Starting phenix.real_space_refine on Sat Apr 26 16:04:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ihk_35447/04_2025/8ihk_35447.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ihk_35447/04_2025/8ihk_35447.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ihk_35447/04_2025/8ihk_35447.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ihk_35447/04_2025/8ihk_35447.map" model { file = "/net/cci-nas-00/data/ceres_data/8ihk_35447/04_2025/8ihk_35447.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ihk_35447/04_2025/8ihk_35447.cif" } resolution = 3.21 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= 0.002 sd= 0.034 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 17 5.16 5 C 1515 2.51 5 N 361 2.21 5 O 360 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 2253 Number of models: 1 Model: "" Number of chains: 2 Chain: "R" Number of atoms: 2237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2237 Classifications: {'peptide': 283} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 9, 'TRANS': 273} Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 5, 'ASN:plan1': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 49 Chain: "R" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'P9X': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.20, per 1000 atoms: 0.98 Number of scatterers: 2253 At special positions: 0 Unit cell: (52.26, 69.42, 73.32, 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 17 16.00 O 360 8.00 N 361 7.00 C 1515 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 18 " - pdb=" SG CYS R 183 " distance=2.03 Simple disulfide: pdb=" SG CYS R 19 " - pdb=" SG CYS R 266 " distance=2.03 Simple disulfide: pdb=" SG CYS R 100 " - pdb=" SG CYS R 177 " distance=1.63 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: 0.62 Conformation dependent library (CDL) restraints added in 280.7 milliseconds 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 544 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 1 sheets defined 77.0% alpha, 1.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'R' and resid 25 through 28 Processing helix chain 'R' and resid 29 through 55 Processing helix chain 'R' and resid 60 through 78 removed outlier: 3.661A pdb=" N PHE R 65 " --> pdb=" O SER R 61 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU R 66 " --> pdb=" O SER R 62 " (cutoff:3.500A) Processing helix chain 'R' and resid 79 through 89 removed outlier: 3.531A pdb=" N TYR R 86 " --> pdb=" O PHE R 82 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N TYR R 87 " --> pdb=" O VAL R 83 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL R 88 " --> pdb=" O MET R 84 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG R 89 " --> pdb=" O ASP R 85 " (cutoff:3.500A) Processing helix chain 'R' and resid 98 through 128 removed outlier: 3.569A pdb=" N LEU R 102 " --> pdb=" O ILE R 98 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N PHE R 107 " --> pdb=" O VAL R 103 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASN R 110 " --> pdb=" O MET R 106 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL R 121 " --> pdb=" O PHE R 117 " (cutoff:3.500A) Processing helix chain 'R' and resid 134 through 139 removed outlier: 3.640A pdb=" N ILE R 139 " --> pdb=" O LEU R 136 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 158 removed outlier: 3.500A pdb=" N SER R 148 " --> pdb=" O ALA R 144 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL R 156 " --> pdb=" O TRP R 152 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU R 158 " --> pdb=" O ILE R 154 " (cutoff:3.500A) Processing helix chain 'R' and resid 160 through 165 removed outlier: 4.004A pdb=" N LYS R 164 " --> pdb=" O VAL R 160 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS R 165 " --> pdb=" O HIS R 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 160 through 165' Processing helix chain 'R' and resid 187 through 218 removed outlier: 3.594A pdb=" N LEU R 194 " --> pdb=" O GLU R 190 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N PHE R 197 " --> pdb=" O PHE R 193 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU R 199 " --> pdb=" O LEU R 195 " (cutoff:3.500A) Proline residue: R 200 - end of helix removed outlier: 3.546A pdb=" N LEU R 205 " --> pdb=" O LEU R 201 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N PHE R 206 " --> pdb=" O GLY R 202 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ARG R 216 " --> pdb=" O ILE R 212 " (cutoff:3.500A) Processing helix chain 'R' and resid 225 through 260 removed outlier: 4.005A pdb=" N ALA R 229 " --> pdb=" O LYS R 225 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET R 234 " --> pdb=" O ILE R 230 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA R 237 " --> pdb=" O ILE R 233 " (cutoff:3.500A) Proline residue: R 246 - end of helix Processing helix chain 'R' and resid 267 through 280 removed outlier: 4.301A pdb=" N SER R 271 " --> pdb=" O GLU R 267 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N VAL R 272 " --> pdb=" O VAL R 268 " (cutoff:3.500A) Processing helix chain 'R' and resid 282 through 294 removed outlier: 3.756A pdb=" N ASN R 286 " --> pdb=" O PHE R 282 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N SER R 287 " --> pdb=" O THR R 283 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N MET R 288 " --> pdb=" O TYR R 284 " (cutoff:3.500A) Proline residue: R 291 - end of helix Processing sheet with id=AA1, first strand: chain 'R' and resid 169 through 171 removed outlier: 3.633A pdb=" N ILE R 169 " --> pdb=" O VAL R 176 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL R 176 " --> pdb=" O ILE R 169 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA R 174 " --> pdb=" O ASN R 171 " (cutoff:3.500A) 134 hydrogen bonds defined for protein. 393 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: 0.47 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: 1.21 - 1.33: 432 1.33 - 1.45: 608 1.45 - 1.57: 1259 1.57 - 1.70: 0 1.70 - 1.82: 23 Bond restraints: 2322 Sorted by residual: bond pdb=" CA TRP R 142 " pdb=" CB TRP R 142 " ideal model delta sigma weight residual 1.529 1.477 0.052 1.55e-02 4.16e+03 1.14e+01 bond pdb=" N TRP R 142 " pdb=" CA TRP R 142 " ideal model delta sigma weight residual 1.459 1.423 0.037 1.19e-02 7.06e+03 9.56e+00 bond pdb=" C5 P9X R 501 " pdb=" O3 P9X R 501 " ideal model delta sigma weight residual 1.248 1.307 -0.059 2.00e-02 2.50e+03 8.82e+00 bond pdb=" C4 P9X R 501 " pdb=" C5 P9X R 501 " ideal model delta sigma weight residual 1.530 1.477 0.053 2.00e-02 2.50e+03 6.99e+00 bond pdb=" C TRP R 142 " pdb=" O TRP R 142 " ideal model delta sigma weight residual 1.236 1.210 0.026 1.15e-02 7.56e+03 5.30e+00 ... (remaining 2317 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.36: 3092 1.36 - 2.72: 47 2.72 - 4.08: 14 4.08 - 5.44: 9 5.44 - 6.80: 5 Bond angle restraints: 3167 Sorted by residual: angle pdb=" N TRP R 142 " pdb=" CA TRP R 142 " pdb=" C TRP R 142 " ideal model delta sigma weight residual 111.07 106.89 4.18 1.07e+00 8.73e-01 1.53e+01 angle pdb=" CA TRP R 142 " pdb=" C TRP R 142 " pdb=" N THR R 143 " ideal model delta sigma weight residual 117.07 120.84 -3.77 1.14e+00 7.69e-01 1.09e+01 angle pdb=" C ASN R 141 " pdb=" N TRP R 142 " pdb=" CA TRP R 142 " ideal model delta sigma weight residual 120.44 117.05 3.39 1.30e+00 5.92e-01 6.80e+00 angle pdb=" N LEU R 167 " pdb=" CA LEU R 167 " pdb=" C LEU R 167 " ideal model delta sigma weight residual 108.34 111.41 -3.07 1.31e+00 5.83e-01 5.51e+00 angle pdb=" CA TRP R 142 " pdb=" C TRP R 142 " pdb=" O TRP R 142 " ideal model delta sigma weight residual 120.82 118.41 2.41 1.05e+00 9.07e-01 5.28e+00 ... (remaining 3162 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 1157 17.97 - 35.93: 150 35.93 - 53.90: 35 53.90 - 71.86: 2 71.86 - 89.83: 3 Dihedral angle restraints: 1347 sinusoidal: 514 harmonic: 833 Sorted by residual: dihedral pdb=" CB CYS R 19 " pdb=" SG CYS R 19 " pdb=" SG CYS R 266 " pdb=" CB CYS R 266 " ideal model delta sinusoidal sigma weight residual 93.00 177.87 -84.87 1 1.00e+01 1.00e-02 8.74e+01 dihedral pdb=" CB CYS R 100 " pdb=" SG CYS R 100 " pdb=" SG CYS R 177 " pdb=" CB CYS R 177 " ideal model delta sinusoidal sigma weight residual 93.00 127.23 -34.23 1 1.00e+01 1.00e-02 1.66e+01 dihedral pdb=" CA CYS R 100 " pdb=" CB CYS R 100 " pdb=" SG CYS R 100 " pdb=" SG CYS R 177 " ideal model delta sinusoidal sigma weight residual 79.00 12.78 66.22 1 2.00e+01 2.50e-03 1.43e+01 ... (remaining 1344 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 203 0.024 - 0.047: 95 0.047 - 0.071: 43 0.071 - 0.095: 18 0.095 - 0.118: 9 Chirality restraints: 368 Sorted by residual: chirality pdb=" CA ILE R 178 " pdb=" N ILE R 178 " pdb=" C ILE R 178 " pdb=" CB ILE R 178 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.51e-01 chirality pdb=" CA VAL R 20 " pdb=" N VAL R 20 " pdb=" C VAL R 20 " pdb=" CB VAL R 20 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.44e-01 chirality pdb=" CG LEU R 257 " pdb=" CB LEU R 257 " pdb=" CD1 LEU R 257 " pdb=" CD2 LEU R 257 " both_signs ideal model delta sigma weight residual False -2.59 -2.47 -0.12 2.00e-01 2.50e+01 3.33e-01 ... (remaining 365 not shown) Planarity restraints: 382 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE R 98 " -0.030 5.00e-02 4.00e+02 4.57e-02 3.35e+00 pdb=" N PRO R 99 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO R 99 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO R 99 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO R 31 " -0.025 5.00e-02 4.00e+02 3.79e-02 2.29e+00 pdb=" N PRO R 32 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO R 32 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO R 32 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU R 30 " -0.019 5.00e-02 4.00e+02 2.80e-02 1.25e+00 pdb=" N PRO R 31 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO R 31 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO R 31 " -0.016 5.00e-02 4.00e+02 ... (remaining 379 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 487 2.78 - 3.31: 2224 3.31 - 3.84: 3584 3.84 - 4.37: 4004 4.37 - 4.90: 6994 Nonbonded interactions: 17293 Sorted by model distance: nonbonded pdb=" OD1 ASN R 68 " pdb=" OG SER R 148 " model vdw 2.246 3.040 nonbonded pdb=" NH2 ARG R 111 " pdb=" O2 P9X R 501 " model vdw 2.393 3.120 nonbonded pdb=" NH2 ARG R 101 " pdb=" O LEU R 163 " model vdw 2.396 3.120 nonbonded pdb=" OD1 ASP R 97 " pdb=" N ILE R 98 " model vdw 2.433 3.120 nonbonded pdb=" NE1 TRP R 93 " pdb=" O GLY R 96 " model vdw 2.459 3.120 ... (remaining 17288 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.450 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: 0.010 Set scattering table: 0.020 Process input model: 10.710 Find NCS groups from input model: 0.020 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: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 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 : 0.009 0.397 2325 Z= 0.453 Angle : 0.729 20.791 3173 Z= 0.360 Chirality : 0.038 0.118 368 Planarity : 0.004 0.046 382 Dihedral : 16.211 89.829 794 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.00 % Allowed : 27.97 % Favored : 72.03 % 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: -0.99 (0.49), residues: 281 helix: -0.13 (0.38), residues: 191 sheet: None (None), residues: 0 loop : -1.61 (0.63), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP R 142 HIS 0.001 0.000 HIS R 161 PHE 0.012 0.001 PHE R 21 TYR 0.011 0.001 TYR R 87 ARG 0.001 0.000 ARG R 216 Details of bonding type rmsd hydrogen bonds : bond 0.27322 ( 134) hydrogen bonds : angle 8.12788 ( 393) SS BOND : bond 0.22928 ( 3) SS BOND : angle 10.50968 ( 6) covalent geometry : bond 0.00343 ( 2322) covalent geometry : angle 0.56854 ( 3167) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.237 Fit side-chains REVERT: R 192 MET cc_start: 0.6068 (ttp) cc_final: 0.5770 (tmm) outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.1514 time to fit residues: 7.4083 Evaluate side-chains 39 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.251 ------------------------------------------------------------------------------- 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: 6.9990 chunk 21 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 7 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 27 optimal weight: 0.3980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 45 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.198924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.154569 restraints weight = 2571.625| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 2.48 r_work: 0.3579 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2325 Z= 0.129 Angle : 0.546 6.541 3173 Z= 0.282 Chirality : 0.042 0.124 368 Planarity : 0.005 0.052 382 Dihedral : 4.594 24.707 325 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.27 % Allowed : 29.24 % Favored : 69.49 % 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: 0.26 (0.52), residues: 281 helix: 0.65 (0.37), residues: 202 sheet: None (None), residues: 0 loop : -0.88 (0.74), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 256 HIS 0.004 0.001 HIS R 253 PHE 0.012 0.001 PHE R 232 TYR 0.007 0.001 TYR R 284 ARG 0.001 0.000 ARG R 218 Details of bonding type rmsd hydrogen bonds : bond 0.05299 ( 134) hydrogen bonds : angle 4.49994 ( 393) SS BOND : bond 0.00344 ( 3) SS BOND : angle 1.25704 ( 6) covalent geometry : bond 0.00273 ( 2322) covalent geometry : angle 0.54393 ( 3167) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 37 time to evaluate : 0.262 Fit side-chains REVERT: R 62 SER cc_start: 0.8934 (t) cc_final: 0.8413 (m) outliers start: 3 outliers final: 2 residues processed: 39 average time/residue: 0.1294 time to fit residues: 6.1780 Evaluate side-chains 36 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 34 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 77 ILE Chi-restraints excluded: chain R residue 220 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 16 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 22 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 286 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.199133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.155720 restraints weight = 2557.113| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 2.37 r_work: 0.3559 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2325 Z= 0.125 Angle : 0.521 6.655 3173 Z= 0.266 Chirality : 0.041 0.121 368 Planarity : 0.004 0.049 382 Dihedral : 4.085 15.612 325 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 4.24 % Allowed : 27.97 % Favored : 67.80 % 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: 0.53 (0.52), residues: 281 helix: 0.89 (0.38), residues: 203 sheet: None (None), residues: 0 loop : -0.91 (0.74), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 256 HIS 0.002 0.001 HIS R 253 PHE 0.008 0.001 PHE R 117 TYR 0.006 0.001 TYR R 294 ARG 0.005 0.000 ARG R 216 Details of bonding type rmsd hydrogen bonds : bond 0.04596 ( 134) hydrogen bonds : angle 4.10505 ( 393) SS BOND : bond 0.00258 ( 3) SS BOND : angle 0.71183 ( 6) covalent geometry : bond 0.00278 ( 2322) covalent geometry : angle 0.52101 ( 3167) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 38 time to evaluate : 0.228 Fit side-chains REVERT: R 21 PHE cc_start: 0.4546 (m-80) cc_final: 0.3959 (m-80) REVERT: R 62 SER cc_start: 0.8945 (t) cc_final: 0.8489 (m) outliers start: 10 outliers final: 6 residues processed: 45 average time/residue: 0.1492 time to fit residues: 8.0911 Evaluate side-chains 43 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 37 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 26 ILE Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 47 LEU Chi-restraints excluded: chain R residue 77 ILE Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 226 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 8 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 17 optimal weight: 7.9990 chunk 12 optimal weight: 0.4980 chunk 5 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 7 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.4278 r_free = 0.4278 target = 0.200428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.156650 restraints weight = 2529.598| |-----------------------------------------------------------------------------| r_work (start): 0.3860 rms_B_bonded: 2.25 r_work: 0.3586 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 2325 Z= 0.110 Angle : 0.527 9.202 3173 Z= 0.261 Chirality : 0.040 0.116 368 Planarity : 0.004 0.050 382 Dihedral : 3.838 15.031 325 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.81 % Allowed : 28.81 % Favored : 67.37 % 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: 0.76 (0.53), residues: 281 helix: 1.09 (0.38), residues: 203 sheet: None (None), residues: 0 loop : -0.93 (0.73), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 256 HIS 0.002 0.000 HIS R 253 PHE 0.016 0.001 PHE R 232 TYR 0.005 0.001 TYR R 87 ARG 0.005 0.000 ARG R 216 Details of bonding type rmsd hydrogen bonds : bond 0.03950 ( 134) hydrogen bonds : angle 3.91715 ( 393) SS BOND : bond 0.00206 ( 3) SS BOND : angle 0.67609 ( 6) covalent geometry : bond 0.00238 ( 2322) covalent geometry : angle 0.52672 ( 3167) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 36 time to evaluate : 0.256 Fit side-chains REVERT: R 21 PHE cc_start: 0.4753 (m-80) cc_final: 0.4205 (m-80) REVERT: R 45 ASN cc_start: 0.7758 (m-40) cc_final: 0.7551 (m-40) REVERT: R 62 SER cc_start: 0.8884 (t) cc_final: 0.8455 (m) REVERT: R 168 LEU cc_start: 0.6395 (OUTLIER) cc_final: 0.5784 (mt) outliers start: 9 outliers final: 7 residues processed: 42 average time/residue: 0.1259 time to fit residues: 6.4818 Evaluate side-chains 44 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 26 ILE Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 47 LEU Chi-restraints excluded: chain R residue 77 ILE Chi-restraints excluded: chain R residue 109 MET Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 168 LEU Chi-restraints excluded: chain R residue 226 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 20 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 19 optimal weight: 0.0060 chunk 18 optimal weight: 0.6980 chunk 9 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- 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 = 0.4268 r_free = 0.4268 target = 0.199499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.155071 restraints weight = 2565.635| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 2.24 r_work: 0.3584 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 2325 Z= 0.109 Angle : 0.509 7.446 3173 Z= 0.253 Chirality : 0.040 0.115 368 Planarity : 0.004 0.050 382 Dihedral : 3.773 14.705 325 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 4.66 % Allowed : 28.81 % Favored : 66.53 % 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: 0.87 (0.53), residues: 281 helix: 1.17 (0.39), residues: 204 sheet: None (None), residues: 0 loop : -0.89 (0.73), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 256 HIS 0.001 0.000 HIS R 253 PHE 0.015 0.001 PHE R 232 TYR 0.005 0.001 TYR R 87 ARG 0.005 0.000 ARG R 216 Details of bonding type rmsd hydrogen bonds : bond 0.03859 ( 134) hydrogen bonds : angle 3.83086 ( 393) SS BOND : bond 0.00106 ( 3) SS BOND : angle 0.59161 ( 6) covalent geometry : bond 0.00237 ( 2322) covalent geometry : angle 0.50922 ( 3167) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 35 time to evaluate : 0.247 Fit side-chains REVERT: R 21 PHE cc_start: 0.4720 (m-80) cc_final: 0.4292 (m-80) REVERT: R 45 ASN cc_start: 0.7667 (m-40) cc_final: 0.7459 (m110) REVERT: R 62 SER cc_start: 0.8874 (OUTLIER) cc_final: 0.8448 (m) REVERT: R 168 LEU cc_start: 0.6401 (OUTLIER) cc_final: 0.5768 (mt) outliers start: 11 outliers final: 9 residues processed: 43 average time/residue: 0.1220 time to fit residues: 6.4966 Evaluate side-chains 46 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 35 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 47 LEU Chi-restraints excluded: chain R residue 62 SER Chi-restraints excluded: chain R residue 77 ILE Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain R residue 109 MET Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 168 LEU Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 226 ILE Chi-restraints excluded: chain R residue 277 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 10 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 1 optimal weight: 0.0010 chunk 20 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 16 optimal weight: 8.9990 chunk 9 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 7 optimal weight: 0.3980 overall best weight: 0.6386 ------------------------------------------------------------------------------- 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 = 0.4277 r_free = 0.4277 target = 0.200450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.156513 restraints weight = 2612.213| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 2.26 r_work: 0.3563 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 2325 Z= 0.107 Angle : 0.511 8.531 3173 Z= 0.252 Chirality : 0.040 0.115 368 Planarity : 0.004 0.049 382 Dihedral : 3.624 14.114 325 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 5.08 % Allowed : 28.81 % Favored : 66.10 % 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: 0.94 (0.53), residues: 281 helix: 1.21 (0.38), residues: 205 sheet: None (None), residues: 0 loop : -0.90 (0.74), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 256 HIS 0.001 0.000 HIS R 253 PHE 0.007 0.001 PHE R 206 TYR 0.005 0.001 TYR R 87 ARG 0.006 0.000 ARG R 216 Details of bonding type rmsd hydrogen bonds : bond 0.03754 ( 134) hydrogen bonds : angle 3.75553 ( 393) SS BOND : bond 0.00104 ( 3) SS BOND : angle 0.56461 ( 6) covalent geometry : bond 0.00235 ( 2322) covalent geometry : angle 0.51107 ( 3167) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 37 time to evaluate : 0.232 Fit side-chains REVERT: R 21 PHE cc_start: 0.4798 (m-80) cc_final: 0.4443 (m-80) REVERT: R 62 SER cc_start: 0.8851 (OUTLIER) cc_final: 0.8440 (m) REVERT: R 168 LEU cc_start: 0.6461 (OUTLIER) cc_final: 0.5795 (mt) REVERT: R 216 ARG cc_start: 0.8385 (ttm-80) cc_final: 0.7552 (mtp85) REVERT: R 220 MET cc_start: 0.8451 (ttm) cc_final: 0.8159 (mtp) outliers start: 12 outliers final: 9 residues processed: 45 average time/residue: 0.1393 time to fit residues: 7.7514 Evaluate side-chains 46 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 35 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 26 ILE Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 47 LEU Chi-restraints excluded: chain R residue 62 SER Chi-restraints excluded: chain R residue 77 ILE Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain R residue 109 MET Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 168 LEU Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 226 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 8 optimal weight: 0.7980 chunk 18 optimal weight: 0.3980 chunk 20 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 27 optimal weight: 0.2980 chunk 4 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 24 optimal weight: 6.9990 chunk 10 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 45 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.199306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.154434 restraints weight = 2592.551| |-----------------------------------------------------------------------------| r_work (start): 0.3832 rms_B_bonded: 2.30 r_work: 0.3564 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 2325 Z= 0.107 Angle : 0.516 8.855 3173 Z= 0.256 Chirality : 0.040 0.114 368 Planarity : 0.004 0.049 382 Dihedral : 3.579 13.895 325 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 5.08 % Allowed : 29.24 % Favored : 65.68 % 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: 0.95 (0.53), residues: 281 helix: 1.23 (0.38), residues: 205 sheet: None (None), residues: 0 loop : -0.91 (0.73), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 256 HIS 0.001 0.000 HIS R 253 PHE 0.013 0.001 PHE R 232 TYR 0.005 0.001 TYR R 87 ARG 0.005 0.000 ARG R 216 Details of bonding type rmsd hydrogen bonds : bond 0.03714 ( 134) hydrogen bonds : angle 3.72866 ( 393) SS BOND : bond 0.00097 ( 3) SS BOND : angle 0.57927 ( 6) covalent geometry : bond 0.00235 ( 2322) covalent geometry : angle 0.51559 ( 3167) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 36 time to evaluate : 0.247 Fit side-chains REVERT: R 21 PHE cc_start: 0.4830 (m-80) cc_final: 0.4458 (m-80) REVERT: R 62 SER cc_start: 0.8850 (OUTLIER) cc_final: 0.8439 (m) REVERT: R 168 LEU cc_start: 0.6466 (OUTLIER) cc_final: 0.5819 (mt) REVERT: R 220 MET cc_start: 0.8452 (ttm) cc_final: 0.8185 (mtp) outliers start: 12 outliers final: 9 residues processed: 45 average time/residue: 0.1226 time to fit residues: 6.7787 Evaluate side-chains 46 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 35 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 47 LEU Chi-restraints excluded: chain R residue 62 SER Chi-restraints excluded: chain R residue 77 ILE Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain R residue 109 MET Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 168 LEU Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 226 ILE Chi-restraints excluded: chain R residue 277 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 15 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 21 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 24 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.4246 r_free = 0.4246 target = 0.197698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.155953 restraints weight = 2687.870| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 2.89 r_work: 0.3537 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2325 Z= 0.126 Angle : 0.532 8.970 3173 Z= 0.264 Chirality : 0.041 0.116 368 Planarity : 0.004 0.048 382 Dihedral : 3.721 15.044 325 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 5.93 % Allowed : 29.24 % Favored : 64.83 % 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: 0.85 (0.53), residues: 281 helix: 1.13 (0.38), residues: 205 sheet: None (None), residues: 0 loop : -0.86 (0.74), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 256 HIS 0.002 0.001 HIS R 161 PHE 0.008 0.001 PHE R 117 TYR 0.010 0.002 TYR R 86 ARG 0.006 0.000 ARG R 216 Details of bonding type rmsd hydrogen bonds : bond 0.04132 ( 134) hydrogen bonds : angle 3.79372 ( 393) SS BOND : bond 0.00119 ( 3) SS BOND : angle 0.52136 ( 6) covalent geometry : bond 0.00290 ( 2322) covalent geometry : angle 0.53182 ( 3167) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 37 time to evaluate : 0.245 Fit side-chains REVERT: R 21 PHE cc_start: 0.4913 (m-80) cc_final: 0.4554 (m-80) REVERT: R 62 SER cc_start: 0.8908 (OUTLIER) cc_final: 0.8480 (m) REVERT: R 168 LEU cc_start: 0.6487 (OUTLIER) cc_final: 0.5823 (mt) REVERT: R 220 MET cc_start: 0.8481 (ttm) cc_final: 0.8184 (mtp) outliers start: 14 outliers final: 10 residues processed: 45 average time/residue: 0.1211 time to fit residues: 6.7229 Evaluate side-chains 49 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 37 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 47 LEU Chi-restraints excluded: chain R residue 62 SER Chi-restraints excluded: chain R residue 77 ILE Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain R residue 95 PHE Chi-restraints excluded: chain R residue 109 MET Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 168 LEU Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 226 ILE Chi-restraints excluded: chain R residue 277 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 25 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 chunk 10 optimal weight: 0.3980 chunk 20 optimal weight: 3.9990 chunk 15 optimal weight: 8.9990 chunk 18 optimal weight: 0.0980 chunk 4 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 24 optimal weight: 0.0570 chunk 27 optimal weight: 0.7980 overall best weight: 0.4298 ------------------------------------------------------------------------------- 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 = 0.4268 r_free = 0.4268 target = 0.199680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.155068 restraints weight = 2600.222| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 2.34 r_work: 0.3596 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 2325 Z= 0.101 Angle : 0.518 9.764 3173 Z= 0.252 Chirality : 0.039 0.117 368 Planarity : 0.004 0.049 382 Dihedral : 3.578 13.804 325 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 5.51 % Allowed : 29.66 % Favored : 64.83 % 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: 0.97 (0.53), residues: 281 helix: 1.20 (0.38), residues: 208 sheet: None (None), residues: 0 loop : -0.85 (0.75), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 142 HIS 0.001 0.000 HIS R 161 PHE 0.012 0.001 PHE R 232 TYR 0.017 0.001 TYR R 86 ARG 0.006 0.000 ARG R 216 Details of bonding type rmsd hydrogen bonds : bond 0.03440 ( 134) hydrogen bonds : angle 3.70015 ( 393) SS BOND : bond 0.00116 ( 3) SS BOND : angle 0.46628 ( 6) covalent geometry : bond 0.00212 ( 2322) covalent geometry : angle 0.51815 ( 3167) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 35 time to evaluate : 0.242 Fit side-chains REVERT: R 21 PHE cc_start: 0.4920 (m-80) cc_final: 0.4542 (m-80) REVERT: R 62 SER cc_start: 0.8816 (OUTLIER) cc_final: 0.8412 (m) REVERT: R 168 LEU cc_start: 0.6524 (OUTLIER) cc_final: 0.5837 (mt) REVERT: R 216 ARG cc_start: 0.8332 (ttm-80) cc_final: 0.7535 (mtp85) REVERT: R 220 MET cc_start: 0.8433 (ttm) cc_final: 0.8017 (mtp) outliers start: 13 outliers final: 10 residues processed: 43 average time/residue: 0.1242 time to fit residues: 6.5696 Evaluate side-chains 47 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 35 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 47 LEU Chi-restraints excluded: chain R residue 62 SER Chi-restraints excluded: chain R residue 77 ILE Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain R residue 95 PHE Chi-restraints excluded: chain R residue 109 MET Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 168 LEU Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 226 ILE Chi-restraints excluded: chain R residue 277 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 20 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 11 optimal weight: 0.2980 chunk 13 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 22 optimal weight: 0.4980 chunk 18 optimal weight: 0.7980 chunk 1 optimal weight: 8.9990 chunk 23 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4261 r_free = 0.4261 target = 0.198810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.154681 restraints weight = 2570.109| |-----------------------------------------------------------------------------| r_work (start): 0.3837 rms_B_bonded: 2.30 r_work: 0.3580 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 2325 Z= 0.108 Angle : 0.524 9.229 3173 Z= 0.256 Chirality : 0.040 0.115 368 Planarity : 0.004 0.048 382 Dihedral : 3.564 13.648 325 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 5.08 % Allowed : 30.51 % Favored : 64.41 % 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: 0.94 (0.52), residues: 281 helix: 1.18 (0.38), residues: 208 sheet: None (None), residues: 0 loop : -0.88 (0.74), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP R 93 HIS 0.001 0.000 HIS R 253 PHE 0.007 0.001 PHE R 206 TYR 0.017 0.002 TYR R 86 ARG 0.005 0.000 ARG R 216 Details of bonding type rmsd hydrogen bonds : bond 0.03663 ( 134) hydrogen bonds : angle 3.70407 ( 393) SS BOND : bond 0.00102 ( 3) SS BOND : angle 0.47157 ( 6) covalent geometry : bond 0.00238 ( 2322) covalent geometry : angle 0.52396 ( 3167) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 36 time to evaluate : 0.252 Fit side-chains REVERT: R 21 PHE cc_start: 0.4926 (m-80) cc_final: 0.4561 (m-80) REVERT: R 62 SER cc_start: 0.8835 (OUTLIER) cc_final: 0.8421 (m) REVERT: R 168 LEU cc_start: 0.6537 (OUTLIER) cc_final: 0.5832 (mt) REVERT: R 216 ARG cc_start: 0.8347 (ttm-80) cc_final: 0.7547 (mtp85) REVERT: R 220 MET cc_start: 0.8473 (ttm) cc_final: 0.8027 (mtp) outliers start: 12 outliers final: 9 residues processed: 43 average time/residue: 0.1290 time to fit residues: 6.8260 Evaluate side-chains 46 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 35 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 47 LEU Chi-restraints excluded: chain R residue 62 SER Chi-restraints excluded: chain R residue 77 ILE Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain R residue 95 PHE Chi-restraints excluded: chain R residue 109 MET Chi-restraints excluded: chain R residue 168 LEU Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 226 ILE Chi-restraints excluded: chain R residue 277 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 22 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 19 optimal weight: 0.2980 chunk 17 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 18 optimal weight: 0.5980 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 = 0.4258 r_free = 0.4258 target = 0.198522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.154120 restraints weight = 2566.737| |-----------------------------------------------------------------------------| r_work (start): 0.3837 rms_B_bonded: 2.35 r_work: 0.3581 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 2325 Z= 0.110 Angle : 0.527 9.069 3173 Z= 0.259 Chirality : 0.040 0.115 368 Planarity : 0.004 0.048 382 Dihedral : 3.567 13.748 325 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 5.08 % Allowed : 30.08 % Favored : 64.83 % 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: 0.98 (0.52), residues: 281 helix: 1.21 (0.38), residues: 208 sheet: None (None), residues: 0 loop : -0.87 (0.75), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP R 142 HIS 0.001 0.000 HIS R 253 PHE 0.019 0.001 PHE R 232 TYR 0.016 0.002 TYR R 86 ARG 0.005 0.000 ARG R 216 Details of bonding type rmsd hydrogen bonds : bond 0.03692 ( 134) hydrogen bonds : angle 3.70736 ( 393) SS BOND : bond 0.00096 ( 3) SS BOND : angle 0.47981 ( 6) covalent geometry : bond 0.00246 ( 2322) covalent geometry : angle 0.52731 ( 3167) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1723.34 seconds wall clock time: 30 minutes 8.82 seconds (1808.82 seconds total)