Starting phenix.real_space_refine on Thu Mar 6 07:00:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8plz_17754/03_2025/8plz_17754.cif Found real_map, /net/cci-nas-00/data/ceres_data/8plz_17754/03_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_17754/03_2025/8plz_17754.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8plz_17754/03_2025/8plz_17754.map" model { file = "/net/cci-nas-00/data/ceres_data/8plz_17754/03_2025/8plz_17754.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8plz_17754/03_2025/8plz_17754.cif" } resolution = 1.9 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= 0.002 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 8.24, per 1000 atoms: 1.56 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: 1.84 Conformation dependent library (CDL) restraints added in 612.5 milliseconds 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: 0.57 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: 1.42 Time building geometry restraints manager: 2.00 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: 62.810 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 22.980 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:15.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.060 ------------------------------------------------------------------------------- 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= 0.342 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (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 TRP 0.014 0.002 TRP J 132 HIS 0.006 0.001 HIS J 131 PHE 0.017 0.002 PHE I 30 TYR 0.020 0.002 TYR I 91 ARG 0.006 0.001 ARG I 102 *********************** 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 : 0.624 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 86 average time/residue: 1.6365 time to fit residues: 146.1307 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 : 0.589 ------------------------------------------------------------------------------- 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 52 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 16 optimal weight: 8.9990 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 18 optimal weight: 7.9990 chunk 29 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 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 = 0.4104 r_free = 0.4104 target = 0.179658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.157900 restraints weight = 4718.007| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 0.94 r_work: 0.3736 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3641 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.0831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5231 Z= 0.179 Angle : 0.593 6.944 7080 Z= 0.305 Chirality : 0.042 0.134 777 Planarity : 0.005 0.036 903 Dihedral : 8.548 111.141 719 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.54 % Rotamer: Outliers : 1.26 % Allowed : 12.27 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.33), residues: 618 helix: 1.83 (0.28), residues: 339 sheet: 0.58 (1.03), residues: 15 loop : -0.22 (0.37), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 132 HIS 0.006 0.001 HIS J 131 PHE 0.017 0.002 PHE I 30 TYR 0.018 0.002 TYR I 91 ARG 0.004 0.000 ARG I 63 *********************** 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 95 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 88 time to evaluate : 0.614 Fit side-chains revert: symmetry clash REVERT: I 192 ASP cc_start: 0.7439 (t70) cc_final: 0.7111 (t70) outliers start: 7 outliers final: 2 residues processed: 92 average time/residue: 1.5020 time to fit residues: 143.3849 Evaluate side-chains 86 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 84 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 290 SER Chi-restraints excluded: chain I residue 129 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 56 optimal weight: 1.9990 chunk 43 optimal weight: 9.9990 chunk 57 optimal weight: 8.9990 chunk 44 optimal weight: 5.9990 chunk 33 optimal weight: 8.9990 chunk 53 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 30 optimal weight: 7.9990 chunk 39 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 chunk 25 optimal weight: 7.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- 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 297 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.176778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.154882 restraints weight = 4693.848| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 0.94 r_work: 0.3697 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3602 rms_B_bonded: 2.51 restraints_weight: 0.2500 r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.0797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 5231 Z= 0.372 Angle : 0.771 7.979 7080 Z= 0.395 Chirality : 0.048 0.152 777 Planarity : 0.006 0.054 903 Dihedral : 8.370 98.052 715 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.10 % Favored : 97.73 % Rotamer: Outliers : 1.81 % Allowed : 13.54 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.32), residues: 618 helix: 1.38 (0.27), residues: 337 sheet: 0.94 (1.10), residues: 15 loop : -0.30 (0.36), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP J 132 HIS 0.010 0.002 HIS J 131 PHE 0.017 0.003 PHE I 71 TYR 0.022 0.003 TYR I 91 ARG 0.006 0.001 ARG I 102 *********************** 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 97 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.635 Fit side-chains REVERT: I 192 ASP cc_start: 0.7455 (t70) cc_final: 0.7098 (t70) REVERT: I 255 MET cc_start: 0.7963 (mtp) cc_final: 0.7621 (ttm) REVERT: J 62 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7858 (tp30) REVERT: J 236 GLN cc_start: 0.7178 (mt0) cc_final: 0.6878 (mt0) outliers start: 10 outliers final: 4 residues processed: 92 average time/residue: 1.4822 time to fit residues: 141.3562 Evaluate side-chains 90 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 85 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 290 SER Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 170 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 40 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 chunk 33 optimal weight: 7.9990 chunk 42 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 35 optimal weight: 8.9990 chunk 15 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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 297 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.178409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.156779 restraints weight = 4835.929| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 0.95 r_work: 0.3723 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3629 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.0948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5231 Z= 0.219 Angle : 0.623 6.755 7080 Z= 0.320 Chirality : 0.043 0.144 777 Planarity : 0.005 0.040 903 Dihedral : 8.363 110.362 715 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.54 % Rotamer: Outliers : 1.99 % Allowed : 13.36 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 618 helix: 1.75 (0.28), residues: 338 sheet: 1.02 (1.23), residues: 15 loop : -0.25 (0.37), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP J 132 HIS 0.006 0.001 HIS J 131 PHE 0.017 0.002 PHE I 30 TYR 0.019 0.002 TYR I 91 ARG 0.003 0.000 ARG J 224 *********************** 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 99 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.592 Fit side-chains REVERT: I 102 ARG cc_start: 0.7639 (OUTLIER) cc_final: 0.7360 (ttt180) REVERT: I 134 LEU cc_start: 0.5913 (OUTLIER) cc_final: 0.5657 (mt) REVERT: I 192 ASP cc_start: 0.7383 (t70) cc_final: 0.7042 (t70) REVERT: I 255 MET cc_start: 0.7981 (mtp) cc_final: 0.7685 (ttm) REVERT: J 236 GLN cc_start: 0.7182 (mt0) cc_final: 0.6855 (mt0) outliers start: 11 outliers final: 3 residues processed: 93 average time/residue: 1.4880 time to fit residues: 143.3853 Evaluate side-chains 92 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 87 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 290 SER Chi-restraints excluded: chain I residue 54 MET Chi-restraints excluded: chain I residue 102 ARG Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 134 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 47 optimal weight: 9.9990 chunk 44 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 31 optimal weight: 6.9990 chunk 1 optimal weight: 0.2980 chunk 57 optimal weight: 6.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 113 HIS J 297 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.180013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.158495 restraints weight = 4783.230| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 0.95 r_work: 0.3745 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3650 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.1117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5231 Z= 0.171 Angle : 0.568 6.859 7080 Z= 0.292 Chirality : 0.042 0.139 777 Planarity : 0.004 0.039 903 Dihedral : 8.110 112.114 715 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.46 % Favored : 98.38 % Rotamer: Outliers : 1.81 % Allowed : 13.90 % 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 (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: 1.58 (0.33), residues: 618 helix: 2.02 (0.28), residues: 338 sheet: 0.87 (1.27), residues: 15 loop : -0.19 (0.37), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 132 HIS 0.005 0.001 HIS J 131 PHE 0.016 0.002 PHE I 30 TYR 0.019 0.001 TYR I 91 ARG 0.005 0.000 ARG I 63 *********************** 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 107 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.629 Fit side-chains REVERT: I 102 ARG cc_start: 0.7647 (OUTLIER) cc_final: 0.7377 (ttt180) REVERT: I 138 LYS cc_start: 0.7456 (ttpt) cc_final: 0.6806 (tptt) REVERT: I 192 ASP cc_start: 0.7375 (t70) cc_final: 0.7034 (t70) REVERT: I 255 MET cc_start: 0.7956 (mtp) cc_final: 0.7685 (ttm) REVERT: J 169 TYR cc_start: 0.6463 (OUTLIER) cc_final: 0.5175 (m-80) REVERT: J 236 GLN cc_start: 0.7116 (mt0) cc_final: 0.6857 (mt0) outliers start: 10 outliers final: 2 residues processed: 100 average time/residue: 1.5492 time to fit residues: 160.3586 Evaluate side-chains 96 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 92 time to evaluate : 0.560 ------------------------------------------------------------------------------- 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 120 MET Chi-restraints excluded: chain J residue 169 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 31 optimal weight: 7.9990 chunk 20 optimal weight: 8.9990 chunk 18 optimal weight: 9.9990 chunk 6 optimal weight: 2.9990 chunk 43 optimal weight: 10.0000 chunk 59 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 39 optimal weight: 8.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 297 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.178223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.156515 restraints weight = 4724.888| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 0.94 r_work: 0.3718 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3623 rms_B_bonded: 2.52 restraints_weight: 0.2500 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.1011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5231 Z= 0.256 Angle : 0.658 7.013 7080 Z= 0.336 Chirality : 0.044 0.141 777 Planarity : 0.005 0.039 903 Dihedral : 8.106 107.798 714 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Rotamer: Outliers : 1.62 % Allowed : 14.44 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 618 helix: 1.82 (0.28), residues: 338 sheet: 0.90 (1.27), residues: 15 loop : -0.25 (0.37), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP J 132 HIS 0.008 0.001 HIS J 131 PHE 0.016 0.002 PHE I 30 TYR 0.020 0.002 TYR I 91 ARG 0.005 0.001 ARG I 21 *********************** 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 99 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 90 time to evaluate : 0.587 Fit side-chains REVERT: I 102 ARG cc_start: 0.7624 (OUTLIER) cc_final: 0.7345 (ttt180) REVERT: I 192 ASP cc_start: 0.7459 (t70) cc_final: 0.7103 (t70) REVERT: I 255 MET cc_start: 0.7963 (mtp) cc_final: 0.7660 (ttm) REVERT: J 236 GLN cc_start: 0.7130 (mt0) cc_final: 0.6822 (mt0) outliers start: 9 outliers final: 2 residues processed: 94 average time/residue: 1.5483 time to fit residues: 150.5802 Evaluate side-chains 88 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 85 time to evaluate : 0.617 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 25 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 9 optimal weight: 6.9990 chunk 53 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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 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 = 0.176932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.155346 restraints weight = 4729.757| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 0.94 r_work: 0.3703 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3608 rms_B_bonded: 2.51 restraints_weight: 0.2500 r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.1027 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= 0.329 Angle : 0.740 7.412 7080 Z= 0.377 Chirality : 0.047 0.151 777 Planarity : 0.006 0.049 903 Dihedral : 8.071 101.378 714 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.78 % Favored : 98.06 % Rotamer: Outliers : 1.62 % Allowed : 14.62 % 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 (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: 1.11 (0.33), residues: 618 helix: 1.55 (0.27), residues: 337 sheet: 1.11 (1.24), residues: 15 loop : -0.29 (0.37), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP J 132 HIS 0.010 0.002 HIS J 131 PHE 0.023 0.003 PHE J 81 TYR 0.022 0.002 TYR I 91 ARG 0.005 0.001 ARG I 21 *********************** 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 98 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 0.659 Fit side-chains REVERT: I 102 ARG cc_start: 0.7630 (OUTLIER) cc_final: 0.7365 (ttt180) REVERT: I 192 ASP cc_start: 0.7479 (t70) cc_final: 0.7114 (t70) REVERT: I 255 MET cc_start: 0.7961 (mtp) cc_final: 0.7649 (ttm) REVERT: J 236 GLN cc_start: 0.7095 (mt0) cc_final: 0.6735 (mt0) outliers start: 9 outliers final: 3 residues processed: 95 average time/residue: 1.5940 time to fit residues: 156.7477 Evaluate side-chains 92 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 88 time to evaluate : 0.620 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain J residue 170 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 27 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 297 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.177582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.156019 restraints weight = 4733.659| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 0.94 r_work: 0.3712 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.3617 rms_B_bonded: 2.51 restraints_weight: 0.2500 r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.1055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5231 Z= 0.287 Angle : 0.704 7.964 7080 Z= 0.358 Chirality : 0.046 0.147 777 Planarity : 0.005 0.040 903 Dihedral : 8.204 106.614 714 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.78 % Favored : 98.06 % Rotamer: Outliers : 1.99 % Allowed : 14.62 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.13 (0.33), residues: 618 helix: 1.59 (0.27), residues: 338 sheet: 1.12 (1.24), residues: 15 loop : -0.32 (0.37), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP J 132 HIS 0.008 0.002 HIS J 131 PHE 0.016 0.002 PHE I 30 TYR 0.021 0.002 TYR I 91 ARG 0.005 0.001 ARG I 21 *********************** 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 101 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.623 Fit side-chains REVERT: I 102 ARG cc_start: 0.7637 (OUTLIER) cc_final: 0.7354 (ttt180) REVERT: I 192 ASP cc_start: 0.7480 (t70) cc_final: 0.7126 (t70) REVERT: I 255 MET cc_start: 0.7954 (mtp) cc_final: 0.7644 (ttm) REVERT: J 236 GLN cc_start: 0.7089 (mt0) cc_final: 0.6720 (mt0) outliers start: 11 outliers final: 3 residues processed: 95 average time/residue: 1.5275 time to fit residues: 150.4738 Evaluate side-chains 92 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 88 time to evaluate : 0.618 ------------------------------------------------------------------------------- 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 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 8 optimal weight: 7.9990 chunk 5 optimal weight: 10.0000 chunk 16 optimal weight: 9.9990 chunk 58 optimal weight: 0.5980 chunk 45 optimal weight: 0.5980 chunk 43 optimal weight: 6.9990 chunk 61 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 52 optimal weight: 0.0980 chunk 20 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 113 HIS J 148 ASN J 297 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.181531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.160310 restraints weight = 4743.631| |-----------------------------------------------------------------------------| r_work (start): 0.3872 rms_B_bonded: 0.94 r_work: 0.3766 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3673 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 5231 Z= 0.158 Angle : 0.588 9.483 7080 Z= 0.298 Chirality : 0.041 0.143 777 Planarity : 0.004 0.038 903 Dihedral : 8.015 113.328 714 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Rotamer: Outliers : 0.72 % Allowed : 15.52 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.34), residues: 618 helix: 2.10 (0.28), residues: 338 sheet: 0.96 (1.25), residues: 15 loop : -0.13 (0.37), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 132 HIS 0.004 0.001 HIS I 281 PHE 0.016 0.001 PHE I 30 TYR 0.017 0.002 TYR I 91 ARG 0.006 0.000 ARG I 21 *********************** 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 100 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 96 time to evaluate : 0.623 Fit side-chains REVERT: I 65 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7425 (mm) REVERT: I 138 LYS cc_start: 0.7416 (ttpt) cc_final: 0.6774 (tptt) REVERT: I 192 ASP cc_start: 0.7425 (t70) cc_final: 0.7079 (t70) REVERT: I 237 MET cc_start: 0.6501 (mmm) cc_final: 0.5200 (tmt) REVERT: I 255 MET cc_start: 0.7951 (mtp) cc_final: 0.7714 (ttm) REVERT: J 169 TYR cc_start: 0.6461 (OUTLIER) cc_final: 0.5170 (m-80) REVERT: J 236 GLN cc_start: 0.7099 (mt0) cc_final: 0.6806 (mt0) REVERT: J 293 LYS cc_start: 0.7748 (mppt) cc_final: 0.7525 (mptp) outliers start: 4 outliers final: 1 residues processed: 99 average time/residue: 1.5118 time to fit residues: 155.1062 Evaluate side-chains 93 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 90 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain J residue 169 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 41 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 28 optimal weight: 9.9990 chunk 58 optimal weight: 0.5980 chunk 56 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 43 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 chunk 48 optimal weight: 0.1980 chunk 35 optimal weight: 9.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 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 = 0.4116 r_free = 0.4116 target = 0.180600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.159056 restraints weight = 4785.897| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 0.95 r_work: 0.3752 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3658 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5231 Z= 0.178 Angle : 0.612 11.001 7080 Z= 0.308 Chirality : 0.042 0.137 777 Planarity : 0.005 0.038 903 Dihedral : 8.004 112.819 714 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Rotamer: Outliers : 0.54 % Allowed : 16.79 % 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 (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: 1.70 (0.34), residues: 618 helix: 2.11 (0.28), residues: 338 sheet: 0.83 (1.25), residues: 15 loop : -0.11 (0.37), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 132 HIS 0.005 0.001 HIS J 131 PHE 0.015 0.002 PHE I 30 TYR 0.018 0.002 TYR I 91 ARG 0.009 0.001 ARG H 268 ********************** 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 93 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 90 time to evaluate : 0.611 Fit side-chains REVERT: I 138 LYS cc_start: 0.7442 (ttpt) cc_final: 0.6767 (tptt) REVERT: I 192 ASP cc_start: 0.7429 (t70) cc_final: 0.7080 (t70) REVERT: I 255 MET cc_start: 0.7943 (mtp) cc_final: 0.7667 (ttm) REVERT: J 236 GLN cc_start: 0.7124 (mt0) cc_final: 0.6839 (mt0) REVERT: J 293 LYS cc_start: 0.7757 (mppt) cc_final: 0.7543 (mptp) outliers start: 3 outliers final: 1 residues processed: 93 average time/residue: 1.5682 time to fit residues: 150.8482 Evaluate side-chains 90 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 89 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 129 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 27 optimal weight: 6.9990 chunk 17 optimal weight: 9.9990 chunk 38 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 54 optimal weight: 0.7980 chunk 25 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 overall best weight: 1.2182 ------------------------------------------------------------------------------- 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 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 = 0.4110 r_free = 0.4110 target = 0.180160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.158545 restraints weight = 4748.253| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 0.95 r_work: 0.3743 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3649 rms_B_bonded: 2.54 restraints_weight: 0.2500 r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5231 Z= 0.196 Angle : 0.631 11.100 7080 Z= 0.317 Chirality : 0.043 0.137 777 Planarity : 0.005 0.038 903 Dihedral : 8.020 111.605 714 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Rotamer: Outliers : 0.54 % Allowed : 16.97 % 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 (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: 1.66 (0.34), residues: 618 helix: 2.07 (0.28), residues: 338 sheet: 0.75 (1.24), residues: 15 loop : -0.13 (0.37), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 132 HIS 0.006 0.001 HIS J 131 PHE 0.017 0.002 PHE J 81 TYR 0.019 0.002 TYR I 91 ARG 0.007 0.001 ARG H 268 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6321.09 seconds wall clock time: 108 minutes 34.01 seconds (6514.01 seconds total)