 HIS B 117 PHE 0.018 0.002 PHE A 252 TYR 0.015 0.002 TYR B 176 ARG 0.004 0.000 ARG B 279 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 0.718 Fit side-chains outliers start: 16 outliers final: 8 residues processed: 102 average time/residue: 0.1747 time to fit residues: 23.9655 Evaluate side-chains 89 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain B residue 154 HIS Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 177 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 37 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 56 optimal weight: 0.0370 chunk 46 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 67 optimal weight: 0.1980 chunk 23 optimal weight: 2.9990 chunk 54 optimal weight: 0.1980 overall best weight: 0.6862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 208 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6561 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6339 Z= 0.169 Angle : 0.565 6.491 8583 Z= 0.293 Chirality : 0.043 0.139 918 Planarity : 0.004 0.051 1095 Dihedral : 4.773 39.264 812 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.06 % Allowed : 25.04 % Favored : 71.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.30), residues: 747 helix: 1.33 (0.38), residues: 177 sheet: 0.43 (0.33), residues: 258 loop : -1.72 (0.31), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 259 HIS 0.005 0.001 HIS B 117 PHE 0.013 0.002 PHE C 252 TYR 0.030 0.001 TYR C 176 ARG 0.004 0.000 ARG A 257 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 89 time to evaluate : 0.686 Fit side-chains REVERT: A 112 ARG cc_start: 0.7407 (mmm160) cc_final: 0.7115 (mtp85) REVERT: B 105 TYR cc_start: 0.6946 (OUTLIER) cc_final: 0.5786 (t80) REVERT: B 144 LEU cc_start: 0.5947 (OUTLIER) cc_final: 0.5147 (pp) REVERT: C 105 TYR cc_start: 0.5311 (t80) cc_final: 0.4931 (t80) REVERT: C 144 LEU cc_start: 0.6088 (OUTLIER) cc_final: 0.5652 (pp) outliers start: 21 outliers final: 13 residues processed: 106 average time/residue: 0.1631 time to fit residues: 23.7374 Evaluate side-chains 97 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 CYS Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 154 HIS Chi-restraints excluded: chain B residue 169 CYS Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 232 LYS Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 169 CYS Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 282 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 67 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 chunk 35 optimal weight: 0.0970 chunk 7 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 72 optimal weight: 6.9990 chunk 64 optimal weight: 0.4980 chunk 19 optimal weight: 0.0270 chunk 60 optimal weight: 3.9990 overall best weight: 0.4636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6531 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 6339 Z= 0.150 Angle : 0.555 6.761 8583 Z= 0.283 Chirality : 0.043 0.133 918 Planarity : 0.004 0.047 1095 Dihedral : 4.642 36.785 812 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.64 % Allowed : 24.60 % Favored : 71.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.30), residues: 747 helix: 1.39 (0.38), residues: 177 sheet: 0.48 (0.33), residues: 258 loop : -1.66 (0.31), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 259 HIS 0.004 0.001 HIS B 117 PHE 0.013 0.001 PHE C 252 TYR 0.018 0.001 TYR C 176 ARG 0.003 0.000 ARG A 291 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 91 time to evaluate : 0.686 Fit side-chains REVERT: A 112 ARG cc_start: 0.7433 (mmm160) cc_final: 0.6942 (mtp85) REVERT: A 324 TRP cc_start: 0.6787 (m100) cc_final: 0.6521 (m-90) REVERT: B 105 TYR cc_start: 0.6914 (OUTLIER) cc_final: 0.5744 (t80) REVERT: C 105 TYR cc_start: 0.5231 (t80) cc_final: 0.4960 (t80) REVERT: C 144 LEU cc_start: 0.6045 (OUTLIER) cc_final: 0.5605 (pp) outliers start: 25 outliers final: 12 residues processed: 110 average time/residue: 0.1609 time to fit residues: 23.9568 Evaluate side-chains 97 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 CYS Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 154 HIS Chi-restraints excluded: chain B residue 169 CYS Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 169 CYS Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 282 THR Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 333 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 41 optimal weight: 0.9980 chunk 1 optimal weight: 0.5980 chunk 53 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6577 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6339 Z= 0.172 Angle : 0.568 6.643 8583 Z= 0.291 Chirality : 0.043 0.144 918 Planarity : 0.004 0.045 1095 Dihedral : 4.643 32.669 812 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 4.08 % Allowed : 24.31 % Favored : 71.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.30), residues: 747 helix: 1.40 (0.38), residues: 177 sheet: 0.63 (0.36), residues: 219 loop : -1.63 (0.29), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 259 HIS 0.005 0.001 HIS B 117 PHE 0.014 0.002 PHE C 252 TYR 0.026 0.002 TYR B 176 ARG 0.003 0.000 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 87 time to evaluate : 0.683 Fit side-chains revert: symmetry clash REVERT: A 111 PHE cc_start: 0.7519 (t80) cc_final: 0.7090 (t80) REVERT: B 105 TYR cc_start: 0.6935 (OUTLIER) cc_final: 0.5795 (t80) REVERT: C 105 TYR cc_start: 0.5283 (t80) cc_final: 0.5023 (t80) REVERT: C 144 LEU cc_start: 0.6112 (OUTLIER) cc_final: 0.5594 (pp) outliers start: 28 outliers final: 22 residues processed: 108 average time/residue: 0.1781 time to fit residues: 26.3702 Evaluate side-chains 106 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 82 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 CYS Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 230 PHE Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 287 PHE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 154 HIS Chi-restraints excluded: chain B residue 169 CYS Chi-restraints excluded: chain B residue 173 ASP Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 169 CYS Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 282 THR Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 333 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 65 optimal weight: 6.9990 chunk 14 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 72 optimal weight: 9.9990 chunk 60 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 6 optimal weight: 0.0970 chunk 24 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 117 HIS B 236 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6618 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6339 Z= 0.195 Angle : 0.584 7.584 8583 Z= 0.301 Chirality : 0.044 0.147 918 Planarity : 0.004 0.044 1095 Dihedral : 4.717 27.692 812 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 4.66 % Allowed : 24.16 % Favored : 71.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.30), residues: 747 helix: 1.37 (0.38), residues: 177 sheet: 0.45 (0.31), residues: 276 loop : -1.70 (0.31), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 324 HIS 0.004 0.001 HIS B 117 PHE 0.016 0.002 PHE B 252 TYR 0.028 0.002 TYR B 176 ARG 0.002 0.000 ARG A 257 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 87 time to evaluate : 0.761 Fit side-chains revert: symmetry clash REVERT: A 111 PHE cc_start: 0.7325 (t80) cc_final: 0.6900 (t80) REVERT: A 143 ARG cc_start: 0.6106 (OUTLIER) cc_final: 0.3900 (ppt-90) REVERT: A 291 ARG cc_start: 0.6670 (OUTLIER) cc_final: 0.5759 (mmt90) REVERT: A 324 TRP cc_start: 0.6917 (m100) cc_final: 0.6566 (m-90) REVERT: B 105 TYR cc_start: 0.6930 (OUTLIER) cc_final: 0.5805 (t80) REVERT: C 144 LEU cc_start: 0.6156 (OUTLIER) cc_final: 0.5679 (pp) outliers start: 32 outliers final: 20 residues processed: 113 average time/residue: 0.2003 time to fit residues: 29.5513 Evaluate side-chains 103 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 79 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain A residue 169 CYS Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 230 PHE Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 291 ARG Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 169 CYS Chi-restraints excluded: chain B residue 173 ASP Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 169 CYS Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 282 THR Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 333 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 8 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 chunk 45 optimal weight: 0.7980 chunk 44 optimal weight: 0.0370 chunk 33 optimal weight: 0.1980 chunk 28 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 overall best weight: 0.5458 ------------------------------------------------------------------------------- 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: 0.6571 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 6339 Z= 0.158 Angle : 0.567 8.061 8583 Z= 0.287 Chirality : 0.043 0.137 918 Planarity : 0.004 0.043 1095 Dihedral : 4.458 21.766 810 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.93 % Allowed : 25.62 % Favored : 70.45 % 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: -0.16 (0.30), residues: 747 helix: 1.38 (0.38), residues: 177 sheet: 0.92 (0.36), residues: 216 loop : -1.62 (0.29), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 324 HIS 0.004 0.001 HIS C 187 PHE 0.013 0.001 PHE C 252 TYR 0.026 0.001 TYR B 176 ARG 0.003 0.000 ARG A 112 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 81 time to evaluate : 0.531 Fit side-chains REVERT: A 111 PHE cc_start: 0.7511 (t80) cc_final: 0.7114 (t80) REVERT: A 112 ARG cc_start: 0.7139 (mmm160) cc_final: 0.6913 (mtp85) REVERT: A 143 ARG cc_start: 0.6137 (OUTLIER) cc_final: 0.3915 (ppt-90) REVERT: A 291 ARG cc_start: 0.6589 (OUTLIER) cc_final: 0.5568 (mmt90) REVERT: A 324 TRP cc_start: 0.6903 (m100) cc_final: 0.6563 (m-90) REVERT: B 105 TYR cc_start: 0.6864 (OUTLIER) cc_final: 0.5724 (t80) REVERT: C 144 LEU cc_start: 0.6018 (OUTLIER) cc_final: 0.5562 (pp) outliers start: 27 outliers final: 19 residues processed: 103 average time/residue: 0.1432 time to fit residues: 19.6367 Evaluate side-chains 99 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 76 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain A residue 169 CYS Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 230 PHE Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 291 ARG Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 169 CYS Chi-restraints excluded: chain B residue 173 ASP Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 169 CYS Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 282 THR Chi-restraints excluded: chain C residue 333 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 21 optimal weight: 0.0470 chunk 14 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 69 optimal weight: 0.1980 chunk 63 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: