Starting phenix.real_space_refine on Wed Mar 5 15:15:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ihk_35447/03_2025/8ihk_35447.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ihk_35447/03_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_35447/03_2025/8ihk_35447.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ihk_35447/03_2025/8ihk_35447.map" model { file = "/net/cci-nas-00/data/ceres_data/8ihk_35447/03_2025/8ihk_35447.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ihk_35447/03_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-5624/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: 2.10, per 1000 atoms: 0.93 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: 0.57 Conformation dependent library (CDL) restraints added in 264.9 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: 0.19 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: 0.50 Time building geometry restraints manager: 0.67 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: 0.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.970 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.530 ------------------------------------------------------------------------------- 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 : 0.003 0.059 2322 Z= 0.253 Angle : 0.569 6.803 3167 Z= 0.287 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 *********************** 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 : 0.248 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: 0.1664 time to fit residues: 8.0582 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 : 0.256 ------------------------------------------------------------------------------- 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: 1.9990 chunk 14 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 16 optimal weight: 9.9990 chunk 25 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 27 optimal weight: 0.3980 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 = 0.4255 r_free = 0.4255 target = 0.197639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.153140 restraints weight = 2604.366| |-----------------------------------------------------------------------------| r_work (start): 0.3835 rms_B_bonded: 2.32 r_work: 0.3576 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2322 Z= 0.207 Angle : 0.554 6.792 3167 Z= 0.287 Chirality : 0.042 0.123 368 Planarity : 0.005 0.052 382 Dihedral : 4.555 22.736 325 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.69 % Allowed : 29.66 % Favored : 68.64 % 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: 0.18 (0.52), residues: 281 helix: 0.66 (0.38), residues: 198 sheet: None (None), residues: 0 loop : -1.05 (0.72), residues: 83 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 0.014 0.001 PHE R 232 TYR 0.008 0.001 TYR R 284 ARG 0.002 0.000 ARG R 218 *********************** 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: 4 poor density : 36 time to evaluate : 0.228 Fit side-chains REVERT: R 62 SER cc_start: 0.8938 (t) cc_final: 0.8408 (m) outliers start: 4 outliers final: 2 residues processed: 39 average time/residue: 0.1385 time to fit residues: 6.6199 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 226 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 16 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 2 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 22 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 3 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.4267 r_free = 0.4267 target = 0.199110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.156181 restraints weight = 2564.594| |-----------------------------------------------------------------------------| r_work (start): 0.3857 rms_B_bonded: 2.75 r_work: 0.3561 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2322 Z= 0.174 Angle : 0.522 6.605 3167 Z= 0.265 Chirality : 0.041 0.122 368 Planarity : 0.004 0.050 382 Dihedral : 4.141 15.411 325 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.81 % Allowed : 27.97 % Favored : 68.22 % 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: 0.45 (0.52), residues: 281 helix: 0.82 (0.38), residues: 203 sheet: None (None), residues: 0 loop : -0.93 (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 0.007 0.001 PHE R 232 TYR 0.006 0.001 TYR R 87 ARG 0.001 0.000 ARG R 218 *********************** 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 47 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 38 time to evaluate : 0.215 Fit side-chains REVERT: R 21 PHE cc_start: 0.4465 (m-80) cc_final: 0.3933 (m-80) REVERT: R 62 SER cc_start: 0.8923 (t) cc_final: 0.8466 (m) REVERT: R 216 ARG cc_start: 0.8266 (ttm-80) cc_final: 0.7625 (mtp85) outliers start: 9 outliers final: 5 residues processed: 44 average time/residue: 0.1366 time to fit residues: 7.2181 Evaluate side-chains 42 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.355 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 21 optimal weight: 0.6980 chunk 17 optimal weight: 7.9990 chunk 12 optimal weight: 0.0670 chunk 5 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 1 optimal weight: 0.0980 chunk 7 optimal weight: 0.0770 overall best weight: 0.3676 ------------------------------------------------------------------------------- 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 = 0.4284 r_free = 0.4284 target = 0.200884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.156300 restraints weight = 2527.669| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 2.34 r_work: 0.3614 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 2322 Z= 0.137 Angle : 0.519 9.425 3167 Z= 0.255 Chirality : 0.040 0.115 368 Planarity : 0.004 0.050 382 Dihedral : 3.750 13.919 325 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.39 % Allowed : 28.81 % 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: 0.81 (0.53), residues: 281 helix: 1.15 (0.38), residues: 203 sheet: None (None), residues: 0 loop : -1.00 (0.72), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.000 TRP R 256 HIS 0.002 0.000 HIS R 253 PHE 0.007 0.001 PHE R 206 TYR 0.005 0.001 TYR R 87 ARG 0.001 0.000 ARG R 101 *********************** 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 46 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.222 Fit side-chains REVERT: R 21 PHE cc_start: 0.4815 (m-80) cc_final: 0.4266 (m-80) REVERT: R 45 ASN cc_start: 0.7753 (m-40) cc_final: 0.7533 (m110) REVERT: R 62 SER cc_start: 0.8832 (t) cc_final: 0.8418 (m) REVERT: R 216 ARG cc_start: 0.8197 (ttm-80) cc_final: 0.7593 (mtp85) outliers start: 8 outliers final: 6 residues processed: 43 average time/residue: 0.1230 time to fit residues: 6.4928 Evaluate side-chains 42 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.241 ------------------------------------------------------------------------------- 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 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: 7.9990 chunk 22 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 9 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.4264 r_free = 0.4264 target = 0.199154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.157442 restraints weight = 2579.973| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 2.66 r_work: 0.3554 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2322 Z= 0.180 Angle : 0.549 7.422 3167 Z= 0.267 Chirality : 0.041 0.116 368 Planarity : 0.004 0.049 382 Dihedral : 3.828 14.393 325 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.81 % Allowed : 29.24 % Favored : 66.95 % 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: 0.78 (0.53), residues: 281 helix: 1.13 (0.38), residues: 203 sheet: None (None), residues: 0 loop : -1.03 (0.72), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 256 HIS 0.002 0.001 HIS R 253 PHE 0.008 0.001 PHE R 117 TYR 0.007 0.001 TYR R 294 ARG 0.001 0.000 ARG R 128 *********************** 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 45 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 36 time to evaluate : 0.218 Fit side-chains REVERT: R 21 PHE cc_start: 0.4741 (m-80) cc_final: 0.4293 (m-80) REVERT: R 45 ASN cc_start: 0.7728 (m-40) cc_final: 0.7475 (m110) REVERT: R 62 SER cc_start: 0.8895 (OUTLIER) cc_final: 0.8472 (m) outliers start: 9 outliers final: 7 residues processed: 42 average time/residue: 0.1290 time to fit residues: 6.6428 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 : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 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 183 CYS Chi-restraints excluded: chain R residue 226 ILE 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: 8.9990 chunk 20 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 12 optimal weight: 0.2980 chunk 16 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 7 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 = 0.4272 r_free = 0.4272 target = 0.199807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.158222 restraints weight = 2612.041| |-----------------------------------------------------------------------------| r_work (start): 0.3873 rms_B_bonded: 2.70 r_work: 0.3559 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2322 Z= 0.165 Angle : 0.538 8.288 3167 Z= 0.263 Chirality : 0.040 0.115 368 Planarity : 0.004 0.049 382 Dihedral : 3.761 14.481 325 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 4.66 % Allowed : 29.24 % 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: 0.86 (0.52), residues: 281 helix: 1.17 (0.38), residues: 204 sheet: None (None), residues: 0 loop : -0.94 (0.72), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 256 HIS 0.002 0.001 HIS R 253 PHE 0.018 0.001 PHE R 232 TYR 0.005 0.001 TYR R 87 ARG 0.005 0.000 ARG R 216 *********************** 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 47 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 36 time to evaluate : 0.243 Fit side-chains REVERT: R 21 PHE cc_start: 0.4728 (m-80) cc_final: 0.4302 (m-80) REVERT: R 62 SER cc_start: 0.8851 (OUTLIER) cc_final: 0.8451 (m) outliers start: 11 outliers final: 9 residues processed: 44 average time/residue: 0.1191 time to fit residues: 6.4584 Evaluate side-chains 45 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 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 183 CYS Chi-restraints excluded: chain R residue 226 ILE Chi-restraints excluded: chain R residue 277 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 8 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 27 optimal weight: 0.0980 chunk 4 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 24 optimal weight: 6.9990 chunk 10 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.200293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.158040 restraints weight = 2611.047| |-----------------------------------------------------------------------------| r_work (start): 0.3872 rms_B_bonded: 2.71 r_work: 0.3564 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 2322 Z= 0.159 Angle : 0.531 8.189 3167 Z= 0.263 Chirality : 0.040 0.115 368 Planarity : 0.004 0.049 382 Dihedral : 3.677 14.262 325 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 3.35 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: 0.86 (0.53), residues: 281 helix: 1.16 (0.38), residues: 205 sheet: None (None), residues: 0 loop : -0.94 (0.73), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 256 HIS 0.002 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 *********************** 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 49 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 37 time to evaluate : 0.244 Fit side-chains REVERT: R 21 PHE cc_start: 0.4786 (m-80) cc_final: 0.4414 (m-80) REVERT: R 62 SER cc_start: 0.8855 (OUTLIER) cc_final: 0.8442 (m) REVERT: R 220 MET cc_start: 0.8439 (ttm) cc_final: 0.8170 (mtp) outliers start: 12 outliers final: 8 residues processed: 45 average time/residue: 0.1185 time to fit residues: 6.5913 Evaluate side-chains 46 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 37 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 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 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: 4.9990 chunk 0 optimal weight: 10.0000 chunk 21 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 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 = 0.4259 r_free = 0.4259 target = 0.198685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.155927 restraints weight = 2677.665| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 2.44 r_work: 0.3568 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2322 Z= 0.163 Angle : 0.543 9.215 3167 Z= 0.266 Chirality : 0.040 0.114 368 Planarity : 0.004 0.049 382 Dihedral : 3.681 14.358 325 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 4.66 % Allowed : 30.08 % Favored : 65.25 % 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 (0.52), residues: 281 helix: 1.17 (0.38), residues: 205 sheet: None (None), residues: 0 loop : -0.95 (0.73), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 256 HIS 0.002 0.000 HIS R 253 PHE 0.014 0.001 PHE R 232 TYR 0.005 0.001 TYR R 87 ARG 0.006 0.000 ARG R 216 *********************** 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 48 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 37 time to evaluate : 0.239 Fit side-chains REVERT: R 21 PHE cc_start: 0.4857 (m-80) cc_final: 0.4488 (m-80) REVERT: R 62 SER cc_start: 0.8830 (OUTLIER) cc_final: 0.8428 (m) REVERT: R 216 ARG cc_start: 0.8423 (ttm-80) cc_final: 0.7584 (mtp85) REVERT: R 220 MET cc_start: 0.8447 (ttm) cc_final: 0.8171 (mtp) outliers start: 11 outliers final: 8 residues processed: 43 average time/residue: 0.1281 time to fit residues: 6.7725 Evaluate side-chains 46 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 37 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 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 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: 1.9990 chunk 7 optimal weight: 5.9990 chunk 6 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 20 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 4 optimal weight: 0.0170 chunk 19 optimal weight: 0.7980 chunk 24 optimal weight: 7.9990 chunk 27 optimal weight: 0.7980 overall best weight: 0.5618 ------------------------------------------------------------------------------- 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 = 0.4271 r_free = 0.4271 target = 0.199820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.155458 restraints weight = 2598.132| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 2.27 r_work: 0.3572 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 2322 Z= 0.150 Angle : 0.537 9.735 3167 Z= 0.263 Chirality : 0.040 0.114 368 Planarity : 0.004 0.049 382 Dihedral : 3.581 13.870 325 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 4.66 % Allowed : 31.36 % Favored : 63.98 % 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 (0.52), residues: 281 helix: 1.26 (0.38), residues: 205 sheet: None (None), residues: 0 loop : -0.98 (0.73), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP R 142 HIS 0.002 0.000 HIS R 253 PHE 0.007 0.001 PHE R 206 TYR 0.005 0.001 TYR R 87 ARG 0.005 0.000 ARG R 216 *********************** 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 49 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 38 time to evaluate : 0.213 Fit side-chains REVERT: R 21 PHE cc_start: 0.4912 (m-80) cc_final: 0.4555 (m-80) REVERT: R 45 ASN cc_start: 0.7806 (m-40) cc_final: 0.7527 (m110) REVERT: R 62 SER cc_start: 0.8826 (OUTLIER) cc_final: 0.8415 (m) REVERT: R 216 ARG cc_start: 0.8389 (ttm-80) cc_final: 0.7546 (mtp85) REVERT: R 220 MET cc_start: 0.8428 (ttm) cc_final: 0.7937 (mtp) outliers start: 11 outliers final: 9 residues processed: 44 average time/residue: 0.1175 time to fit residues: 6.4090 Evaluate side-chains 47 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 37 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 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 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: 0.6980 chunk 13 optimal weight: 0.8980 chunk 3 optimal weight: 0.4980 chunk 21 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 1 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 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 = 0.4258 r_free = 0.4258 target = 0.198580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.155164 restraints weight = 2582.257| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 2.25 r_work: 0.3576 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2322 Z= 0.161 Angle : 0.537 9.261 3167 Z= 0.262 Chirality : 0.040 0.115 368 Planarity : 0.004 0.048 382 Dihedral : 3.608 13.995 325 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 4.24 % Allowed : 30.93 % 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: 0.96 (0.53), residues: 281 helix: 1.24 (0.38), residues: 205 sheet: None (None), residues: 0 loop : -0.93 (0.74), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP R 142 HIS 0.002 0.000 HIS R 253 PHE 0.015 0.001 PHE R 232 TYR 0.009 0.001 TYR R 86 ARG 0.005 0.000 ARG R 216 ********************** 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 46 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 36 time to evaluate : 0.221 Fit side-chains REVERT: R 21 PHE cc_start: 0.4932 (m-80) cc_final: 0.4565 (m-80) REVERT: R 62 SER cc_start: 0.8817 (OUTLIER) cc_final: 0.8417 (m) REVERT: R 216 ARG cc_start: 0.8369 (ttm-80) cc_final: 0.7519 (mtp85) REVERT: R 220 MET cc_start: 0.8458 (ttm) cc_final: 0.7973 (mtp) outliers start: 10 outliers final: 9 residues processed: 41 average time/residue: 0.1088 time to fit residues: 5.5874 Evaluate side-chains 46 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 36 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 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 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: 0.1980 chunk 7 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 14 optimal weight: 5.9990 chunk 18 optimal weight: 0.1980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.4265 r_free = 0.4265 target = 0.199447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.155416 restraints weight = 2571.238| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 2.21 r_work: 0.3570 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 2322 Z= 0.150 Angle : 0.529 9.091 3167 Z= 0.258 Chirality : 0.040 0.115 368 Planarity : 0.004 0.049 382 Dihedral : 3.571 13.651 325 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 4.24 % Allowed : 30.93 % 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: 0.96 (0.52), residues: 281 helix: 1.21 (0.38), residues: 208 sheet: None (None), residues: 0 loop : -0.89 (0.74), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP R 142 HIS 0.002 0.000 HIS R 253 PHE 0.007 0.001 PHE R 206 TYR 0.017 0.001 TYR R 86 ARG 0.005 0.000 ARG R 216 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1605.25 seconds wall clock time: 28 minutes 12.66 seconds (1692.66 seconds total)