Starting phenix.real_space_refine on Tue Feb 11 08:27:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xqi_38578/02_2025/8xqi_38578.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xqi_38578/02_2025/8xqi_38578.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xqi_38578/02_2025/8xqi_38578.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xqi_38578/02_2025/8xqi_38578.map" model { file = "/net/cci-nas-00/data/ceres_data/8xqi_38578/02_2025/8xqi_38578.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xqi_38578/02_2025/8xqi_38578.cif" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.015 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 41 5.16 5 C 3225 2.51 5 N 768 2.21 5 O 808 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 4842 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2330 Classifications: {'peptide': 291} Link IDs: {'PTRANS': 11, 'TRANS': 279} Chain breaks: 1 Chain: "B" Number of atoms: 2456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2456 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 11, 'TRANS': 294} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.65, per 1000 atoms: 0.75 Number of scatterers: 4842 At special positions: 0 Unit cell: (105.04, 56.16, 81.12, 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 41 16.00 O 808 8.00 N 768 7.00 C 3225 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 102 " - pdb=" SG CYS A 181 " distance=2.04 Simple disulfide: pdb=" SG CYS B 19 " - pdb=" SG CYS B 281 " distance=2.03 Simple disulfide: pdb=" SG CYS B 102 " - pdb=" SG CYS B 181 " distance=2.04 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: 1.38 Conformation dependent library (CDL) restraints added in 607.6 milliseconds 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1140 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 2 sheets defined 85.1% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 29 through 56 Processing helix chain 'A' and resid 62 through 91 removed outlier: 4.051A pdb=" N ILE A 66 " --> pdb=" O ARG A 62 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N PHE A 67 " --> pdb=" O SER A 63 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N THR A 81 " --> pdb=" O THR A 77 " (cutoff:3.500A) Proline residue: A 83 - end of helix Processing helix chain 'A' and resid 97 through 132 removed outlier: 4.343A pdb=" N PHE A 101 " --> pdb=" O PHE A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 144 removed outlier: 3.516A pdb=" N ARG A 139 " --> pdb=" O VAL A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 167 Proline residue: A 163 - end of helix Processing helix chain 'A' and resid 172 through 176 removed outlier: 3.518A pdb=" N ASN A 175 " --> pdb=" O ASP A 172 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N THR A 176 " --> pdb=" O LEU A 173 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 172 through 176' Processing helix chain 'A' and resid 193 through 210 Processing helix chain 'A' and resid 210 through 232 Processing helix chain 'A' and resid 242 through 278 removed outlier: 4.173A pdb=" N LEU A 246 " --> pdb=" O LYS A 242 " (cutoff:3.500A) Proline residue: A 263 - end of helix Processing helix chain 'A' and resid 280 through 313 Proline residue: A 292 - end of helix removed outlier: 4.541A pdb=" N SER A 302 " --> pdb=" O SER A 298 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N CYS A 303 " --> pdb=" O TYR A 299 " (cutoff:3.500A) Proline residue: A 306 - end of helix Processing helix chain 'A' and resid 313 through 322 Processing helix chain 'B' and resid 29 through 56 Processing helix chain 'B' and resid 62 through 91 removed outlier: 3.908A pdb=" N ILE B 66 " --> pdb=" O ARG B 62 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N PHE B 67 " --> pdb=" O SER B 63 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N THR B 81 " --> pdb=" O THR B 77 " (cutoff:3.500A) Proline residue: B 83 - end of helix Processing helix chain 'B' and resid 98 through 132 Processing helix chain 'B' and resid 134 through 144 removed outlier: 4.532A pdb=" N ALA B 138 " --> pdb=" O PRO B 134 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ARG B 139 " --> pdb=" O VAL B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 167 Proline residue: B 163 - end of helix Processing helix chain 'B' and resid 172 through 176 removed outlier: 3.611A pdb=" N ASN B 175 " --> pdb=" O ASP B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 210 Processing helix chain 'B' and resid 210 through 232 removed outlier: 3.782A pdb=" N HIS B 231 " --> pdb=" O THR B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 278 removed outlier: 5.880A pdb=" N LEU B 246 " --> pdb=" O LYS B 242 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N LEU B 247 " --> pdb=" O ARG B 243 " (cutoff:3.500A) Proline residue: B 263 - end of helix removed outlier: 3.909A pdb=" N LEU B 276 " --> pdb=" O MET B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 310 Proline residue: B 292 - end of helix removed outlier: 4.469A pdb=" N SER B 302 " --> pdb=" O SER B 298 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N CYS B 303 " --> pdb=" O TYR B 299 " (cutoff:3.500A) Proline residue: B 306 - end of helix Processing helix chain 'B' and resid 314 through 322 Processing sheet with id=AA1, first strand: chain 'A' and resid 168 through 171 Processing sheet with id=AA2, first strand: chain 'B' and resid 168 through 171 378 hydrogen bonds defined for protein. 1125 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: 1.41 Time building geometry restraints manager: 1.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1418 1.35 - 1.47: 1388 1.47 - 1.58: 2119 1.58 - 1.70: 0 1.70 - 1.82: 61 Bond restraints: 4986 Sorted by residual: bond pdb=" N GLN A 318 " pdb=" CA GLN A 318 " ideal model delta sigma weight residual 1.459 1.486 -0.026 1.19e-02 7.06e+03 4.92e+00 bond pdb=" N GLN B 318 " pdb=" CA GLN B 318 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.28e-02 6.10e+03 4.90e+00 bond pdb=" N CYS A 320 " pdb=" CA CYS A 320 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.19e-02 7.06e+03 4.66e+00 bond pdb=" N CYS B 320 " pdb=" CA CYS B 320 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.23e-02 6.61e+03 4.33e+00 bond pdb=" N ALA A 319 " pdb=" CA ALA A 319 " ideal model delta sigma weight residual 1.459 1.481 -0.022 1.21e-02 6.83e+03 3.37e+00 ... (remaining 4981 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 6658 1.84 - 3.68: 128 3.68 - 5.52: 20 5.52 - 7.36: 6 7.36 - 9.20: 2 Bond angle restraints: 6814 Sorted by residual: angle pdb=" CB MET A 36 " pdb=" CG MET A 36 " pdb=" SD MET A 36 " ideal model delta sigma weight residual 112.70 121.90 -9.20 3.00e+00 1.11e-01 9.41e+00 angle pdb=" CA THR A 321 " pdb=" CB THR A 321 " pdb=" OG1 THR A 321 " ideal model delta sigma weight residual 109.60 105.68 3.92 1.50e+00 4.44e-01 6.84e+00 angle pdb=" CA CYS A 320 " pdb=" C CYS A 320 " pdb=" O CYS A 320 " ideal model delta sigma weight residual 120.82 118.12 2.70 1.05e+00 9.07e-01 6.61e+00 angle pdb=" CA THR B 321 " pdb=" CB THR B 321 " pdb=" OG1 THR B 321 " ideal model delta sigma weight residual 109.60 105.75 3.85 1.50e+00 4.44e-01 6.58e+00 angle pdb=" N THR B 321 " pdb=" CA THR B 321 " pdb=" C THR B 321 " ideal model delta sigma weight residual 111.28 108.64 2.64 1.09e+00 8.42e-01 5.85e+00 ... (remaining 6809 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.16: 2529 13.16 - 26.33: 284 26.33 - 39.49: 109 39.49 - 52.65: 36 52.65 - 65.82: 11 Dihedral angle restraints: 2969 sinusoidal: 1204 harmonic: 1765 Sorted by residual: dihedral pdb=" CA PHE B 210 " pdb=" C PHE B 210 " pdb=" N VAL B 211 " pdb=" CA VAL B 211 " ideal model delta harmonic sigma weight residual 180.00 -163.21 -16.79 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CA PHE A 210 " pdb=" C PHE A 210 " pdb=" N VAL A 211 " pdb=" CA VAL A 211 " ideal model delta harmonic sigma weight residual -180.00 -163.93 -16.07 0 5.00e+00 4.00e-02 1.03e+01 dihedral pdb=" CA ILE A 228 " pdb=" C ILE A 228 " pdb=" N ALA A 229 " pdb=" CA ALA A 229 " ideal model delta harmonic sigma weight residual 180.00 164.55 15.45 0 5.00e+00 4.00e-02 9.55e+00 ... (remaining 2966 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 591 0.040 - 0.080: 148 0.080 - 0.121: 53 0.121 - 0.161: 6 0.161 - 0.201: 1 Chirality restraints: 799 Sorted by residual: chirality pdb=" CB VAL B 79 " pdb=" CA VAL B 79 " pdb=" CG1 VAL B 79 " pdb=" CG2 VAL B 79 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CG LEU A 304 " pdb=" CB LEU A 304 " pdb=" CD1 LEU A 304 " pdb=" CD2 LEU A 304 " both_signs ideal model delta sigma weight residual False -2.59 -2.75 0.16 2.00e-01 2.50e+01 6.42e-01 chirality pdb=" CB THR A 170 " pdb=" CA THR A 170 " pdb=" OG1 THR A 170 " pdb=" CG2 THR A 170 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.16 2.00e-01 2.50e+01 6.01e-01 ... (remaining 796 not shown) Planarity restraints: 806 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET B 162 " -0.026 5.00e-02 4.00e+02 3.84e-02 2.36e+00 pdb=" N PRO B 163 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO B 163 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 163 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 162 " 0.025 5.00e-02 4.00e+02 3.78e-02 2.28e+00 pdb=" N PRO A 163 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 163 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 163 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 305 " -0.025 5.00e-02 4.00e+02 3.74e-02 2.24e+00 pdb=" N PRO B 306 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO B 306 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 306 " -0.021 5.00e-02 4.00e+02 ... (remaining 803 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 543 2.74 - 3.28: 5065 3.28 - 3.82: 8515 3.82 - 4.36: 9763 4.36 - 4.90: 16657 Nonbonded interactions: 40543 Sorted by model distance: nonbonded pdb=" O MET B 272 " pdb=" OG SER B 275 " model vdw 2.204 3.040 nonbonded pdb=" O GLY B 200 " pdb=" OG SER B 204 " model vdw 2.249 3.040 nonbonded pdb=" O GLY A 200 " pdb=" OG SER A 204 " model vdw 2.332 3.040 nonbonded pdb=" O MET A 272 " pdb=" OG SER A 275 " model vdw 2.397 3.040 nonbonded pdb=" NH2 ARG B 168 " pdb=" O CYS B 181 " model vdw 2.423 3.120 ... (remaining 40538 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' and (resid 24 through 234 or resid 243 through 322 or resid 401)) } 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: 0.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.420 Find NCS groups from input model: 0.190 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 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 0.041 4986 Z= 0.273 Angle : 0.664 9.202 6814 Z= 0.366 Chirality : 0.042 0.201 799 Planarity : 0.005 0.038 806 Dihedral : 13.883 65.815 1820 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.00 % Allowed : 19.54 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.34), residues: 591 helix: 1.47 (0.23), residues: 459 sheet: -0.69 (1.80), residues: 10 loop : -2.06 (0.54), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 154 HIS 0.003 0.001 HIS A 265 PHE 0.017 0.002 PHE B 67 TYR 0.011 0.001 TYR B 107 ARG 0.007 0.000 ARG B 55 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.545 Fit side-chains REVERT: B 288 MET cc_start: 0.6589 (tmm) cc_final: 0.6333 (tmm) REVERT: B 309 TYR cc_start: 0.7402 (m-80) cc_final: 0.7008 (m-80) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.1796 time to fit residues: 21.7548 Evaluate side-chains 97 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 49 optimal weight: 0.0980 chunk 44 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 34 optimal weight: 0.2980 chunk 53 optimal weight: 0.3980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.152905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.130653 restraints weight = 5940.490| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.60 r_work: 0.3443 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.0670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4986 Z= 0.240 Angle : 0.560 7.639 6814 Z= 0.286 Chirality : 0.039 0.134 799 Planarity : 0.005 0.036 806 Dihedral : 5.143 36.309 791 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.72 % Allowed : 17.24 % Favored : 81.03 % 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 (0.34), residues: 591 helix: 1.62 (0.23), residues: 466 sheet: -0.84 (1.76), residues: 10 loop : -2.03 (0.56), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 154 HIS 0.003 0.001 HIS A 265 PHE 0.015 0.001 PHE A 307 TYR 0.010 0.001 TYR B 107 ARG 0.005 0.000 ARG B 55 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 106 time to evaluate : 0.518 Fit side-chains REVERT: B 288 MET cc_start: 0.7312 (tmm) cc_final: 0.7002 (tmm) REVERT: B 309 TYR cc_start: 0.7449 (m-80) cc_final: 0.6982 (m-80) outliers start: 9 outliers final: 7 residues processed: 111 average time/residue: 0.1747 time to fit residues: 24.5412 Evaluate side-chains 109 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 102 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 277 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 55 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 40 optimal weight: 0.2980 chunk 46 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 chunk 41 optimal weight: 7.9990 chunk 25 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.151084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.129263 restraints weight = 5886.094| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 1.58 r_work: 0.3419 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.0958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 4986 Z= 0.326 Angle : 0.588 8.151 6814 Z= 0.300 Chirality : 0.041 0.163 799 Planarity : 0.005 0.034 806 Dihedral : 5.142 34.378 791 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.53 % Allowed : 18.97 % Favored : 79.50 % 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: 1.10 (0.33), residues: 591 helix: 1.47 (0.23), residues: 466 sheet: -0.94 (1.73), residues: 10 loop : -2.17 (0.55), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 154 HIS 0.005 0.001 HIS A 265 PHE 0.011 0.002 PHE B 67 TYR 0.011 0.001 TYR B 107 ARG 0.006 0.000 ARG B 133 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 114 time to evaluate : 0.543 Fit side-chains REVERT: B 288 MET cc_start: 0.7323 (tmm) cc_final: 0.7027 (tmm) REVERT: B 309 TYR cc_start: 0.7577 (m-80) cc_final: 0.7097 (m-80) outliers start: 8 outliers final: 7 residues processed: 119 average time/residue: 0.1682 time to fit residues: 25.7234 Evaluate side-chains 117 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 110 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 277 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 39 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 44 optimal weight: 0.0070 chunk 19 optimal weight: 0.3980 chunk 51 optimal weight: 0.0470 chunk 50 optimal weight: 0.5980 chunk 46 optimal weight: 0.4980 chunk 41 optimal weight: 6.9990 chunk 0 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 49 optimal weight: 0.4980 overall best weight: 0.2896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.153060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.131624 restraints weight = 6020.243| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 1.53 r_work: 0.3462 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.1155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4986 Z= 0.194 Angle : 0.530 7.189 6814 Z= 0.271 Chirality : 0.038 0.156 799 Planarity : 0.004 0.035 806 Dihedral : 4.848 33.495 791 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.30 % Allowed : 19.35 % Favored : 78.35 % 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 (0.33), residues: 591 helix: 1.68 (0.23), residues: 467 sheet: -0.94 (1.68), residues: 10 loop : -2.23 (0.54), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 279 HIS 0.001 0.000 HIS A 265 PHE 0.016 0.001 PHE A 307 TYR 0.009 0.001 TYR B 107 ARG 0.003 0.000 ARG A 91 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 0.540 Fit side-chains REVERT: B 133 ARG cc_start: 0.7002 (ptp90) cc_final: 0.6691 (ptt-90) REVERT: B 288 MET cc_start: 0.7355 (tmm) cc_final: 0.7042 (tmm) REVERT: B 308 LEU cc_start: 0.8322 (mt) cc_final: 0.8121 (mt) REVERT: B 309 TYR cc_start: 0.7550 (m-80) cc_final: 0.6854 (m-80) outliers start: 12 outliers final: 7 residues processed: 118 average time/residue: 0.1571 time to fit residues: 24.0267 Evaluate side-chains 114 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 107 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 296 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 31 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 4 optimal weight: 0.2980 chunk 56 optimal weight: 0.9990 chunk 38 optimal weight: 0.4980 chunk 47 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 22 optimal weight: 0.2980 chunk 51 optimal weight: 10.0000 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.151757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.130009 restraints weight = 5962.401| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 1.59 r_work: 0.3431 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 4986 Z= 0.265 Angle : 0.560 7.609 6814 Z= 0.283 Chirality : 0.040 0.160 799 Planarity : 0.005 0.036 806 Dihedral : 4.870 32.216 791 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.07 % Allowed : 20.31 % Favored : 76.63 % 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: 1.37 (0.33), residues: 591 helix: 1.67 (0.22), residues: 468 sheet: -0.89 (1.61), residues: 10 loop : -2.21 (0.54), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 197 HIS 0.003 0.001 HIS A 265 PHE 0.009 0.001 PHE B 101 TYR 0.009 0.001 TYR B 107 ARG 0.002 0.000 ARG B 133 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 0.508 Fit side-chains REVERT: B 133 ARG cc_start: 0.7040 (ptp90) cc_final: 0.6569 (ptp90) REVERT: B 288 MET cc_start: 0.7321 (tmm) cc_final: 0.7014 (tmm) REVERT: B 309 TYR cc_start: 0.7613 (m-80) cc_final: 0.6938 (m-80) outliers start: 16 outliers final: 11 residues processed: 122 average time/residue: 0.1683 time to fit residues: 26.1832 Evaluate side-chains 117 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 106 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ARG Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 197 TRP Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 296 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 31 optimal weight: 0.6980 chunk 35 optimal weight: 0.1980 chunk 42 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.151210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.129565 restraints weight = 5970.364| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 1.58 r_work: 0.3426 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 4986 Z= 0.288 Angle : 0.569 7.664 6814 Z= 0.289 Chirality : 0.041 0.179 799 Planarity : 0.005 0.033 806 Dihedral : 4.914 32.350 791 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.87 % Allowed : 20.88 % Favored : 76.25 % 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 (0.33), residues: 591 helix: 1.59 (0.22), residues: 468 sheet: -0.75 (1.58), residues: 10 loop : -2.27 (0.53), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 24 HIS 0.004 0.001 HIS A 265 PHE 0.018 0.002 PHE A 222 TYR 0.010 0.001 TYR B 107 ARG 0.003 0.000 ARG B 133 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 0.480 Fit side-chains REVERT: A 129 LEU cc_start: 0.6166 (mt) cc_final: 0.5940 (mt) REVERT: B 133 ARG cc_start: 0.7094 (ptp90) cc_final: 0.6725 (ptp90) REVERT: B 288 MET cc_start: 0.7341 (tmm) cc_final: 0.7032 (tmm) REVERT: B 309 TYR cc_start: 0.7659 (m-80) cc_final: 0.6998 (m-80) outliers start: 15 outliers final: 11 residues processed: 128 average time/residue: 0.1707 time to fit residues: 28.4559 Evaluate side-chains 123 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 112 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ARG Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 296 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 11 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 30 optimal weight: 0.0870 chunk 3 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 chunk 9 optimal weight: 0.3980 chunk 41 optimal weight: 8.9990 chunk 14 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 8 optimal weight: 0.0980 chunk 36 optimal weight: 0.3980 overall best weight: 0.3158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.151914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.129742 restraints weight = 5912.118| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 1.61 r_work: 0.3435 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4986 Z= 0.201 Angle : 0.532 7.200 6814 Z= 0.272 Chirality : 0.039 0.163 799 Planarity : 0.004 0.034 806 Dihedral : 4.707 31.361 791 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.07 % Allowed : 20.88 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.33), residues: 591 helix: 1.75 (0.22), residues: 470 sheet: None (None), residues: 0 loop : -2.24 (0.50), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 195 HIS 0.002 0.000 HIS A 265 PHE 0.014 0.001 PHE A 307 TYR 0.008 0.001 TYR B 107 ARG 0.003 0.000 ARG A 91 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 0.662 Fit side-chains REVERT: A 127 ARG cc_start: 0.6394 (mmm160) cc_final: 0.5917 (mmp-170) REVERT: A 188 VAL cc_start: 0.8344 (m) cc_final: 0.8026 (p) REVERT: A 222 PHE cc_start: 0.8096 (t80) cc_final: 0.7865 (t80) REVERT: B 133 ARG cc_start: 0.7040 (ptp90) cc_final: 0.6753 (ptp90) REVERT: B 288 MET cc_start: 0.7330 (tmm) cc_final: 0.7024 (tmm) REVERT: B 309 TYR cc_start: 0.7594 (m-80) cc_final: 0.6832 (m-80) outliers start: 16 outliers final: 12 residues processed: 122 average time/residue: 0.2128 time to fit residues: 33.4504 Evaluate side-chains 120 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ARG Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 197 TRP Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 296 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 54 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 19 optimal weight: 0.0970 chunk 53 optimal weight: 0.0770 chunk 25 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 33 optimal weight: 4.9990 chunk 13 optimal weight: 0.5980 overall best weight: 0.4536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.151894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.130175 restraints weight = 5938.655| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 1.58 r_work: 0.3423 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 4986 Z= 0.245 Angle : 0.557 7.476 6814 Z= 0.283 Chirality : 0.040 0.167 799 Planarity : 0.004 0.035 806 Dihedral : 4.723 30.570 791 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.68 % Allowed : 21.84 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.33), residues: 591 helix: 1.70 (0.22), residues: 470 sheet: None (None), residues: 0 loop : -2.23 (0.50), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 197 HIS 0.003 0.001 HIS A 265 PHE 0.012 0.001 PHE B 307 TYR 0.009 0.001 TYR B 107 ARG 0.004 0.000 ARG B 168 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 113 time to evaluate : 0.498 Fit side-chains REVERT: A 127 ARG cc_start: 0.6344 (mmm160) cc_final: 0.5906 (mmp-170) REVERT: A 188 VAL cc_start: 0.8365 (m) cc_final: 0.8053 (p) REVERT: B 133 ARG cc_start: 0.7051 (ptp90) cc_final: 0.6772 (ptp90) REVERT: B 288 MET cc_start: 0.7334 (tmm) cc_final: 0.7024 (tmm) REVERT: B 309 TYR cc_start: 0.7658 (m-80) cc_final: 0.6934 (m-80) outliers start: 14 outliers final: 12 residues processed: 122 average time/residue: 0.1745 time to fit residues: 26.9703 Evaluate side-chains 125 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 113 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ARG Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 197 TRP Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 296 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 5 optimal weight: 0.7980 chunk 51 optimal weight: 0.4980 chunk 12 optimal weight: 1.9990 chunk 9 optimal weight: 0.0970 chunk 41 optimal weight: 9.9990 chunk 58 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 45 optimal weight: 0.7980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.151280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.129330 restraints weight = 5855.097| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 1.59 r_work: 0.3421 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 4986 Z= 0.282 Angle : 0.582 7.497 6814 Z= 0.294 Chirality : 0.041 0.174 799 Planarity : 0.005 0.035 806 Dihedral : 4.785 30.966 791 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.68 % Allowed : 21.65 % Favored : 75.67 % 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: 1.31 (0.33), residues: 591 helix: 1.62 (0.22), residues: 470 sheet: None (None), residues: 0 loop : -2.17 (0.50), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 24 HIS 0.003 0.001 HIS A 265 PHE 0.016 0.001 PHE A 307 TYR 0.010 0.001 TYR B 107 ARG 0.006 0.000 ARG A 241 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 113 time to evaluate : 0.438 Fit side-chains REVERT: A 25 LYS cc_start: 0.4138 (OUTLIER) cc_final: 0.3854 (tmtt) REVERT: A 127 ARG cc_start: 0.6318 (mmm160) cc_final: 0.5902 (mmp-170) REVERT: A 188 VAL cc_start: 0.8408 (m) cc_final: 0.8120 (p) REVERT: B 133 ARG cc_start: 0.7070 (ptp90) cc_final: 0.6812 (ptp90) REVERT: B 288 MET cc_start: 0.7339 (tmm) cc_final: 0.7034 (tmm) REVERT: B 309 TYR cc_start: 0.7697 (m-80) cc_final: 0.7015 (m-80) outliers start: 14 outliers final: 12 residues processed: 122 average time/residue: 0.1837 time to fit residues: 28.2649 Evaluate side-chains 127 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 114 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LYS Chi-restraints excluded: chain A residue 55 ARG Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 197 TRP Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 296 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 54 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 9 optimal weight: 0.3980 chunk 22 optimal weight: 0.0980 chunk 0 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 58 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.151605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.129512 restraints weight = 5973.742| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 1.62 r_work: 0.3421 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 4986 Z= 0.255 Angle : 0.581 8.763 6814 Z= 0.293 Chirality : 0.040 0.169 799 Planarity : 0.004 0.036 806 Dihedral : 4.730 30.823 791 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.68 % Allowed : 22.41 % Favored : 74.90 % 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: 1.35 (0.33), residues: 591 helix: 1.64 (0.22), residues: 470 sheet: None (None), residues: 0 loop : -2.13 (0.50), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 195 HIS 0.003 0.001 HIS A 265 PHE 0.017 0.001 PHE A 307 TYR 0.009 0.001 TYR B 107 ARG 0.003 0.000 ARG A 91 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 0.538 Fit side-chains REVERT: A 25 LYS cc_start: 0.3938 (OUTLIER) cc_final: 0.3168 (tmtt) REVERT: A 127 ARG cc_start: 0.6299 (mmm160) cc_final: 0.5916 (mmp-170) REVERT: A 188 VAL cc_start: 0.8406 (m) cc_final: 0.8120 (p) REVERT: B 133 ARG cc_start: 0.7064 (ptp90) cc_final: 0.6854 (ptp90) REVERT: B 288 MET cc_start: 0.7350 (tmm) cc_final: 0.7031 (tmm) REVERT: B 309 TYR cc_start: 0.7709 (m-80) cc_final: 0.7025 (m-80) outliers start: 14 outliers final: 11 residues processed: 124 average time/residue: 0.1699 time to fit residues: 26.8274 Evaluate side-chains 124 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 112 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LYS Chi-restraints excluded: chain A residue 55 ARG Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 197 TRP Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 296 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 48 optimal weight: 0.0770 chunk 56 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 22 optimal weight: 0.2980 chunk 53 optimal weight: 0.2980 chunk 38 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 39 optimal weight: 0.5980 chunk 58 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 1 optimal weight: 0.4980 overall best weight: 0.3538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.152282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.130248 restraints weight = 5997.112| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 1.61 r_work: 0.3436 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4986 Z= 0.218 Angle : 0.573 8.766 6814 Z= 0.289 Chirality : 0.039 0.161 799 Planarity : 0.005 0.041 806 Dihedral : 4.667 30.424 791 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.30 % Allowed : 22.80 % Favored : 74.90 % 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: 1.38 (0.33), residues: 591 helix: 1.66 (0.22), residues: 470 sheet: None (None), residues: 0 loop : -2.11 (0.50), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 195 HIS 0.001 0.000 HIS B 265 PHE 0.010 0.001 PHE B 101 TYR 0.008 0.001 TYR B 107 ARG 0.003 0.000 ARG A 91 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2524.69 seconds wall clock time: 45 minutes 34.54 seconds (2734.54 seconds total)