Starting phenix.real_space_refine on Mon Feb 10 20:20:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ggj_40010/02_2025/8ggj_40010.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ggj_40010/02_2025/8ggj_40010.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ggj_40010/02_2025/8ggj_40010.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ggj_40010/02_2025/8ggj_40010.map" model { file = "/net/cci-nas-00/data/ceres_data/8ggj_40010/02_2025/8ggj_40010.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ggj_40010/02_2025/8ggj_40010.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.027 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 15 5.16 5 C 1471 2.51 5 N 351 2.21 5 O 364 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 2201 Number of models: 1 Model: "" Number of chains: 2 Chain: "R" Number of atoms: 2185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2185 Classifications: {'peptide': 286} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 7, 'TRANS': 278} Chain breaks: 1 Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 5, 'GLU:plan': 6, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 79 Chain: "R" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} Time building chain proxies: 2.75, per 1000 atoms: 1.25 Number of scatterers: 2201 At special positions: 0 Unit cell: (59.8713, 85.9023, 62.4744, 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 15 16.00 O 364 8.00 N 351 7.00 C 1471 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 191 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.59 Conformation dependent library (CDL) restraints added in 276.0 milliseconds 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 548 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 0 sheets defined 86.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'R' and resid 31 through 61 removed outlier: 3.581A pdb=" N GLY R 37 " --> pdb=" O VAL R 33 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE R 38 " --> pdb=" O VAL R 34 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL R 39 " --> pdb=" O GLY R 35 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU R 53 " --> pdb=" O PHE R 49 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL R 54 " --> pdb=" O GLY R 50 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ILE R 55 " --> pdb=" O ASN R 51 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 86 removed outlier: 4.463A pdb=" N PHE R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) Processing helix chain 'R' and resid 86 through 97 Processing helix chain 'R' and resid 103 through 137 removed outlier: 4.287A pdb=" N GLU R 107 " --> pdb=" O ASN R 103 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE R 108 " --> pdb=" O PHE R 104 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE R 121 " --> pdb=" O VAL R 117 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLU R 122 " --> pdb=" O THR R 118 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N THR R 123 " --> pdb=" O ALA R 119 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LEU R 124 " --> pdb=" O SER R 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 145 Processing helix chain 'R' and resid 146 through 163 removed outlier: 3.775A pdb=" N ARG R 151 " --> pdb=" O LYS R 147 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL R 152 " --> pdb=" O ASN R 148 " (cutoff:3.500A) Processing helix chain 'R' and resid 166 through 171 Processing helix chain 'R' and resid 178 through 187 Processing helix chain 'R' and resid 196 through 208 Processing helix chain 'R' and resid 208 through 237 Processing helix chain 'R' and resid 269 through 281 removed outlier: 3.821A pdb=" N THR R 281 " --> pdb=" O ILE R 277 " (cutoff:3.500A) Processing helix chain 'R' and resid 282 through 296 Proline residue: R 288 - end of helix removed outlier: 3.626A pdb=" N VAL R 292 " --> pdb=" O PRO R 288 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ILE R 294 " --> pdb=" O PHE R 290 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 315 removed outlier: 3.602A pdb=" N GLY R 315 " --> pdb=" O LEU R 311 " (cutoff:3.500A) Processing helix chain 'R' and resid 316 through 320 Processing helix chain 'R' and resid 321 through 327 Processing helix chain 'R' and resid 329 through 340 160 hydrogen bonds defined for protein. 474 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: 0.67 Time building geometry restraints manager: 0.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 651 1.34 - 1.46: 518 1.46 - 1.58: 1068 1.58 - 1.69: 0 1.69 - 1.81: 21 Bond restraints: 2258 Sorted by residual: bond pdb=" CAC G1I R 501 " pdb=" CAD G1I R 501 " ideal model delta sigma weight residual 1.397 1.449 -0.052 2.00e-02 2.50e+03 6.67e+00 bond pdb=" CAD G1I R 501 " pdb=" CAE G1I R 501 " ideal model delta sigma weight residual 1.394 1.438 -0.044 2.00e-02 2.50e+03 4.89e+00 bond pdb=" CAI G1I R 501 " pdb=" CAJ G1I R 501 " ideal model delta sigma weight residual 1.523 1.566 -0.043 2.00e-02 2.50e+03 4.63e+00 bond pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " ideal model delta sigma weight residual 1.520 1.562 -0.042 2.00e-02 2.50e+03 4.33e+00 bond pdb=" CAD G1I R 501 " pdb=" OAK G1I R 501 " ideal model delta sigma weight residual 1.353 1.319 0.034 2.00e-02 2.50e+03 2.85e+00 ... (remaining 2253 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.11: 2971 1.11 - 2.21: 95 2.21 - 3.32: 12 3.32 - 4.43: 7 4.43 - 5.54: 6 Bond angle restraints: 3091 Sorted by residual: angle pdb=" C THR R 96 " pdb=" N LYS R 97 " pdb=" CA LYS R 97 " ideal model delta sigma weight residual 121.54 127.08 -5.54 1.91e+00 2.74e-01 8.40e+00 angle pdb=" C LEU R 84 " pdb=" N ALA R 85 " pdb=" CA ALA R 85 " ideal model delta sigma weight residual 122.79 119.15 3.64 1.78e+00 3.16e-01 4.19e+00 angle pdb=" CAE G1I R 501 " pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " ideal model delta sigma weight residual 112.63 117.92 -5.29 3.00e+00 1.11e-01 3.11e+00 angle pdb=" N SER R 236 " pdb=" CA SER R 236 " pdb=" C SER R 236 " ideal model delta sigma weight residual 111.40 113.41 -2.01 1.22e+00 6.72e-01 2.72e+00 angle pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " pdb=" CAI G1I R 501 " ideal model delta sigma weight residual 110.89 115.70 -4.81 3.00e+00 1.11e-01 2.58e+00 ... (remaining 3086 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.64: 1067 10.64 - 21.28: 140 21.28 - 31.92: 59 31.92 - 42.56: 23 42.56 - 53.19: 5 Dihedral angle restraints: 1294 sinusoidal: 451 harmonic: 843 Sorted by residual: dihedral pdb=" CA PHE R 208 " pdb=" C PHE R 208 " pdb=" N TYR R 209 " pdb=" CA TYR R 209 " ideal model delta harmonic sigma weight residual -180.00 -160.78 -19.22 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CG ARG R 175 " pdb=" CD ARG R 175 " pdb=" NE ARG R 175 " pdb=" CZ ARG R 175 " ideal model delta sinusoidal sigma weight residual 180.00 138.69 41.31 2 1.50e+01 4.44e-03 9.30e+00 dihedral pdb=" CA HIS R 178 " pdb=" C HIS R 178 " pdb=" N GLN R 179 " pdb=" CA GLN R 179 " ideal model delta harmonic sigma weight residual -180.00 -164.98 -15.02 0 5.00e+00 4.00e-02 9.03e+00 ... (remaining 1291 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 229 0.030 - 0.060: 100 0.060 - 0.089: 36 0.089 - 0.119: 13 0.119 - 0.149: 1 Chirality restraints: 379 Sorted by residual: chirality pdb=" CAJ G1I R 501 " pdb=" CAF G1I R 501 " pdb=" CAI G1I R 501 " pdb=" OAM G1I R 501 " both_signs ideal model delta sigma weight residual False 2.40 2.55 -0.15 2.00e-01 2.50e+01 5.56e-01 chirality pdb=" CA PRO R 288 " pdb=" N PRO R 288 " pdb=" C PRO R 288 " pdb=" CB PRO R 288 " both_signs ideal model delta sigma weight residual False 2.72 2.62 0.10 2.00e-01 2.50e+01 2.57e-01 chirality pdb=" CA PRO R 138 " pdb=" N PRO R 138 " pdb=" C PRO R 138 " pdb=" CB PRO R 138 " both_signs ideal model delta sigma weight residual False 2.72 2.62 0.10 2.00e-01 2.50e+01 2.52e-01 ... (remaining 376 not shown) Planarity restraints: 368 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL R 87 " -0.022 5.00e-02 4.00e+02 3.35e-02 1.79e+00 pdb=" N PRO R 88 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO R 88 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO R 88 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN R 322 " 0.020 5.00e-02 4.00e+02 2.97e-02 1.41e+00 pdb=" N PRO R 323 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO R 323 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO R 323 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL R 210 " 0.016 5.00e-02 4.00e+02 2.37e-02 9.01e-01 pdb=" N PRO R 211 " -0.041 5.00e-02 4.00e+02 pdb=" CA PRO R 211 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO R 211 " 0.013 5.00e-02 4.00e+02 ... (remaining 365 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 464 2.78 - 3.31: 2093 3.31 - 3.84: 3475 3.84 - 4.37: 3624 4.37 - 4.90: 6840 Nonbonded interactions: 16496 Sorted by model distance: nonbonded pdb=" OG SER R 203 " pdb=" OAL G1I R 501 " model vdw 2.245 3.040 nonbonded pdb=" N GLU R 306 " pdb=" OE1 GLU R 306 " model vdw 2.294 3.120 nonbonded pdb=" O SER R 111 " pdb=" OG SER R 165 " model vdw 2.312 3.040 nonbonded pdb=" O ILE R 47 " pdb=" ND2 ASN R 51 " model vdw 2.315 3.120 nonbonded pdb=" OD2 ASP R 113 " pdb=" OAM G1I R 501 " model vdw 2.368 3.040 ... (remaining 16491 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.710 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 12.260 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:2.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 2258 Z= 0.255 Angle : 0.533 5.536 3091 Z= 0.287 Chirality : 0.040 0.149 379 Planarity : 0.004 0.033 368 Dihedral : 13.044 53.194 743 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.52), residues: 282 helix: 1.82 (0.36), residues: 220 sheet: None (None), residues: 0 loop : -0.58 (0.83), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 313 HIS 0.003 0.001 HIS R 178 PHE 0.008 0.001 PHE R 240 TYR 0.010 0.001 TYR R 132 ARG 0.002 0.000 ARG R 239 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.239 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.2634 time to fit residues: 8.2535 Evaluate side-chains 23 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 23 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.111990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.097103 restraints weight = 2970.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.099389 restraints weight = 1771.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.100913 restraints weight = 1255.152| |-----------------------------------------------------------------------------| r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3004 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3004 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.0746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 2258 Z= 0.235 Angle : 0.480 4.741 3091 Z= 0.264 Chirality : 0.039 0.108 379 Planarity : 0.004 0.028 368 Dihedral : 4.442 19.309 319 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 0.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 1.36 % Allowed : 5.43 % Favored : 93.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.52), residues: 282 helix: 1.98 (0.36), residues: 225 sheet: None (None), residues: 0 loop : -0.19 (0.90), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 158 HIS 0.007 0.002 HIS R 296 PHE 0.007 0.001 PHE R 282 TYR 0.006 0.001 TYR R 174 ARG 0.002 0.000 ARG R 239 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 22 time to evaluate : 0.234 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 24 average time/residue: 0.2286 time to fit residues: 6.3095 Evaluate side-chains 21 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 20 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 94 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 21 optimal weight: 0.3980 chunk 15 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 chunk 5 optimal weight: 0.0770 chunk 10 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.113121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.098350 restraints weight = 2938.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.100610 restraints weight = 1756.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.102048 restraints weight = 1250.509| |-----------------------------------------------------------------------------| r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3015 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3015 r_free = 0.3015 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3015 r_free = 0.3015 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3015 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.0929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 2258 Z= 0.186 Angle : 0.443 4.628 3091 Z= 0.242 Chirality : 0.038 0.102 379 Planarity : 0.003 0.026 368 Dihedral : 4.277 19.216 319 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 0.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 1.36 % Allowed : 9.05 % Favored : 89.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.47 (0.52), residues: 282 helix: 2.14 (0.35), residues: 225 sheet: None (None), residues: 0 loop : -0.40 (0.89), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 158 HIS 0.007 0.002 HIS R 296 PHE 0.006 0.001 PHE R 282 TYR 0.006 0.001 TYR R 209 ARG 0.002 0.000 ARG R 239 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 24 time to evaluate : 0.243 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 26 average time/residue: 0.2210 time to fit residues: 6.6293 Evaluate side-chains 24 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 22 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 145 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 10 optimal weight: 0.2980 chunk 5 optimal weight: 0.0670 chunk 24 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 3 optimal weight: 0.0470 chunk 27 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 overall best weight: 0.3416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.115908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.101083 restraints weight = 2847.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.103390 restraints weight = 1717.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.104898 restraints weight = 1231.312| |-----------------------------------------------------------------------------| r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3052 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3052 r_free = 0.3052 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3052 r_free = 0.3052 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3052 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 2258 Z= 0.148 Angle : 0.411 4.561 3091 Z= 0.224 Chirality : 0.037 0.101 379 Planarity : 0.003 0.025 368 Dihedral : 4.059 19.153 319 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 0.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 2.26 % Allowed : 11.76 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.67 (0.53), residues: 282 helix: 2.33 (0.36), residues: 225 sheet: None (None), residues: 0 loop : -0.57 (0.87), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 158 HIS 0.006 0.001 HIS R 296 PHE 0.005 0.001 PHE R 193 TYR 0.006 0.001 TYR R 209 ARG 0.001 0.000 ARG R 175 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 26 time to evaluate : 0.230 Fit side-chains REVERT: R 72 ILE cc_start: 0.8452 (OUTLIER) cc_final: 0.7997 (mp) outliers start: 5 outliers final: 2 residues processed: 29 average time/residue: 0.2267 time to fit residues: 7.4224 Evaluate side-chains 25 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 22 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 72 ILE Chi-restraints excluded: chain R residue 82 MET Chi-restraints excluded: chain R residue 145 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 14 optimal weight: 0.4980 chunk 8 optimal weight: 0.4980 chunk 2 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 13 optimal weight: 0.0980 chunk 22 optimal weight: 1.9990 chunk 23 optimal weight: 0.2980 chunk 18 optimal weight: 0.8980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.115434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.100457 restraints weight = 2962.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.102559 restraints weight = 1780.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.104177 restraints weight = 1292.948| |-----------------------------------------------------------------------------| r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3044 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3044 r_free = 0.3044 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3044 r_free = 0.3044 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3044 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2258 Z= 0.168 Angle : 0.432 4.572 3091 Z= 0.234 Chirality : 0.037 0.100 379 Planarity : 0.003 0.035 368 Dihedral : 4.069 19.114 319 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 1.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 1.36 % Allowed : 15.84 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.72 (0.52), residues: 282 helix: 2.37 (0.36), residues: 226 sheet: None (None), residues: 0 loop : -0.64 (0.85), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 158 HIS 0.005 0.002 HIS R 296 PHE 0.006 0.001 PHE R 282 TYR 0.006 0.001 TYR R 209 ARG 0.002 0.000 ARG R 239 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 22 time to evaluate : 0.246 Fit side-chains REVERT: R 72 ILE cc_start: 0.8436 (OUTLIER) cc_final: 0.7973 (mp) outliers start: 3 outliers final: 2 residues processed: 25 average time/residue: 0.2703 time to fit residues: 7.6118 Evaluate side-chains 24 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 21 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 72 ILE Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 218 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 20 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 18 optimal weight: 0.1980 chunk 26 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 3 optimal weight: 0.0970 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.114286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.099444 restraints weight = 2876.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.101716 restraints weight = 1745.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.103239 restraints weight = 1252.711| |-----------------------------------------------------------------------------| r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3032 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3032 r_free = 0.3032 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3032 r_free = 0.3032 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3032 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2258 Z= 0.175 Angle : 0.422 4.580 3091 Z= 0.230 Chirality : 0.037 0.100 379 Planarity : 0.003 0.024 368 Dihedral : 4.040 19.083 319 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 1.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Rotamer: Outliers : 1.36 % Allowed : 16.29 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.72 (0.52), residues: 282 helix: 2.42 (0.36), residues: 225 sheet: None (None), residues: 0 loop : -0.80 (0.83), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 158 HIS 0.005 0.002 HIS R 296 PHE 0.007 0.001 PHE R 282 TYR 0.006 0.001 TYR R 209 ARG 0.001 0.000 ARG R 239 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 21 time to evaluate : 0.240 Fit side-chains REVERT: R 72 ILE cc_start: 0.8514 (OUTLIER) cc_final: 0.8062 (mp) outliers start: 3 outliers final: 2 residues processed: 24 average time/residue: 0.2405 time to fit residues: 6.5795 Evaluate side-chains 24 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 21 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 72 ILE Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 218 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 17 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 5 optimal weight: 0.4980 chunk 13 optimal weight: 0.3980 chunk 8 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 26 optimal weight: 0.3980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.113890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.099016 restraints weight = 2940.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.101141 restraints weight = 1770.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.102663 restraints weight = 1281.242| |-----------------------------------------------------------------------------| r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3025 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3025 r_free = 0.3025 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3025 r_free = 0.3025 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3025 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2258 Z= 0.181 Angle : 0.437 4.596 3091 Z= 0.237 Chirality : 0.038 0.100 379 Planarity : 0.003 0.023 368 Dihedral : 4.031 19.041 319 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 1.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 2.26 % Allowed : 15.84 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.71 (0.52), residues: 282 helix: 2.41 (0.36), residues: 225 sheet: None (None), residues: 0 loop : -0.81 (0.82), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 158 HIS 0.005 0.002 HIS R 296 PHE 0.007 0.001 PHE R 282 TYR 0.006 0.001 TYR R 209 ARG 0.002 0.000 ARG R 239 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 22 time to evaluate : 0.240 Fit side-chains REVERT: R 72 ILE cc_start: 0.8473 (OUTLIER) cc_final: 0.8016 (mp) REVERT: R 113 ASP cc_start: 0.8406 (OUTLIER) cc_final: 0.8155 (t0) outliers start: 5 outliers final: 1 residues processed: 27 average time/residue: 0.2197 time to fit residues: 6.8315 Evaluate side-chains 24 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 21 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 72 ILE Chi-restraints excluded: chain R residue 113 ASP Chi-restraints excluded: chain R residue 218 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 4 optimal weight: 1.9990 chunk 18 optimal weight: 0.1980 chunk 26 optimal weight: 0.2980 chunk 5 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.113419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.098324 restraints weight = 3021.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.100648 restraints weight = 1807.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.102246 restraints weight = 1287.937| |-----------------------------------------------------------------------------| r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3020 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3020 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 2258 Z= 0.187 Angle : 0.428 4.613 3091 Z= 0.233 Chirality : 0.038 0.100 379 Planarity : 0.003 0.023 368 Dihedral : 4.048 18.987 319 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 1.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 1.81 % Allowed : 15.84 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.68 (0.52), residues: 282 helix: 2.40 (0.36), residues: 225 sheet: None (None), residues: 0 loop : -0.83 (0.81), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 158 HIS 0.005 0.002 HIS R 296 PHE 0.007 0.001 PHE R 282 TYR 0.006 0.001 TYR R 209 ARG 0.001 0.000 ARG R 239 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 22 time to evaluate : 0.187 Fit side-chains REVERT: R 72 ILE cc_start: 0.8476 (OUTLIER) cc_final: 0.8013 (mp) REVERT: R 113 ASP cc_start: 0.8427 (OUTLIER) cc_final: 0.8181 (t0) outliers start: 4 outliers final: 1 residues processed: 26 average time/residue: 0.2527 time to fit residues: 7.3653 Evaluate side-chains 25 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 22 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 72 ILE Chi-restraints excluded: chain R residue 113 ASP Chi-restraints excluded: chain R residue 218 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 15 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 3 optimal weight: 0.4980 chunk 26 optimal weight: 0.4980 chunk 19 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.112905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.097807 restraints weight = 2969.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.099963 restraints weight = 1784.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.101475 restraints weight = 1302.388| |-----------------------------------------------------------------------------| r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3008 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3008 r_free = 0.3008 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3008 r_free = 0.3008 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3008 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 2258 Z= 0.194 Angle : 0.436 4.620 3091 Z= 0.237 Chirality : 0.038 0.101 379 Planarity : 0.003 0.023 368 Dihedral : 4.104 18.959 319 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 1.36 % Allowed : 16.74 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.63 (0.52), residues: 282 helix: 2.39 (0.36), residues: 225 sheet: None (None), residues: 0 loop : -0.98 (0.78), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 158 HIS 0.005 0.002 HIS R 296 PHE 0.008 0.001 PHE R 240 TYR 0.006 0.001 TYR R 209 ARG 0.002 0.000 ARG R 239 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 22 time to evaluate : 0.221 Fit side-chains REVERT: R 72 ILE cc_start: 0.8482 (OUTLIER) cc_final: 0.8019 (mp) REVERT: R 113 ASP cc_start: 0.8433 (OUTLIER) cc_final: 0.8197 (t0) outliers start: 3 outliers final: 1 residues processed: 25 average time/residue: 0.2588 time to fit residues: 7.2788 Evaluate side-chains 25 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 22 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 72 ILE Chi-restraints excluded: chain R residue 113 ASP Chi-restraints excluded: chain R residue 218 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 13 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.111129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.096177 restraints weight = 2982.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.098296 restraints weight = 1805.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.099861 restraints weight = 1301.215| |-----------------------------------------------------------------------------| r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2989 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2989 r_free = 0.2989 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2989 r_free = 0.2989 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2989 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 2258 Z= 0.237 Angle : 0.465 4.662 3091 Z= 0.254 Chirality : 0.039 0.103 379 Planarity : 0.003 0.026 368 Dihedral : 4.211 18.862 319 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 1.36 % Allowed : 16.29 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.49 (0.52), residues: 282 helix: 2.28 (0.36), residues: 225 sheet: None (None), residues: 0 loop : -1.00 (0.77), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 109 HIS 0.006 0.002 HIS R 296 PHE 0.008 0.001 PHE R 282 TYR 0.006 0.001 TYR R 209 ARG 0.003 0.000 ARG R 239 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 24 time to evaluate : 0.266 Fit side-chains REVERT: R 72 ILE cc_start: 0.8511 (OUTLIER) cc_final: 0.8048 (mp) REVERT: R 113 ASP cc_start: 0.8482 (OUTLIER) cc_final: 0.8252 (t0) outliers start: 3 outliers final: 1 residues processed: 27 average time/residue: 0.2683 time to fit residues: 8.2712 Evaluate side-chains 27 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 24 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 72 ILE Chi-restraints excluded: chain R residue 113 ASP Chi-restraints excluded: chain R residue 218 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 6 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 18 optimal weight: 0.4980 chunk 5 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 chunk 13 optimal weight: 0.0980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.112633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.097568 restraints weight = 2930.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.099724 restraints weight = 1774.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.101233 restraints weight = 1290.750| |-----------------------------------------------------------------------------| r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3004 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3004 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 2258 Z= 0.197 Angle : 0.466 5.263 3091 Z= 0.253 Chirality : 0.038 0.110 379 Planarity : 0.003 0.023 368 Dihedral : 4.201 19.025 319 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 1.36 % Allowed : 16.29 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.52 (0.52), residues: 282 helix: 2.35 (0.36), residues: 224 sheet: None (None), residues: 0 loop : -1.16 (0.77), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 109 HIS 0.005 0.002 HIS R 296 PHE 0.007 0.001 PHE R 282 TYR 0.006 0.001 TYR R 209 ARG 0.002 0.000 ARG R 304 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1144.52 seconds wall clock time: 21 minutes 3.02 seconds (1263.02 seconds total)