Starting phenix.real_space_refine on Fri Aug 22 15:45:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8plz_17754/08_2025/8plz_17754.cif Found real_map, /net/cci-nas-00/data/ceres_data/8plz_17754/08_2025/8plz_17754.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8plz_17754/08_2025/8plz_17754.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8plz_17754/08_2025/8plz_17754.map" model { file = "/net/cci-nas-00/data/ceres_data/8plz_17754/08_2025/8plz_17754.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8plz_17754/08_2025/8plz_17754.cif" } resolution = 1.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.002 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 31 5.16 5 C 3292 2.51 5 N 870 2.21 5 O 1078 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5271 Number of models: 1 Model: "" Number of chains: 7 Chain: "H" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 512 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 5, 'TRANS': 59} Chain: "I" Number of atoms: 2281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2281 Unusual residues: {'ACE': 1} Classifications: {'peptide': 279, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 264} Chain breaks: 1 Chain: "J" Number of atoms: 2283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2283 Classifications: {'peptide': 286} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 267} Chain breaks: 2 Chain: "J" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ZQ6': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "I" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 65 Classifications: {'water': 65} Link IDs: {None: 64} Chain: "J" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 81 Classifications: {'water': 81} Link IDs: {None: 80} Time building chain proxies: 1.56, per 1000 atoms: 0.30 Number of scatterers: 5271 At special positions: 0 Unit cell: (83.3625, 94.05, 67.6875, 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 31 16.00 O 1078 8.00 N 870 7.00 C 3292 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.45 Conformation dependent library (CDL) restraints added in 198.7 milliseconds Enol-peptide restraints added in 1.2 microseconds 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1196 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 3 sheets defined 61.3% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'H' and resid 270 through 275 removed outlier: 3.555A pdb=" N ASN H 273 " --> pdb=" O GLY H 270 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL H 275 " --> pdb=" O LEU H 272 " (cutoff:3.500A) Processing helix chain 'H' and resid 279 through 285 Processing helix chain 'H' and resid 288 through 302 removed outlier: 3.953A pdb=" N ALA H 292 " --> pdb=" O THR H 288 " (cutoff:3.500A) Processing helix chain 'I' and resid 1 through 4 removed outlier: 3.537A pdb=" N ASN I 4 " --> pdb=" O MET I 1 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 1 through 4' Processing helix chain 'I' and resid 5 through 11 Processing helix chain 'I' and resid 15 through 38 Processing helix chain 'I' and resid 49 through 70 Processing helix chain 'I' and resid 76 through 93 removed outlier: 4.079A pdb=" N ASN I 93 " --> pdb=" O ARG I 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 100 through 116 removed outlier: 3.596A pdb=" N LEU I 106 " --> pdb=" O ARG I 102 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS I 114 " --> pdb=" O PHE I 110 " (cutoff:3.500A) Processing helix chain 'I' and resid 121 through 127 Processing helix chain 'I' and resid 132 through 154 removed outlier: 4.765A pdb=" N LEU I 148 " --> pdb=" O LEU I 144 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N LEU I 149 " --> pdb=" O GLU I 145 " (cutoff:3.500A) Processing helix chain 'I' and resid 163 through 178 Processing helix chain 'I' and resid 183 through 186 Processing helix chain 'I' and resid 187 through 201 removed outlier: 3.612A pdb=" N LEU I 200 " --> pdb=" O ASN I 196 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR I 201 " --> pdb=" O ARG I 197 " (cutoff:3.500A) Processing helix chain 'I' and resid 202 through 206 Processing helix chain 'I' and resid 208 through 224 Processing helix chain 'I' and resid 228 through 234 Processing helix chain 'I' and resid 237 through 240 removed outlier: 3.581A pdb=" N GLU I 240 " --> pdb=" O MET I 237 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 237 through 240' Processing helix chain 'I' and resid 241 through 261 Processing helix chain 'I' and resid 266 through 283 Processing helix chain 'J' and resid 56 through 68 removed outlier: 3.995A pdb=" N GLU J 68 " --> pdb=" O LYS J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 98 through 104 Processing helix chain 'J' and resid 110 through 131 Processing helix chain 'J' and resid 139 through 141 No H-bonds generated for 'chain 'J' and resid 139 through 141' Processing helix chain 'J' and resid 175 through 179 Processing helix chain 'J' and resid 180 through 185 Processing helix chain 'J' and resid 192 through 209 removed outlier: 3.807A pdb=" N ALA J 198 " --> pdb=" O VAL J 194 " (cutoff:3.500A) Processing helix chain 'J' and resid 217 through 230 Processing helix chain 'J' and resid 239 through 243 Processing helix chain 'J' and resid 256 through 261 Processing helix chain 'J' and resid 265 through 276 Processing helix chain 'J' and resid 285 through 291 Processing helix chain 'J' and resid 292 through 297 removed outlier: 3.618A pdb=" N SER J 296 " --> pdb=" O MET J 292 " (cutoff:3.500A) Processing helix chain 'J' and resid 303 through 307 Processing sheet with id=AA1, first strand: chain 'J' and resid 14 through 21 removed outlier: 5.786A pdb=" N PHE J 17 " --> pdb=" O LYS J 28 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N LYS J 28 " --> pdb=" O PHE J 17 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP J 79 " --> pdb=" O VAL J 90 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ASP J 92 " --> pdb=" O LEU J 77 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N LEU J 77 " --> pdb=" O ASP J 92 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'J' and resid 96 through 97 Processing sheet with id=AA3, first strand: chain 'J' and resid 133 through 134 267 hydrogen bonds defined for protein. 756 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: 0.79 Time building geometry restraints manager: 0.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1641 1.34 - 1.46: 1145 1.46 - 1.58: 2395 1.58 - 1.70: 1 1.70 - 1.82: 49 Bond restraints: 5231 Sorted by residual: bond pdb=" C11 ZQ6 J 401 " pdb=" N10 ZQ6 J 401 " ideal model delta sigma weight residual 1.339 1.455 -0.116 2.00e-02 2.50e+03 3.37e+01 bond pdb=" C13 ZQ6 J 401 " pdb=" N14 ZQ6 J 401 " ideal model delta sigma weight residual 1.350 1.448 -0.098 2.00e-02 2.50e+03 2.40e+01 bond pdb=" C24 ZQ6 J 401 " pdb=" N28 ZQ6 J 401 " ideal model delta sigma weight residual 1.376 1.296 0.080 2.00e-02 2.50e+03 1.60e+01 bond pdb=" N27 ZQ6 J 401 " pdb=" N28 ZQ6 J 401 " ideal model delta sigma weight residual 1.344 1.400 -0.056 2.00e-02 2.50e+03 7.95e+00 bond pdb=" C15 ZQ6 J 401 " pdb=" C16 ZQ6 J 401 " ideal model delta sigma weight residual 1.530 1.584 -0.054 2.00e-02 2.50e+03 7.37e+00 ... (remaining 5226 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 6893 2.04 - 4.07: 155 4.07 - 6.11: 26 6.11 - 8.15: 5 8.15 - 10.18: 1 Bond angle restraints: 7080 Sorted by residual: angle pdb=" CB MET J 189 " pdb=" CG MET J 189 " pdb=" SD MET J 189 " ideal model delta sigma weight residual 112.70 122.88 -10.18 3.00e+00 1.11e-01 1.15e+01 angle pdb=" CB ARG I 102 " pdb=" CG ARG I 102 " pdb=" CD ARG I 102 " ideal model delta sigma weight residual 111.30 118.90 -7.60 2.30e+00 1.89e-01 1.09e+01 angle pdb=" CA GLU I 17 " pdb=" CB GLU I 17 " pdb=" CG GLU I 17 " ideal model delta sigma weight residual 114.10 120.40 -6.30 2.00e+00 2.50e-01 9.91e+00 angle pdb=" C LEU I 65 " pdb=" N GLU I 66 " pdb=" CA GLU I 66 " ideal model delta sigma weight residual 121.14 115.74 5.40 1.75e+00 3.27e-01 9.53e+00 angle pdb=" C PHE I 90 " pdb=" N TYR I 91 " pdb=" CA TYR I 91 " ideal model delta sigma weight residual 122.38 116.95 5.43 1.81e+00 3.05e-01 9.01e+00 ... (remaining 7075 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.18: 2949 24.18 - 48.37: 173 48.37 - 72.55: 32 72.55 - 96.73: 15 96.73 - 120.92: 1 Dihedral angle restraints: 3170 sinusoidal: 1323 harmonic: 1847 Sorted by residual: dihedral pdb=" C17 ZQ6 J 401 " pdb=" C18 ZQ6 J 401 " pdb=" N19 ZQ6 J 401 " pdb=" C20 ZQ6 J 401 " ideal model delta sinusoidal sigma weight residual -70.42 50.50 -120.92 1 3.00e+01 1.11e-03 1.61e+01 dihedral pdb=" CA ILE I 180 " pdb=" C ILE I 180 " pdb=" N LEU I 181 " pdb=" CA LEU I 181 " ideal model delta harmonic sigma weight residual 180.00 161.82 18.18 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA GLU J 20 " pdb=" C GLU J 20 " pdb=" N GLY J 21 " pdb=" CA GLY J 21 " ideal model delta harmonic sigma weight residual 180.00 163.40 16.60 0 5.00e+00 4.00e-02 1.10e+01 ... (remaining 3167 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 400 0.029 - 0.058: 227 0.058 - 0.087: 95 0.087 - 0.116: 39 0.116 - 0.145: 16 Chirality restraints: 777 Sorted by residual: chirality pdb=" CA PRO J 238 " pdb=" N PRO J 238 " pdb=" C PRO J 238 " pdb=" CB PRO J 238 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.14 2.00e-01 2.50e+01 5.24e-01 chirality pdb=" CA GLU I 66 " pdb=" N GLU I 66 " pdb=" C GLU I 66 " pdb=" CB GLU I 66 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.20e-01 chirality pdb=" CA VAL I 120 " pdb=" N VAL I 120 " pdb=" C VAL I 120 " pdb=" CB VAL I 120 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.08e-01 ... (remaining 774 not shown) Planarity restraints: 903 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C11 ZQ6 J 401 " -0.002 2.00e-02 2.50e+03 1.27e-02 3.22e+00 pdb=" C24 ZQ6 J 401 " -0.004 2.00e-02 2.50e+03 pdb=" C25 ZQ6 J 401 " 0.032 2.00e-02 2.50e+03 pdb=" C26 ZQ6 J 401 " -0.006 2.00e-02 2.50e+03 pdb=" C29 ZQ6 J 401 " -0.015 2.00e-02 2.50e+03 pdb=" N23 ZQ6 J 401 " -0.001 2.00e-02 2.50e+03 pdb=" N27 ZQ6 J 401 " -0.003 2.00e-02 2.50e+03 pdb=" N28 ZQ6 J 401 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN I 162 " -0.027 5.00e-02 4.00e+02 4.05e-02 2.62e+00 pdb=" N PRO I 163 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO I 163 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO I 163 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS J 201 " 0.008 2.00e-02 2.50e+03 1.52e-02 2.30e+00 pdb=" C CYS J 201 " -0.026 2.00e-02 2.50e+03 pdb=" O CYS J 201 " 0.010 2.00e-02 2.50e+03 pdb=" N ILE J 202 " 0.009 2.00e-02 2.50e+03 ... (remaining 900 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 686 2.75 - 3.29: 5435 3.29 - 3.82: 9882 3.82 - 4.36: 11948 4.36 - 4.90: 19207 Nonbonded interactions: 47158 Sorted by model distance: nonbonded pdb=" O HOH J 567 " pdb=" O HOH J 573 " model vdw 2.212 3.040 nonbonded pdb=" O HOH J 577 " pdb=" O HOH J 581 " model vdw 2.218 3.040 nonbonded pdb=" O HOH H 413 " pdb=" O HOH H 417 " model vdw 2.250 3.040 nonbonded pdb=" OD1 ASN J 279 " pdb=" O HOH J 501 " model vdw 2.256 3.040 nonbonded pdb=" O ARG J 283 " pdb=" O HOH J 502 " model vdw 2.267 3.040 ... (remaining 47153 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 4.880 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.250 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:6.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 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 : 0.005 0.116 5231 Z= 0.239 Angle : 0.766 10.185 7080 Z= 0.398 Chirality : 0.046 0.145 777 Planarity : 0.006 0.043 903 Dihedral : 16.791 120.919 1974 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Rotamer: Outliers : 0.90 % Allowed : 13.36 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.88 (0.32), residues: 618 helix: 1.23 (0.28), residues: 337 sheet: 0.74 (0.96), residues: 15 loop : -0.17 (0.36), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 102 TYR 0.020 0.002 TYR I 91 PHE 0.017 0.002 PHE I 30 TRP 0.014 0.002 TRP J 132 HIS 0.006 0.001 HIS J 131 Details of bonding type rmsd covalent geometry : bond 0.00496 ( 5231) covalent geometry : angle 0.76586 ( 7080) hydrogen bonds : bond 0.13799 ( 267) hydrogen bonds : angle 5.92797 ( 756) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 83 time to evaluate : 0.214 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 86 average time/residue: 0.6997 time to fit residues: 62.2976 Evaluate side-chains 85 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 81 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 290 SER Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain J residue 120 MET Chi-restraints excluded: chain J residue 170 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 54 optimal weight: 10.0000 chunk 24 optimal weight: 7.9990 chunk 48 optimal weight: 0.9990 chunk 56 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 16 optimal weight: 8.9990 chunk 61 optimal weight: 8.9990 chunk 32 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 247 GLN J 236 GLN J 297 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.180233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.158456 restraints weight = 4798.143| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 0.95 r_work: 0.3743 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3648 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.0847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 5231 Z= 0.120 Angle : 0.575 7.020 7080 Z= 0.297 Chirality : 0.042 0.131 777 Planarity : 0.004 0.036 903 Dihedral : 8.625 113.319 719 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.54 % Rotamer: Outliers : 0.72 % Allowed : 12.45 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.42 (0.33), residues: 618 helix: 1.87 (0.28), residues: 341 sheet: 0.54 (1.02), residues: 15 loop : -0.23 (0.37), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 63 TYR 0.018 0.001 TYR I 91 PHE 0.017 0.002 PHE I 30 TRP 0.010 0.001 TRP J 132 HIS 0.005 0.001 HIS J 131 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 5231) covalent geometry : angle 0.57524 ( 7080) hydrogen bonds : bond 0.04867 ( 267) hydrogen bonds : angle 4.69485 ( 756) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 90 time to evaluate : 0.220 Fit side-chains revert: symmetry clash REVERT: I 192 ASP cc_start: 0.7419 (t70) cc_final: 0.7091 (t70) outliers start: 4 outliers final: 1 residues processed: 92 average time/residue: 0.7295 time to fit residues: 69.4146 Evaluate side-chains 86 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 85 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 290 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 32 optimal weight: 9.9990 chunk 13 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 28 optimal weight: 9.9990 chunk 42 optimal weight: 1.9990 chunk 39 optimal weight: 9.9990 chunk 17 optimal weight: 6.9990 chunk 49 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 55 optimal weight: 7.9990 chunk 59 optimal weight: 0.0370 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 247 GLN J 113 HIS J 236 GLN J 297 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.181908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.160260 restraints weight = 4768.409| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 0.95 r_work: 0.3764 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3671 rms_B_bonded: 2.56 restraints_weight: 0.2500 r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 5231 Z= 0.107 Angle : 0.538 6.619 7080 Z= 0.275 Chirality : 0.041 0.130 777 Planarity : 0.004 0.040 903 Dihedral : 7.967 113.645 713 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Rotamer: Outliers : 1.26 % Allowed : 13.18 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.70 (0.33), residues: 618 helix: 2.12 (0.28), residues: 341 sheet: 0.50 (1.04), residues: 15 loop : -0.13 (0.37), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 63 TYR 0.017 0.001 TYR I 91 PHE 0.016 0.001 PHE I 30 TRP 0.008 0.001 TRP J 132 HIS 0.004 0.001 HIS J 131 Details of bonding type rmsd covalent geometry : bond 0.00220 ( 5231) covalent geometry : angle 0.53767 ( 7080) hydrogen bonds : bond 0.04275 ( 267) hydrogen bonds : angle 4.44432 ( 756) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 96 time to evaluate : 0.245 Fit side-chains REVERT: H 307 GLN cc_start: 0.7667 (mm110) cc_final: 0.7443 (mm110) REVERT: I 138 LYS cc_start: 0.7505 (ttpt) cc_final: 0.6797 (tptt) REVERT: I 192 ASP cc_start: 0.7378 (t70) cc_final: 0.7044 (t70) REVERT: J 169 TYR cc_start: 0.6374 (OUTLIER) cc_final: 0.5144 (m-80) outliers start: 7 outliers final: 2 residues processed: 98 average time/residue: 0.7295 time to fit residues: 74.1543 Evaluate side-chains 86 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 83 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain J residue 120 MET Chi-restraints excluded: chain J residue 169 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 61 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 chunk 16 optimal weight: 9.9990 chunk 27 optimal weight: 0.3980 chunk 17 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 8 optimal weight: 9.9990 chunk 1 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 39 optimal weight: 9.9990 chunk 31 optimal weight: 0.7980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 247 GLN J 113 HIS J 236 GLN J 297 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.179745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.157771 restraints weight = 4717.213| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 0.95 r_work: 0.3732 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3638 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.1071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5231 Z= 0.139 Angle : 0.590 6.668 7080 Z= 0.302 Chirality : 0.042 0.135 777 Planarity : 0.005 0.039 903 Dihedral : 7.922 111.524 712 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.46 % Favored : 98.38 % Rotamer: Outliers : 1.44 % Allowed : 14.08 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.65 (0.33), residues: 618 helix: 2.07 (0.28), residues: 338 sheet: 0.38 (1.10), residues: 15 loop : -0.09 (0.37), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 63 TYR 0.019 0.002 TYR I 91 PHE 0.016 0.002 PHE I 30 TRP 0.010 0.001 TRP J 132 HIS 0.006 0.001 HIS J 131 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 5231) covalent geometry : angle 0.58992 ( 7080) hydrogen bonds : bond 0.04852 ( 267) hydrogen bonds : angle 4.56114 ( 756) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.266 Fit side-chains REVERT: H 307 GLN cc_start: 0.7656 (mm110) cc_final: 0.7435 (mm110) REVERT: I 102 ARG cc_start: 0.7595 (OUTLIER) cc_final: 0.7355 (ttt180) REVERT: I 138 LYS cc_start: 0.7519 (ttpt) cc_final: 0.6828 (tptt) REVERT: I 192 ASP cc_start: 0.7366 (t70) cc_final: 0.7021 (t70) REVERT: I 255 MET cc_start: 0.7912 (mtm) cc_final: 0.7621 (ttm) outliers start: 8 outliers final: 1 residues processed: 88 average time/residue: 0.7796 time to fit residues: 70.9519 Evaluate side-chains 83 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 81 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 102 ARG Chi-restraints excluded: chain I residue 129 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 20 optimal weight: 8.9990 chunk 30 optimal weight: 6.9990 chunk 33 optimal weight: 8.9990 chunk 49 optimal weight: 7.9990 chunk 44 optimal weight: 7.9990 chunk 21 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 chunk 28 optimal weight: 7.9990 chunk 36 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 247 GLN J 236 GLN J 297 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.177175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.155014 restraints weight = 4781.038| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 0.96 r_work: 0.3698 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3604 rms_B_bonded: 2.54 restraints_weight: 0.2500 r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.0941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 5231 Z= 0.235 Angle : 0.733 7.543 7080 Z= 0.375 Chirality : 0.047 0.146 777 Planarity : 0.006 0.050 903 Dihedral : 7.749 100.536 712 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.78 % Favored : 98.06 % Rotamer: Outliers : 1.62 % Allowed : 14.08 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.21 (0.33), residues: 618 helix: 1.63 (0.27), residues: 337 sheet: 0.64 (1.09), residues: 15 loop : -0.21 (0.37), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 165 TYR 0.023 0.002 TYR I 91 PHE 0.018 0.003 PHE J 81 TRP 0.015 0.003 TRP J 132 HIS 0.010 0.002 HIS J 131 Details of bonding type rmsd covalent geometry : bond 0.00521 ( 5231) covalent geometry : angle 0.73278 ( 7080) hydrogen bonds : bond 0.05947 ( 267) hydrogen bonds : angle 4.88435 ( 756) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 90 time to evaluate : 0.235 Fit side-chains REVERT: I 102 ARG cc_start: 0.7646 (OUTLIER) cc_final: 0.7368 (ttt180) REVERT: I 138 LYS cc_start: 0.7525 (ttpt) cc_final: 0.6863 (tptt) REVERT: I 192 ASP cc_start: 0.7439 (t70) cc_final: 0.7093 (t70) REVERT: I 269 GLU cc_start: 0.7172 (tp30) cc_final: 0.6622 (tp30) REVERT: J 236 GLN cc_start: 0.7169 (mt0) cc_final: 0.6886 (mt0) outliers start: 9 outliers final: 2 residues processed: 93 average time/residue: 0.8021 time to fit residues: 77.1309 Evaluate side-chains 90 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 87 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 102 ARG Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain I residue 129 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 30 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 34 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 61 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 247 GLN J 113 HIS J 297 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.180543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.158860 restraints weight = 4850.195| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 0.96 r_work: 0.3749 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3655 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.1202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5231 Z= 0.119 Angle : 0.568 6.972 7080 Z= 0.291 Chirality : 0.041 0.139 777 Planarity : 0.004 0.038 903 Dihedral : 7.920 112.098 712 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.46 % Favored : 98.38 % Rotamer: Outliers : 1.44 % Allowed : 14.80 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.65 (0.34), residues: 618 helix: 2.07 (0.28), residues: 338 sheet: 0.92 (1.26), residues: 15 loop : -0.15 (0.37), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 63 TYR 0.019 0.001 TYR I 91 PHE 0.017 0.002 PHE I 30 TRP 0.010 0.001 TRP J 132 HIS 0.005 0.001 HIS J 131 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 5231) covalent geometry : angle 0.56776 ( 7080) hydrogen bonds : bond 0.04501 ( 267) hydrogen bonds : angle 4.48522 ( 756) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 93 time to evaluate : 0.220 Fit side-chains REVERT: I 65 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7471 (mm) REVERT: I 102 ARG cc_start: 0.7589 (OUTLIER) cc_final: 0.7307 (ttt180) REVERT: I 138 LYS cc_start: 0.7500 (ttpt) cc_final: 0.6826 (tptt) REVERT: I 192 ASP cc_start: 0.7412 (t70) cc_final: 0.7085 (t70) REVERT: I 255 MET cc_start: 0.7915 (mtm) cc_final: 0.7611 (ttm) outliers start: 8 outliers final: 2 residues processed: 96 average time/residue: 0.7854 time to fit residues: 77.8682 Evaluate side-chains 90 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 86 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 102 ARG Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain J residue 120 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 44 optimal weight: 7.9990 chunk 52 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 27 optimal weight: 7.9990 chunk 23 optimal weight: 4.9990 chunk 4 optimal weight: 8.9990 chunk 54 optimal weight: 10.0000 chunk 60 optimal weight: 6.9990 chunk 40 optimal weight: 8.9990 chunk 21 optimal weight: 8.9990 chunk 55 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 247 GLN J 148 ASN J 236 GLN J 297 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.175695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.153943 restraints weight = 4730.815| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 0.94 r_work: 0.3688 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3593 rms_B_bonded: 2.50 restraints_weight: 0.2500 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.065 5231 Z= 0.385 Angle : 0.929 8.982 7080 Z= 0.476 Chirality : 0.055 0.175 777 Planarity : 0.008 0.080 903 Dihedral : 6.126 51.590 712 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.78 % Favored : 98.06 % Rotamer: Outliers : 2.17 % Allowed : 14.62 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.49 (0.32), residues: 618 helix: 0.91 (0.26), residues: 343 sheet: 1.52 (1.28), residues: 15 loop : -0.44 (0.37), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.002 ARG J 188 TYR 0.025 0.004 TYR I 91 PHE 0.023 0.004 PHE J 81 TRP 0.020 0.005 TRP J 132 HIS 0.012 0.003 HIS J 131 Details of bonding type rmsd covalent geometry : bond 0.00855 ( 5231) covalent geometry : angle 0.92864 ( 7080) hydrogen bonds : bond 0.07063 ( 267) hydrogen bonds : angle 5.19924 ( 756) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 0.243 Fit side-chains REVERT: I 102 ARG cc_start: 0.7660 (OUTLIER) cc_final: 0.7434 (ttt180) REVERT: I 138 LYS cc_start: 0.7573 (ttpt) cc_final: 0.6886 (tptt) REVERT: I 192 ASP cc_start: 0.7492 (t70) cc_final: 0.7122 (t70) REVERT: J 13 GLU cc_start: 0.5995 (OUTLIER) cc_final: 0.5792 (pt0) REVERT: J 236 GLN cc_start: 0.7146 (OUTLIER) cc_final: 0.6744 (mt0) outliers start: 12 outliers final: 4 residues processed: 97 average time/residue: 0.7931 time to fit residues: 79.5047 Evaluate side-chains 95 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 88 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 290 SER Chi-restraints excluded: chain I residue 102 ARG Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain J residue 13 GLU Chi-restraints excluded: chain J residue 170 THR Chi-restraints excluded: chain J residue 236 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 46 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 39 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 57 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 307 GLN I 247 GLN J 148 ASN J 297 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.179982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.158515 restraints weight = 4731.612| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 0.94 r_work: 0.3744 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3650 rms_B_bonded: 2.54 restraints_weight: 0.2500 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.1243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5231 Z= 0.130 Angle : 0.614 7.631 7080 Z= 0.316 Chirality : 0.043 0.142 777 Planarity : 0.005 0.037 903 Dihedral : 4.940 48.607 712 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.54 % Rotamer: Outliers : 1.44 % Allowed : 15.88 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.44 (0.33), residues: 618 helix: 1.88 (0.28), residues: 338 sheet: 1.27 (1.30), residues: 15 loop : -0.24 (0.37), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 63 TYR 0.019 0.002 TYR I 91 PHE 0.021 0.002 PHE J 81 TRP 0.011 0.001 TRP J 237 HIS 0.005 0.001 HIS J 131 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 5231) covalent geometry : angle 0.61356 ( 7080) hydrogen bonds : bond 0.04708 ( 267) hydrogen bonds : angle 4.63714 ( 756) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 91 time to evaluate : 0.200 Fit side-chains REVERT: I 102 ARG cc_start: 0.7600 (OUTLIER) cc_final: 0.7305 (ttt180) REVERT: I 138 LYS cc_start: 0.7464 (ttpt) cc_final: 0.6797 (tptt) REVERT: I 192 ASP cc_start: 0.7445 (t70) cc_final: 0.7098 (t70) REVERT: I 255 MET cc_start: 0.7907 (mtm) cc_final: 0.7596 (ttm) outliers start: 8 outliers final: 2 residues processed: 96 average time/residue: 0.7104 time to fit residues: 70.2909 Evaluate side-chains 95 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 92 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 102 ARG Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain J residue 170 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 41 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 16 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 chunk 15 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 34 optimal weight: 0.8980 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 247 GLN J 148 ASN J 297 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.177115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.155478 restraints weight = 4789.118| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 0.94 r_work: 0.3706 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3612 rms_B_bonded: 2.52 restraints_weight: 0.2500 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 5231 Z= 0.233 Angle : 0.749 8.710 7080 Z= 0.383 Chirality : 0.047 0.146 777 Planarity : 0.006 0.048 903 Dihedral : 5.348 49.789 712 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.78 % Favored : 98.06 % Rotamer: Outliers : 1.08 % Allowed : 16.06 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.12 (0.33), residues: 618 helix: 1.55 (0.27), residues: 337 sheet: 1.35 (1.31), residues: 15 loop : -0.28 (0.37), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG J 188 TYR 0.022 0.002 TYR I 91 PHE 0.016 0.003 PHE I 30 TRP 0.015 0.003 TRP J 132 HIS 0.010 0.002 HIS J 131 Details of bonding type rmsd covalent geometry : bond 0.00515 ( 5231) covalent geometry : angle 0.74924 ( 7080) hydrogen bonds : bond 0.05879 ( 267) hydrogen bonds : angle 4.90080 ( 756) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 90 time to evaluate : 0.172 Fit side-chains REVERT: I 102 ARG cc_start: 0.7627 (OUTLIER) cc_final: 0.7346 (ttt180) REVERT: I 138 LYS cc_start: 0.7508 (ttpt) cc_final: 0.6848 (tptt) REVERT: I 192 ASP cc_start: 0.7502 (t70) cc_final: 0.7143 (t70) outliers start: 6 outliers final: 2 residues processed: 93 average time/residue: 0.7218 time to fit residues: 69.2618 Evaluate side-chains 92 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 89 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 102 ARG Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain J residue 170 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 59 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 33 optimal weight: 6.9990 chunk 28 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 18 optimal weight: 7.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 247 GLN J 148 ASN J 236 GLN J 297 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.178845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.157200 restraints weight = 4747.908| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 0.94 r_work: 0.3727 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3633 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.1160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5231 Z= 0.163 Angle : 0.672 10.358 7080 Z= 0.343 Chirality : 0.044 0.161 777 Planarity : 0.005 0.039 903 Dihedral : 5.045 48.871 712 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Rotamer: Outliers : 1.26 % Allowed : 15.88 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.29 (0.33), residues: 618 helix: 1.75 (0.28), residues: 338 sheet: 1.09 (1.32), residues: 15 loop : -0.28 (0.37), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG J 224 TYR 0.020 0.002 TYR I 91 PHE 0.020 0.002 PHE J 81 TRP 0.013 0.002 TRP J 132 HIS 0.007 0.001 HIS J 131 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 5231) covalent geometry : angle 0.67232 ( 7080) hydrogen bonds : bond 0.05142 ( 267) hydrogen bonds : angle 4.72699 ( 756) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 92 time to evaluate : 0.230 Fit side-chains REVERT: I 102 ARG cc_start: 0.7629 (OUTLIER) cc_final: 0.7358 (ttt180) REVERT: I 138 LYS cc_start: 0.7462 (ttpt) cc_final: 0.6813 (tptt) REVERT: I 192 ASP cc_start: 0.7456 (t70) cc_final: 0.7109 (t70) outliers start: 7 outliers final: 2 residues processed: 94 average time/residue: 0.7313 time to fit residues: 71.0710 Evaluate side-chains 92 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 89 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 102 ARG Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain J residue 170 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 60 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 43 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 chunk 50 optimal weight: 7.9990 chunk 2 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 247 GLN J 148 ASN J 236 GLN J 297 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.179663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.157960 restraints weight = 4750.502| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 0.95 r_work: 0.3736 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3641 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5231 Z= 0.143 Angle : 0.644 11.287 7080 Z= 0.327 Chirality : 0.043 0.147 777 Planarity : 0.005 0.038 903 Dihedral : 4.914 48.380 712 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.78 % Favored : 98.06 % Rotamer: Outliers : 0.72 % Allowed : 16.79 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.50 (0.34), residues: 618 helix: 1.93 (0.28), residues: 338 sheet: 1.01 (1.35), residues: 15 loop : -0.19 (0.37), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 63 TYR 0.019 0.002 TYR I 91 PHE 0.016 0.002 PHE I 30 TRP 0.012 0.001 TRP J 132 HIS 0.006 0.001 HIS J 131 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 5231) covalent geometry : angle 0.64382 ( 7080) hydrogen bonds : bond 0.04850 ( 267) hydrogen bonds : angle 4.63356 ( 756) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2953.52 seconds wall clock time: 50 minutes 58.98 seconds (3058.98 seconds total)