Starting phenix.real_space_refine on Fri May 9 13:43:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ggj_40010/05_2025/8ggj_40010.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ggj_40010/05_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_40010/05_2025/8ggj_40010.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ggj_40010/05_2025/8ggj_40010.map" model { file = "/net/cci-nas-00/data/ceres_data/8ggj_40010/05_2025/8ggj_40010.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ggj_40010/05_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-5687/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: 2.66, per 1000 atoms: 1.21 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: 0.58 Conformation dependent library (CDL) restraints added in 270.4 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: 0.22 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: 0.58 Time building geometry restraints manager: 0.68 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: 1.870 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: 0.030 Process input model: 11.240 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.000 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.940 ------------------------------------------------------------------------------- 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 : 0.220 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.2601 time to fit residues: 8.1546 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 : 0.227 ------------------------------------------------------------------------------- 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 : 0.239 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 24 average time/residue: 0.2229 time to fit residues: 6.1680 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 : 0.230 ------------------------------------------------------------------------------- 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 2259 Z= 0.122 Angle : 0.443 4.628 3093 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 Details of bonding type rmsd hydrogen bonds : bond 0.04510 ( 160) hydrogen bonds : angle 3.99778 ( 474) SS BOND : bond 0.00377 ( 1) SS BOND : angle 0.30076 ( 2) covalent geometry : bond 0.00288 ( 2258) covalent geometry : angle 0.44304 ( 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 27 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 24 time to evaluate : 0.248 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 26 average time/residue: 0.2087 time to fit residues: 6.3137 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 : 0.242 ------------------------------------------------------------------------------- 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 2259 Z= 0.100 Angle : 0.412 4.561 3093 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 Details of bonding type rmsd hydrogen bonds : bond 0.03823 ( 160) hydrogen bonds : angle 3.79280 ( 474) SS BOND : bond 0.00274 ( 1) SS BOND : angle 0.83550 ( 2) covalent geometry : bond 0.00224 ( 2258) covalent geometry : angle 0.41124 ( 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: 5 poor density : 26 time to evaluate : 0.217 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: 0.2339 time to fit residues: 7.6591 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 : 0.229 ------------------------------------------------------------------------------- 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: 0.4980 chunk 8 optimal weight: 0.4980 chunk 2 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 7 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 23 optimal weight: 0.2980 chunk 18 optimal weight: 0.8980 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 = 0.3163 r_free = 0.3163 target = 0.113729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.098619 restraints weight = 2982.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.100902 restraints weight = 1761.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.102459 restraints weight = 1257.875| |-----------------------------------------------------------------------------| r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3018 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3018 r_free = 0.3018 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 = 0.3018 r_free = 0.3018 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3018 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 2259 Z= 0.126 Angle : 0.447 4.604 3093 Z= 0.243 Chirality : 0.038 0.101 379 Planarity : 0.003 0.031 368 Dihedral : 4.126 19.115 319 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 1.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 1.36 % Allowed : 15.38 % Favored : 83.26 % 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: 2.62 (0.52), residues: 282 helix: 2.34 (0.36), residues: 225 sheet: None (None), residues: 0 loop : -0.80 (0.84), 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 0.004 0.000 ARG R 239 Details of bonding type rmsd hydrogen bonds : bond 0.04399 ( 160) hydrogen bonds : angle 3.82733 ( 474) SS BOND : bond 0.00226 ( 1) SS BOND : angle 0.85913 ( 2) covalent geometry : bond 0.00306 ( 2258) covalent geometry : angle 0.44644 ( 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 26 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 23 time to evaluate : 0.209 Fit side-chains REVERT: R 72 ILE cc_start: 0.8438 (OUTLIER) cc_final: 0.7974 (mp) outliers start: 3 outliers final: 2 residues processed: 26 average time/residue: 0.2504 time to fit residues: 7.3251 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 : 0.218 ------------------------------------------------------------------------------- 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: 0.9980 chunk 5 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 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 = 0.3135 r_free = 0.3135 target = 0.111366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.096348 restraints weight = 2954.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.098408 restraints weight = 1794.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.099936 restraints weight = 1315.124| |-----------------------------------------------------------------------------| r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2985 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2985 r_free = 0.2985 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 = 0.2985 r_free = 0.2985 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2985 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.1214 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= 0.144 Angle : 0.458 4.642 3093 Z= 0.250 Chirality : 0.039 0.102 379 Planarity : 0.003 0.028 368 Dihedral : 4.223 18.996 319 Min Nonbonded Distance : 2.632 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: 2.49 (0.52), residues: 282 helix: 2.25 (0.36), residues: 225 sheet: None (None), residues: 0 loop : -0.86 (0.81), 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 0.004 0.000 ARG R 239 Details of bonding type rmsd hydrogen bonds : bond 0.04868 ( 160) hydrogen bonds : angle 3.92234 ( 474) SS BOND : bond 0.00321 ( 1) SS BOND : angle 0.84629 ( 2) covalent geometry : bond 0.00357 ( 2258) covalent geometry : angle 0.45783 ( 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 30 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 25 time to evaluate : 0.242 Fit side-chains REVERT: R 72 ILE cc_start: 0.8552 (OUTLIER) cc_final: 0.8095 (mp) outliers start: 5 outliers final: 2 residues processed: 29 average time/residue: 0.2379 time to fit residues: 7.8116 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 : 0.211 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 17 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 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 = 0.3125 r_free = 0.3125 target = 0.110907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.096024 restraints weight = 2967.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.098108 restraints weight = 1781.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.099689 restraints weight = 1290.279| |-----------------------------------------------------------------------------| r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2983 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2983 r_free = 0.2983 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 = 0.2983 r_free = 0.2983 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2983 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.1237 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= 0.147 Angle : 0.468 4.642 3093 Z= 0.255 Chirality : 0.039 0.102 379 Planarity : 0.003 0.024 368 Dihedral : 4.211 19.037 319 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 1.38 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: 2.41 (0.52), residues: 282 helix: 2.23 (0.36), residues: 225 sheet: None (None), residues: 0 loop : -1.03 (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 0.001 0.000 ARG R 328 Details of bonding type rmsd hydrogen bonds : bond 0.04888 ( 160) hydrogen bonds : angle 3.93619 ( 474) SS BOND : bond 0.00295 ( 1) SS BOND : angle 0.80417 ( 2) covalent geometry : bond 0.00366 ( 2258) covalent geometry : angle 0.46750 ( 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 28 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 24 time to evaluate : 0.210 Fit side-chains REVERT: R 72 ILE cc_start: 0.8476 (OUTLIER) cc_final: 0.8008 (mp) REVERT: R 113 ASP cc_start: 0.8474 (OUTLIER) cc_final: 0.8237 (t0) outliers start: 4 outliers final: 1 residues processed: 27 average time/residue: 0.2469 time to fit residues: 7.5038 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 : 0.241 ------------------------------------------------------------------------------- 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: 0.8980 chunk 26 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3120 r_free = 0.3120 target = 0.110614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.095615 restraints weight = 3048.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.097722 restraints weight = 1818.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.099367 restraints weight = 1310.243| |-----------------------------------------------------------------------------| r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2979 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2979 r_free = 0.2979 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2979 r_free = 0.2979 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2979 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1287 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= 0.152 Angle : 0.465 4.643 3093 Z= 0.254 Chirality : 0.039 0.102 379 Planarity : 0.003 0.024 368 Dihedral : 4.255 19.044 319 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 1.61 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: 2.31 (0.52), residues: 282 helix: 2.17 (0.36), residues: 225 sheet: None (None), residues: 0 loop : -1.14 (0.76), 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 0.001 0.000 ARG R 175 Details of bonding type rmsd hydrogen bonds : bond 0.04999 ( 160) hydrogen bonds : angle 3.96306 ( 474) SS BOND : bond 0.00330 ( 1) SS BOND : angle 0.80227 ( 2) covalent geometry : bond 0.00379 ( 2258) covalent geometry : angle 0.46432 ( 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 29 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 25 time to evaluate : 0.235 Fit side-chains REVERT: R 72 ILE cc_start: 0.8454 (OUTLIER) cc_final: 0.7987 (mp) REVERT: R 113 ASP cc_start: 0.8492 (OUTLIER) cc_final: 0.8260 (t0) outliers start: 4 outliers final: 2 residues processed: 29 average time/residue: 0.2394 time to fit residues: 7.8527 Evaluate side-chains 29 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 25 time to evaluate : 0.268 ------------------------------------------------------------------------------- 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: 0.0470 chunk 1 optimal weight: 1.9990 chunk 16 optimal weight: 0.1980 chunk 3 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 5 optimal weight: 0.3980 chunk 13 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 overall best weight: 0.4078 ------------------------------------------------------------------------------- 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 = 0.3164 r_free = 0.3164 target = 0.113715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.098568 restraints weight = 2962.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.100757 restraints weight = 1773.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.102235 restraints weight = 1291.638| |-----------------------------------------------------------------------------| r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3022 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 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 = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3022 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1321 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= 0.114 Angle : 0.460 4.979 3093 Z= 0.248 Chirality : 0.038 0.101 379 Planarity : 0.004 0.044 368 Dihedral : 4.185 19.237 319 Min Nonbonded Distance : 2.542 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: 2.51 (0.52), residues: 282 helix: 2.33 (0.36), residues: 225 sheet: None (None), residues: 0 loop : -1.17 (0.77), residues: 57 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 0.006 0.001 PHE R 282 TYR 0.005 0.001 TYR R 209 ARG 0.005 0.001 ARG R 239 Details of bonding type rmsd hydrogen bonds : bond 0.04224 ( 160) hydrogen bonds : angle 3.81769 ( 474) SS BOND : bond 0.00224 ( 1) SS BOND : angle 0.60129 ( 2) covalent geometry : bond 0.00263 ( 2258) covalent geometry : angle 0.45982 ( 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 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: 0.8431 (OUTLIER) cc_final: 0.7932 (mp) REVERT: R 113 ASP cc_start: 0.8416 (OUTLIER) cc_final: 0.8175 (t0) outliers start: 3 outliers final: 1 residues processed: 25 average time/residue: 0.2835 time to fit residues: 8.0130 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 : 0.232 ------------------------------------------------------------------------------- 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: 0.2980 chunk 6 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.112424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.097220 restraints weight = 2957.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.099533 restraints weight = 1759.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.101105 restraints weight = 1251.751| |-----------------------------------------------------------------------------| r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3003 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3003 r_free = 0.3003 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 = 0.3002 r_free = 0.3002 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3002 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1344 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= 0.128 Angle : 0.447 4.600 3093 Z= 0.244 Chirality : 0.038 0.100 379 Planarity : 0.004 0.044 368 Dihedral : 4.223 19.166 319 Min Nonbonded Distance : 2.636 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: 2.51 (0.52), residues: 282 helix: 2.31 (0.36), residues: 225 sheet: None (None), residues: 0 loop : -1.09 (0.77), 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 0.009 0.001 ARG R 239 Details of bonding type rmsd hydrogen bonds : bond 0.04500 ( 160) hydrogen bonds : angle 3.83643 ( 474) SS BOND : bond 0.00311 ( 1) SS BOND : angle 0.62849 ( 2) covalent geometry : bond 0.00310 ( 2258) covalent geometry : angle 0.44638 ( 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 25 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 22 time to evaluate : 0.226 Fit side-chains REVERT: R 72 ILE cc_start: 0.8473 (OUTLIER) cc_final: 0.7987 (mp) REVERT: R 113 ASP cc_start: 0.8458 (OUTLIER) cc_final: 0.8226 (t0) outliers start: 3 outliers final: 1 residues processed: 25 average time/residue: 0.3673 time to fit residues: 10.2800 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 : 0.465 ------------------------------------------------------------------------------- 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: 0.6980 chunk 12 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 18 optimal weight: 0.0980 chunk 5 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 13 optimal weight: 0.0270 overall best weight: 0.4438 ------------------------------------------------------------------------------- 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 = 0.113886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.098780 restraints weight = 2912.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.101082 restraints weight = 1756.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.102613 restraints weight = 1264.094| |-----------------------------------------------------------------------------| r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3018 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3018 r_free = 0.3018 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 = 0.3019 r_free = 0.3019 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3019 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.1360 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= 0.115 Angle : 0.446 5.083 3093 Z= 0.243 Chirality : 0.037 0.104 379 Planarity : 0.003 0.035 368 Dihedral : 4.128 19.266 319 Min Nonbonded Distance : 2.523 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: 2.61 (0.52), residues: 282 helix: 2.41 (0.36), residues: 224 sheet: None (None), residues: 0 loop : -1.10 (0.77), residues: 58 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 0.007 0.001 PHE R 282 TYR 0.006 0.001 TYR R 209 ARG 0.007 0.001 ARG R 239 Details of bonding type rmsd hydrogen bonds : bond 0.04134 ( 160) hydrogen bonds : angle 3.76993 ( 474) SS BOND : bond 0.00247 ( 1) SS BOND : angle 0.56722 ( 2) covalent geometry : bond 0.00268 ( 2258) covalent geometry : angle 0.44635 ( 3091) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1188.67 seconds wall clock time: 21 minutes 23.82 seconds (1283.82 seconds total)