Starting phenix.real_space_refine on Sat Apr 26 16:03:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ggj_40010/04_2025/8ggj_40010.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ggj_40010/04_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_40010/04_2025/8ggj_40010.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ggj_40010/04_2025/8ggj_40010.map" model { file = "/net/cci-nas-00/data/ceres_data/8ggj_40010/04_2025/8ggj_40010.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ggj_40010/04_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-5669/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: 2.99, per 1000 atoms: 1.36 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 298.2 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: 0.27 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: 0.64 Time building geometry restraints manager: 0.70 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: 1.420 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.710 Find NCS groups from input model: 0.020 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: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.180 ------------------------------------------------------------------------------- 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 2259 Z= 0.184 Angle : 0.533 5.536 3093 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 Details of bonding type rmsd hydrogen bonds : bond 0.15697 ( 160) hydrogen bonds : angle 5.71552 ( 474) SS BOND : bond 0.00198 ( 1) SS BOND : angle 0.48873 ( 2) covalent geometry : bond 0.00403 ( 2258) covalent geometry : angle 0.53331 ( 3091) *********************** 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 : 0.238 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.2652 time to fit residues: 8.3336 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 : 0.245 ------------------------------------------------------------------------------- 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 2259 Z= 0.149 Angle : 0.480 4.741 3093 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 Details of bonding type rmsd hydrogen bonds : bond 0.05237 ( 160) hydrogen bonds : angle 4.27835 ( 474) SS BOND : bond 0.00483 ( 1) SS BOND : angle 0.30992 ( 2) covalent geometry : bond 0.00365 ( 2258) covalent geometry : angle 0.48003 ( 3091) *********************** 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 : 0.247 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 24 average time/residue: 0.2389 time to fit residues: 6.6030 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 : 0.234 ------------------------------------------------------------------------------- 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: 0.7980 chunk 5 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3139 r_free = 0.3139 target = 0.111633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.096604 restraints weight = 2998.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.098911 restraints weight = 1774.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.100433 restraints weight = 1270.798| |-----------------------------------------------------------------------------| r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2991 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2991 r_free = 0.2991 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 = 0.2991 r_free = 0.2991 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2991 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.0914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 2259 Z= 0.142 Angle : 0.463 4.659 3093 Z= 0.254 Chirality : 0.038 0.104 379 Planarity : 0.003 0.027 368 Dihedral : 4.349 19.233 319 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 0.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 1.36 % Allowed : 9.50 % Favored : 89.14 % 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: 2.36 (0.52), residues: 282 helix: 2.05 (0.35), residues: 225 sheet: None (None), residues: 0 loop : -0.36 (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 209 ARG 0.002 0.000 ARG R 239 Details of bonding type rmsd hydrogen bonds : bond 0.04912 ( 160) hydrogen bonds : angle 4.08667 ( 474) SS BOND : bond 0.00468 ( 1) SS BOND : angle 0.32315 ( 2) covalent geometry : bond 0.00345 ( 2258) covalent geometry : angle 0.46291 ( 3091) *********************** 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 25 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 22 time to evaluate : 0.251 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 24 average time/residue: 0.2283 time to fit residues: 6.3278 Evaluate side-chains 22 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 20 time to evaluate : 0.239 ------------------------------------------------------------------------------- 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: 0.7980 chunk 5 optimal weight: 0.3980 chunk 24 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 22 optimal weight: 0.3980 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 = 0.3145 r_free = 0.3145 target = 0.112712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.098008 restraints weight = 2882.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.100198 restraints weight = 1735.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.101709 restraints weight = 1246.353| |-----------------------------------------------------------------------------| r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3012 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3012 r_free = 0.3012 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 = 0.3012 r_free = 0.3012 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3012 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 2259 Z= 0.124 Angle : 0.438 4.625 3093 Z= 0.240 Chirality : 0.038 0.100 379 Planarity : 0.003 0.026 368 Dihedral : 4.223 19.212 319 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 0.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 2.71 % Allowed : 11.31 % 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: 2.47 (0.52), residues: 282 helix: 2.16 (0.36), residues: 225 sheet: None (None), residues: 0 loop : -0.52 (0.87), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 158 HIS 0.006 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 175 Details of bonding type rmsd hydrogen bonds : bond 0.04497 ( 160) hydrogen bonds : angle 3.95552 ( 474) SS BOND : bond 0.00332 ( 1) SS BOND : angle 0.89661 ( 2) covalent geometry : bond 0.00294 ( 2258) covalent geometry : angle 0.43792 ( 3091) *********************** 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: 6 poor density : 25 time to evaluate : 0.249 Fit side-chains REVERT: R 72 ILE cc_start: 0.8433 (OUTLIER) cc_final: 0.7969 (mp) outliers start: 6 outliers final: 2 residues processed: 28 average time/residue: 0.2535 time to fit residues: 8.0045 Evaluate side-chains 26 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 23 time to evaluate : 0.229 ------------------------------------------------------------------------------- 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: 0.7980 chunk 8 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3115 r_free = 0.3115 target = 0.110268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.095593 restraints weight = 2956.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.097759 restraints weight = 1775.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.099265 restraints weight = 1273.769| |-----------------------------------------------------------------------------| r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2980 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2980 r_free = 0.2980 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 = 0.2980 r_free = 0.2980 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2980 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 2259 Z= 0.158 Angle : 0.477 4.684 3093 Z= 0.261 Chirality : 0.039 0.102 379 Planarity : 0.003 0.025 368 Dihedral : 4.303 19.093 319 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 0.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 2.26 % Allowed : 14.03 % Favored : 83.71 % 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: 2.25 (0.51), residues: 282 helix: 2.09 (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 0.005 0.001 TRP R 158 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 0.001 0.000 ARG R 328 Details of bonding type rmsd hydrogen bonds : bond 0.05129 ( 160) hydrogen bonds : angle 4.02709 ( 474) SS BOND : bond 0.00344 ( 1) SS BOND : angle 1.03582 ( 2) covalent geometry : bond 0.00394 ( 2258) covalent geometry : angle 0.47688 ( 3091) *********************** 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 29 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 24 time to evaluate : 0.251 Fit side-chains REVERT: R 72 ILE cc_start: 0.8453 (OUTLIER) cc_final: 0.7990 (mp) outliers start: 5 outliers final: 2 residues processed: 27 average time/residue: 0.2127 time to fit residues: 6.6509 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 : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 72 ILE Chi-restraints excluded: chain R residue 94 ILE 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: 0.8980 chunk 17 optimal weight: 0.9990 chunk 5 optimal weight: 0.4980 chunk 6 optimal weight: 0.1980 chunk 18 optimal weight: 0.4980 chunk 26 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 25 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 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 = 0.3149 r_free = 0.3149 target = 0.112882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.097990 restraints weight = 2888.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.100149 restraints weight = 1749.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.101757 restraints weight = 1266.620| |-----------------------------------------------------------------------------| r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3010 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3010 r_free = 0.3010 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 = 0.3009 r_free = 0.3009 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3009 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 2259 Z= 0.118 Angle : 0.427 4.601 3093 Z= 0.234 Chirality : 0.038 0.101 379 Planarity : 0.003 0.025 368 Dihedral : 4.128 19.193 319 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 0.92 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: 2.44 (0.52), residues: 282 helix: 2.23 (0.36), residues: 225 sheet: None (None), residues: 0 loop : -0.96 (0.79), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 158 HIS 0.006 0.002 HIS R 296 PHE 0.006 0.001 PHE R 282 TYR 0.006 0.001 TYR R 209 ARG 0.001 0.000 ARG R 328 Details of bonding type rmsd hydrogen bonds : bond 0.04329 ( 160) hydrogen bonds : angle 3.88298 ( 474) SS BOND : bond 0.00238 ( 1) SS BOND : angle 0.71060 ( 2) covalent geometry : bond 0.00277 ( 2258) covalent geometry : angle 0.42720 ( 3091) *********************** 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 29 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 26 time to evaluate : 0.257 Fit side-chains REVERT: R 72 ILE cc_start: 0.8433 (OUTLIER) cc_final: 0.7963 (mp) outliers start: 3 outliers final: 1 residues processed: 28 average time/residue: 0.2428 time to fit residues: 7.6698 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 : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 72 ILE 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: 0.6980 chunk 21 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.111264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.096425 restraints weight = 2966.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.098592 restraints weight = 1779.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.100119 restraints weight = 1285.565| |-----------------------------------------------------------------------------| r_work (final): 0.2990 ------------------------------------------------------------------------------- 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: 0.8438 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 2259 Z= 0.143 Angle : 0.464 4.642 3093 Z= 0.253 Chirality : 0.038 0.101 379 Planarity : 0.003 0.025 368 Dihedral : 4.195 19.073 319 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 1.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 2.71 % Allowed : 15.38 % 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: 2.36 (0.52), residues: 282 helix: 2.17 (0.36), residues: 225 sheet: None (None), residues: 0 loop : -0.96 (0.79), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 158 HIS 0.006 0.002 HIS R 296 PHE 0.007 0.001 PHE R 282 TYR 0.006 0.001 TYR R 308 ARG 0.001 0.000 ARG R 304 Details of bonding type rmsd hydrogen bonds : bond 0.04814 ( 160) hydrogen bonds : angle 3.92773 ( 474) SS BOND : bond 0.00354 ( 1) SS BOND : angle 0.73130 ( 2) covalent geometry : bond 0.00354 ( 2258) covalent geometry : angle 0.46361 ( 3091) *********************** 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 30 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 24 time to evaluate : 0.251 Fit side-chains REVERT: R 72 ILE cc_start: 0.8496 (OUTLIER) cc_final: 0.8010 (mp) REVERT: R 113 ASP cc_start: 0.8479 (OUTLIER) cc_final: 0.8254 (t0) outliers start: 6 outliers final: 2 residues processed: 30 average time/residue: 0.2424 time to fit residues: 8.2499 Evaluate side-chains 28 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 24 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 72 ILE Chi-restraints excluded: chain R residue 94 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: 0.6980 chunk 26 optimal weight: 0.6980 chunk 5 optimal weight: 0.4980 chunk 27 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.111069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.095874 restraints weight = 3045.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.098213 restraints weight = 1794.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.099830 restraints weight = 1268.928| |-----------------------------------------------------------------------------| r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2988 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2988 r_free = 0.2988 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 = 0.2988 r_free = 0.2988 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2988 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 2259 Z= 0.141 Angle : 0.451 4.637 3093 Z= 0.247 Chirality : 0.039 0.101 379 Planarity : 0.003 0.024 368 Dihedral : 4.207 19.091 319 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 1.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 1.81 % Allowed : 16.29 % 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: 2.33 (0.52), residues: 282 helix: 2.17 (0.36), residues: 225 sheet: None (None), residues: 0 loop : -1.07 (0.77), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 158 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 0.001 0.000 ARG R 131 Details of bonding type rmsd hydrogen bonds : bond 0.04794 ( 160) hydrogen bonds : angle 3.92844 ( 474) SS BOND : bond 0.00338 ( 1) SS BOND : angle 0.74352 ( 2) covalent geometry : bond 0.00348 ( 2258) covalent geometry : angle 0.45124 ( 3091) *********************** 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 28 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 24 time to evaluate : 0.255 Fit side-chains REVERT: R 72 ILE cc_start: 0.8477 (OUTLIER) cc_final: 0.8007 (mp) REVERT: R 113 ASP cc_start: 0.8472 (OUTLIER) cc_final: 0.8236 (t0) outliers start: 4 outliers final: 2 residues processed: 28 average time/residue: 0.2449 time to fit residues: 7.7740 Evaluate side-chains 28 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 24 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 72 ILE Chi-restraints excluded: chain R residue 94 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: 2.9990 chunk 1 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 5 optimal weight: 0.0370 chunk 13 optimal weight: 0.2980 chunk 12 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 overall best weight: 0.4458 ------------------------------------------------------------------------------- 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 = 0.3154 r_free = 0.3154 target = 0.113392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.098407 restraints weight = 2912.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.100644 restraints weight = 1756.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.102208 restraints weight = 1261.377| |-----------------------------------------------------------------------------| r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3016 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3016 r_free = 0.3016 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 = 0.3016 r_free = 0.3016 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3016 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2259 Z= 0.116 Angle : 0.449 4.976 3093 Z= 0.244 Chirality : 0.038 0.103 379 Planarity : 0.003 0.024 368 Dihedral : 4.117 19.265 319 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 1.15 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: 2.49 (0.52), residues: 282 helix: 2.30 (0.36), residues: 225 sheet: None (None), residues: 0 loop : -1.07 (0.78), 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 304 Details of bonding type rmsd hydrogen bonds : bond 0.04212 ( 160) hydrogen bonds : angle 3.82119 ( 474) SS BOND : bond 0.00255 ( 1) SS BOND : angle 0.60959 ( 2) covalent geometry : bond 0.00270 ( 2258) covalent geometry : angle 0.44839 ( 3091) *********************** 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 27 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 24 time to evaluate : 0.223 Fit side-chains REVERT: R 72 ILE cc_start: 0.8466 (OUTLIER) cc_final: 0.7979 (mp) REVERT: R 113 ASP cc_start: 0.8424 (OUTLIER) cc_final: 0.8190 (t0) outliers start: 3 outliers final: 1 residues processed: 27 average time/residue: 0.2515 time to fit residues: 7.6517 Evaluate side-chains 26 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 23 time to evaluate : 0.234 ------------------------------------------------------------------------------- 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: 0.6980 chunk 6 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 27 optimal weight: 0.0870 chunk 21 optimal weight: 0.5980 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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 = 0.3144 r_free = 0.3144 target = 0.112512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.097673 restraints weight = 2961.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.099798 restraints weight = 1769.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.101390 restraints weight = 1275.594| |-----------------------------------------------------------------------------| r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3009 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3009 r_free = 0.3009 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 = 0.3009 r_free = 0.3009 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3009 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 2259 Z= 0.127 Angle : 0.443 4.604 3093 Z= 0.242 Chirality : 0.038 0.102 379 Planarity : 0.003 0.024 368 Dihedral : 4.175 19.198 319 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 1.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 1.81 % Allowed : 16.29 % 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: 2.47 (0.52), residues: 282 helix: 2.30 (0.36), residues: 225 sheet: None (None), residues: 0 loop : -1.14 (0.77), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 158 HIS 0.006 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 175 Details of bonding type rmsd hydrogen bonds : bond 0.04429 ( 160) hydrogen bonds : angle 3.83443 ( 474) SS BOND : bond 0.00303 ( 1) SS BOND : angle 0.61999 ( 2) covalent geometry : bond 0.00306 ( 2258) covalent geometry : angle 0.44317 ( 3091) ********************** 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: 4 poor density : 23 time to evaluate : 0.227 Fit side-chains REVERT: R 72 ILE cc_start: 0.8478 (OUTLIER) cc_final: 0.7992 (mp) REVERT: R 113 ASP cc_start: 0.8456 (OUTLIER) cc_final: 0.8224 (t0) outliers start: 4 outliers final: 1 residues processed: 26 average time/residue: 0.2570 time to fit residues: 7.5184 Evaluate side-chains 26 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 23 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: 1.9990 chunk 25 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 18 optimal weight: 0.0270 chunk 5 optimal weight: 0.0030 chunk 2 optimal weight: 0.0970 chunk 3 optimal weight: 0.8980 chunk 13 optimal weight: 0.3980 overall best weight: 0.2246 ------------------------------------------------------------------------------- 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 = 0.3205 r_free = 0.3205 target = 0.117386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.102362 restraints weight = 2875.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.104692 restraints weight = 1738.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.105827 restraints weight = 1236.752| |-----------------------------------------------------------------------------| r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3070 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3070 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 2259 Z= 0.099 Angle : 0.434 5.797 3093 Z= 0.235 Chirality : 0.037 0.106 379 Planarity : 0.003 0.025 368 Dihedral : 4.050 19.827 319 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 1.61 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: 2.78 (0.52), residues: 282 helix: 2.65 (0.36), residues: 219 sheet: None (None), residues: 0 loop : -1.24 (0.75), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 158 HIS 0.005 0.001 HIS R 296 PHE 0.005 0.001 PHE R 282 TYR 0.005 0.001 TYR R 219 ARG 0.002 0.000 ARG R 239 Details of bonding type rmsd hydrogen bonds : bond 0.03427 ( 160) hydrogen bonds : angle 3.66509 ( 474) SS BOND : bond 0.00145 ( 1) SS BOND : angle 0.43882 ( 2) covalent geometry : bond 0.00210 ( 2258) covalent geometry : angle 0.43377 ( 3091) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1205.43 seconds wall clock time: 21 minutes 32.17 seconds (1292.17 seconds total)