Starting phenix.real_space_refine on Mon Feb 10 20:16:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iyx_35832/02_2025/8iyx_35832.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iyx_35832/02_2025/8iyx_35832.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8iyx_35832/02_2025/8iyx_35832.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iyx_35832/02_2025/8iyx_35832.map" model { file = "/net/cci-nas-00/data/ceres_data/8iyx_35832/02_2025/8iyx_35832.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iyx_35832/02_2025/8iyx_35832.cif" } resolution = 3.34 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= 0.001 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 20 5.16 5 Cl 1 4.86 5 C 1489 2.51 5 N 344 2.21 5 O 353 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-5592/modules/chem_data/mon_lib" Total number of atoms: 2207 Number of models: 1 Model: "" Number of chains: 2 Chain: "C" Number of atoms: 2165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2165 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 3, 'TRANS': 262} Chain breaks: 3 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'S6R': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.34, per 1000 atoms: 1.06 Number of scatterers: 2207 At special positions: 0 Unit cell: (59.5, 72.25, 58.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 20 16.00 O 353 8.00 N 344 7.00 C 1489 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 127 " - pdb=" SG CYS C 204 " distance=2.04 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: 0.61 Conformation dependent library (CDL) restraints added in 264.4 milliseconds 516 Ramachandran restraints generated. 258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 508 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 0 sheets defined 88.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'C' and resid 51 through 83 removed outlier: 3.586A pdb=" N ILE C 82 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N HIS C 83 " --> pdb=" O PHE C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 116 Proline residue: C 108 - end of helix Processing helix chain 'C' and resid 124 through 157 removed outlier: 3.683A pdb=" N SER C 149 " --> pdb=" O LEU C 145 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LYS C 155 " --> pdb=" O ASP C 151 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE C 156 " --> pdb=" O ARG C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 195 removed outlier: 3.883A pdb=" N TRP C 179 " --> pdb=" O CYS C 175 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET C 189 " --> pdb=" O GLY C 185 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE C 190 " --> pdb=" O PHE C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 242 removed outlier: 3.637A pdb=" N TRP C 228 " --> pdb=" O VAL C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 279 removed outlier: 3.587A pdb=" N PHE C 269 " --> pdb=" O ALA C 265 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ILE C 270 " --> pdb=" O ARG C 266 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL C 271 " --> pdb=" O ASN C 267 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU C 272 " --> pdb=" O SER C 268 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE C 279 " --> pdb=" O PHE C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 294 removed outlier: 3.505A pdb=" N ARG C 286 " --> pdb=" O TYR C 282 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE C 287 " --> pdb=" O HIS C 283 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ILE C 288 " --> pdb=" O ALA C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 317 removed outlier: 3.714A pdb=" N GLU C 303 " --> pdb=" O CYS C 299 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU C 310 " --> pdb=" O HIS C 306 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE C 311 " --> pdb=" O LYS C 307 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL C 314 " --> pdb=" O GLU C 310 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU C 315 " --> pdb=" O ILE C 311 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER C 316 " --> pdb=" O MET C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 331 Proline residue: C 324 - end of helix removed outlier: 3.641A pdb=" N LEU C 329 " --> pdb=" O VAL C 325 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER C 331 " --> pdb=" O TYR C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 343 removed outlier: 3.694A pdb=" N ARG C 335 " --> pdb=" O SER C 331 " (cutoff:3.500A) 163 hydrogen bonds defined for protein. 489 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: 0.53 Time building geometry restraints manager: 0.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 304 1.31 - 1.43: 653 1.43 - 1.56: 1270 1.56 - 1.68: 1 1.68 - 1.81: 32 Bond restraints: 2260 Sorted by residual: bond pdb=" C26 S6R C 401 " pdb=" N25 S6R C 401 " ideal model delta sigma weight residual 1.347 1.462 -0.115 2.00e-02 2.50e+03 3.29e+01 bond pdb=" C02 S6R C 401 " pdb=" N18 S6R C 401 " ideal model delta sigma weight residual 1.348 1.453 -0.105 2.00e-02 2.50e+03 2.78e+01 bond pdb=" CA SER C 141 " pdb=" CB SER C 141 " ideal model delta sigma weight residual 1.528 1.476 0.053 1.56e-02 4.11e+03 1.15e+01 bond pdb=" CA SER C 149 " pdb=" CB SER C 149 " ideal model delta sigma weight residual 1.530 1.478 0.052 1.57e-02 4.06e+03 1.09e+01 bond pdb=" C19 S6R C 401 " pdb=" C23 S6R C 401 " ideal model delta sigma weight residual 1.538 1.475 0.063 2.00e-02 2.50e+03 9.91e+00 ... (remaining 2255 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 2860 1.41 - 2.83: 127 2.83 - 4.24: 44 4.24 - 5.66: 21 5.66 - 7.07: 6 Bond angle restraints: 3058 Sorted by residual: angle pdb=" C LEU C 150 " pdb=" N ASP C 151 " pdb=" CA ASP C 151 " ideal model delta sigma weight residual 120.28 113.26 7.02 1.34e+00 5.57e-01 2.74e+01 angle pdb=" CA SER C 141 " pdb=" C SER C 141 " pdb=" O SER C 141 " ideal model delta sigma weight residual 120.55 116.25 4.30 1.06e+00 8.90e-01 1.64e+01 angle pdb=" N LEU C 150 " pdb=" CA LEU C 150 " pdb=" C LEU C 150 " ideal model delta sigma weight residual 111.11 106.36 4.75 1.20e+00 6.94e-01 1.57e+01 angle pdb=" N LEU C 145 " pdb=" CA LEU C 145 " pdb=" C LEU C 145 " ideal model delta sigma weight residual 112.23 107.64 4.59 1.26e+00 6.30e-01 1.33e+01 angle pdb=" CA TYR C 139 " pdb=" C TYR C 139 " pdb=" O TYR C 139 " ideal model delta sigma weight residual 120.42 116.63 3.79 1.06e+00 8.90e-01 1.28e+01 ... (remaining 3053 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.98: 1153 15.98 - 31.97: 119 31.97 - 47.95: 39 47.95 - 63.93: 16 63.93 - 79.92: 2 Dihedral angle restraints: 1329 sinusoidal: 544 harmonic: 785 Sorted by residual: dihedral pdb=" CB CYS C 127 " pdb=" SG CYS C 127 " pdb=" SG CYS C 204 " pdb=" CB CYS C 204 " ideal model delta sinusoidal sigma weight residual -86.00 -138.93 52.93 1 1.00e+01 1.00e-02 3.81e+01 dihedral pdb=" C TYR C 139 " pdb=" N TYR C 139 " pdb=" CA TYR C 139 " pdb=" CB TYR C 139 " ideal model delta harmonic sigma weight residual -122.60 -132.66 10.06 0 2.50e+00 1.60e-01 1.62e+01 dihedral pdb=" CA ILE C 82 " pdb=" C ILE C 82 " pdb=" N HIS C 83 " pdb=" CA HIS C 83 " ideal model delta harmonic sigma weight residual 180.00 -162.99 -17.01 0 5.00e+00 4.00e-02 1.16e+01 ... (remaining 1326 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 324 0.069 - 0.138: 34 0.138 - 0.206: 2 0.206 - 0.275: 2 0.275 - 0.344: 1 Chirality restraints: 363 Sorted by residual: chirality pdb=" CA TYR C 139 " pdb=" N TYR C 139 " pdb=" C TYR C 139 " pdb=" CB TYR C 139 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.95e+00 chirality pdb=" CA ILE C 140 " pdb=" N ILE C 140 " pdb=" C ILE C 140 " pdb=" CB ILE C 140 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" C19 S6R C 401 " pdb=" C20 S6R C 401 " pdb=" C23 S6R C 401 " pdb=" C42 S6R C 401 " both_signs ideal model delta sigma weight residual False 2.88 2.67 0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 360 not shown) Planarity restraints: 353 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY C 146 " -0.011 2.00e-02 2.50e+03 2.31e-02 5.33e+00 pdb=" C GLY C 146 " 0.040 2.00e-02 2.50e+03 pdb=" O GLY C 146 " -0.015 2.00e-02 2.50e+03 pdb=" N PHE C 147 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 205 " -0.012 2.00e-02 2.50e+03 1.36e-02 3.26e+00 pdb=" CG PHE C 205 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE C 205 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE C 205 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE C 205 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 205 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE C 205 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 152 " 0.009 2.00e-02 2.50e+03 1.69e-02 2.85e+00 pdb=" C ARG C 152 " -0.029 2.00e-02 2.50e+03 pdb=" O ARG C 152 " 0.011 2.00e-02 2.50e+03 pdb=" N TYR C 153 " 0.010 2.00e-02 2.50e+03 ... (remaining 350 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 501 2.78 - 3.31: 2279 3.31 - 3.84: 3484 3.84 - 4.37: 3862 4.37 - 4.90: 6550 Nonbonded interactions: 16676 Sorted by model distance: nonbonded pdb=" O LEU C 192 " pdb=" N LYS C 196 " model vdw 2.252 3.120 nonbonded pdb=" OH TYR C 282 " pdb=" NH2 ARG C 286 " model vdw 2.263 3.120 nonbonded pdb=" O ALA C 99 " pdb=" ND2 ASN C 137 " model vdw 2.308 3.120 nonbonded pdb=" O ARG C 208 " pdb=" NE2 GLN C 293 " model vdw 2.348 3.120 nonbonded pdb=" OD1 ASN C 95 " pdb=" NE1 TRP C 179 " model vdw 2.353 3.120 ... (remaining 16671 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: 0.770 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: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.820 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 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 : 0.007 0.115 2260 Z= 0.420 Angle : 0.857 7.071 3058 Z= 0.509 Chirality : 0.050 0.344 363 Planarity : 0.004 0.031 353 Dihedral : 15.492 79.918 818 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.39 % Allowed : 3.49 % Favored : 96.12 % Rotamer: Outliers : 4.08 % Allowed : 1.63 % Favored : 94.29 % 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 (0.50), residues: 258 helix: 1.32 (0.34), residues: 207 sheet: None (None), residues: 0 loop : -2.10 (0.83), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 228 HIS 0.002 0.001 HIS C 206 PHE 0.032 0.002 PHE C 205 TYR 0.021 0.002 TYR C 139 ARG 0.002 0.000 ARG C 110 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 516 Ramachandran restraints generated. 258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 516 Ramachandran restraints generated. 258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.252 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 83 average time/residue: 0.1711 time to fit residues: 16.0223 Evaluate side-chains 67 residues out of total 245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 62 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain C residue 264 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 21 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 15 optimal weight: 10.0000 chunk 23 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.4189 r_free = 0.4189 target = 0.161381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.129850 restraints weight = 3517.353| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 2.66 r_work: 0.3589 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 2260 Z= 0.224 Angle : 0.684 7.228 3058 Z= 0.354 Chirality : 0.042 0.113 363 Planarity : 0.005 0.041 353 Dihedral : 9.343 57.917 331 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 4.49 % Allowed : 15.10 % Favored : 80.41 % 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: 2.27 (0.50), residues: 258 helix: 2.03 (0.33), residues: 222 sheet: None (None), residues: 0 loop : -1.94 (0.86), residues: 36 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 228 HIS 0.004 0.001 HIS C 206 PHE 0.017 0.002 PHE C 221 TYR 0.014 0.002 TYR C 238 ARG 0.002 0.001 ARG C 110 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 516 Ramachandran restraints generated. 258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 516 Ramachandran restraints generated. 258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.364 Fit side-chains outliers start: 11 outliers final: 3 residues processed: 75 average time/residue: 0.1879 time to fit residues: 15.9509 Evaluate side-chains 64 residues out of total 245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 61 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 137 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 18 optimal weight: 6.9990 chunk 2 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 15 optimal weight: 7.9990 chunk 5 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 = 0.3938 r_free = 0.3938 target = 0.149949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.115536 restraints weight = 3495.714| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.65 r_work: 0.3273 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 2260 Z= 0.253 Angle : 0.659 7.739 3058 Z= 0.339 Chirality : 0.042 0.150 363 Planarity : 0.004 0.037 353 Dihedral : 7.016 45.955 323 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.45 % Allowed : 20.00 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.49), residues: 258 helix: 2.14 (0.32), residues: 222 sheet: None (None), residues: 0 loop : -2.03 (0.86), residues: 36 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 120 HIS 0.002 0.001 HIS C 114 PHE 0.014 0.002 PHE C 205 TYR 0.010 0.001 TYR C 77 ARG 0.004 0.001 ARG C 110 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 516 Ramachandran restraints generated. 258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 516 Ramachandran restraints generated. 258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.266 Fit side-chains REVERT: C 195 LYS cc_start: 0.4614 (mmtt) cc_final: 0.4169 (mptt) REVERT: C 232 LEU cc_start: 0.9154 (tp) cc_final: 0.8858 (tp) REVERT: C 236 LEU cc_start: 0.9464 (mp) cc_final: 0.9207 (mp) outliers start: 6 outliers final: 6 residues processed: 68 average time/residue: 0.1404 time to fit residues: 11.2752 Evaluate side-chains 65 residues out of total 245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 343 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 14 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 20 optimal weight: 0.4980 chunk 4 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 21 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 3 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 83 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.153916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.119843 restraints weight = 3482.480| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 2.64 r_work: 0.3337 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.3750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2260 Z= 0.183 Angle : 0.618 8.699 3058 Z= 0.312 Chirality : 0.039 0.130 363 Planarity : 0.004 0.041 353 Dihedral : 6.555 42.974 323 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.27 % Allowed : 20.41 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.71 (0.50), residues: 258 helix: 2.43 (0.33), residues: 221 sheet: None (None), residues: 0 loop : -2.44 (0.82), residues: 37 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 120 HIS 0.004 0.001 HIS C 206 PHE 0.009 0.001 PHE C 221 TYR 0.010 0.001 TYR C 173 ARG 0.003 0.000 ARG C 110 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 516 Ramachandran restraints generated. 258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 516 Ramachandran restraints generated. 258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 0.196 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 65 average time/residue: 0.1430 time to fit residues: 10.9011 Evaluate side-chains 63 residues out of total 245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 58 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 136 MET Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 337 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 24 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 25 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 4 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.3984 r_free = 0.3984 target = 0.153112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.118222 restraints weight = 3577.835| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 2.65 r_work: 0.3327 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.3859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2260 Z= 0.200 Angle : 0.595 6.532 3058 Z= 0.302 Chirality : 0.039 0.112 363 Planarity : 0.004 0.042 353 Dihedral : 6.278 39.563 323 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.86 % Allowed : 21.22 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.86 (0.50), residues: 258 helix: 2.53 (0.33), residues: 222 sheet: None (None), residues: 0 loop : -2.50 (0.84), residues: 36 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 120 HIS 0.002 0.001 HIS C 114 PHE 0.011 0.001 PHE C 205 TYR 0.013 0.001 TYR C 238 ARG 0.002 0.000 ARG C 110 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 516 Ramachandran restraints generated. 258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 516 Ramachandran restraints generated. 258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.245 Fit side-chains REVERT: C 173 TYR cc_start: 0.7717 (m-10) cc_final: 0.7346 (m-80) outliers start: 7 outliers final: 5 residues processed: 62 average time/residue: 0.1354 time to fit residues: 9.8592 Evaluate side-chains 60 residues out of total 245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 136 MET Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 343 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 13 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 83 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.155093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.120223 restraints weight = 3590.650| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.75 r_work: 0.3302 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.4158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 2260 Z= 0.224 Angle : 0.661 11.446 3058 Z= 0.322 Chirality : 0.040 0.113 363 Planarity : 0.004 0.042 353 Dihedral : 6.125 37.222 323 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.86 % Allowed : 21.22 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.77 (0.50), residues: 258 helix: 2.48 (0.33), residues: 222 sheet: None (None), residues: 0 loop : -2.63 (0.82), residues: 36 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 120 HIS 0.001 0.001 HIS C 114 PHE 0.008 0.001 PHE C 134 TYR 0.015 0.001 TYR C 238 ARG 0.002 0.000 ARG C 110 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 516 Ramachandran restraints generated. 258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 516 Ramachandran restraints generated. 258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.266 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 7 residues processed: 64 average time/residue: 0.1408 time to fit residues: 10.6323 Evaluate side-chains 64 residues out of total 245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 136 MET Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 269 PHE Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 343 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 10 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 9 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3974 r_free = 0.3974 target = 0.152184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.115887 restraints weight = 3663.052| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.92 r_work: 0.3311 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.4245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2260 Z= 0.199 Angle : 0.626 7.408 3058 Z= 0.309 Chirality : 0.039 0.122 363 Planarity : 0.003 0.041 353 Dihedral : 5.975 35.442 323 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.27 % Allowed : 24.90 % Favored : 71.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.93 (0.51), residues: 258 helix: 2.60 (0.33), residues: 222 sheet: None (None), residues: 0 loop : -2.66 (0.80), residues: 36 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 120 HIS 0.002 0.001 HIS C 206 PHE 0.011 0.001 PHE C 205 TYR 0.011 0.001 TYR C 238 ARG 0.002 0.000 ARG C 110 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 516 Ramachandran restraints generated. 258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 516 Ramachandran restraints generated. 258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.261 Fit side-chains REVERT: C 195 LYS cc_start: 0.4384 (mptt) cc_final: 0.3175 (tppt) outliers start: 8 outliers final: 6 residues processed: 59 average time/residue: 0.1460 time to fit residues: 10.1000 Evaluate side-chains 59 residues out of total 245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 136 MET Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 343 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 9 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 13 optimal weight: 0.0050 chunk 25 optimal weight: 4.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 83 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.154290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.119285 restraints weight = 3791.132| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.89 r_work: 0.3341 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.4375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2260 Z= 0.186 Angle : 0.651 13.000 3058 Z= 0.314 Chirality : 0.039 0.139 363 Planarity : 0.004 0.042 353 Dihedral : 5.942 34.348 323 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.86 % Allowed : 24.08 % Favored : 73.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.91 (0.51), residues: 258 helix: 2.60 (0.33), residues: 222 sheet: None (None), residues: 0 loop : -2.73 (0.80), residues: 36 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 120 HIS 0.002 0.001 HIS C 206 PHE 0.009 0.001 PHE C 205 TYR 0.021 0.001 TYR C 238 ARG 0.002 0.000 ARG C 110 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 516 Ramachandran restraints generated. 258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 516 Ramachandran restraints generated. 258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.245 Fit side-chains REVERT: C 195 LYS cc_start: 0.4489 (mptt) cc_final: 0.3295 (tppt) outliers start: 7 outliers final: 5 residues processed: 59 average time/residue: 0.1453 time to fit residues: 10.0708 Evaluate side-chains 56 residues out of total 245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 136 MET Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 339 CYS Chi-restraints excluded: chain C residue 341 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 25 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 10 optimal weight: 8.9990 chunk 18 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 9 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 = 0.3990 r_free = 0.3990 target = 0.152998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.118272 restraints weight = 3681.598| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.82 r_work: 0.3312 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.4470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2260 Z= 0.221 Angle : 0.638 7.539 3058 Z= 0.315 Chirality : 0.039 0.139 363 Planarity : 0.004 0.041 353 Dihedral : 5.913 32.035 323 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.27 % Allowed : 23.27 % Favored : 73.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.86 (0.51), residues: 258 helix: 2.53 (0.33), residues: 223 sheet: None (None), residues: 0 loop : -2.68 (0.81), residues: 35 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 120 HIS 0.002 0.001 HIS C 114 PHE 0.012 0.001 PHE C 205 TYR 0.009 0.001 TYR C 139 ARG 0.002 0.000 ARG C 286 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 516 Ramachandran restraints generated. 258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 516 Ramachandran restraints generated. 258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.259 Fit side-chains REVERT: C 195 LYS cc_start: 0.4575 (mptt) cc_final: 0.3409 (tppt) outliers start: 8 outliers final: 6 residues processed: 58 average time/residue: 0.1498 time to fit residues: 10.2067 Evaluate side-chains 57 residues out of total 245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 136 MET Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 339 CYS Chi-restraints excluded: chain C residue 341 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 3 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 23 optimal weight: 0.3980 chunk 4 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 83 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.158850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.125828 restraints weight = 3669.972| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 2.77 r_work: 0.3559 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.4667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2260 Z= 0.200 Angle : 0.672 15.792 3058 Z= 0.317 Chirality : 0.039 0.116 363 Planarity : 0.003 0.041 353 Dihedral : 5.898 35.740 323 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.86 % Allowed : 24.90 % Favored : 72.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.99 (0.51), residues: 258 helix: 2.62 (0.33), residues: 223 sheet: None (None), residues: 0 loop : -2.61 (0.82), residues: 35 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 120 HIS 0.002 0.001 HIS C 83 PHE 0.009 0.001 PHE C 205 TYR 0.012 0.001 TYR C 238 ARG 0.002 0.000 ARG C 286 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 516 Ramachandran restraints generated. 258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 516 Ramachandran restraints generated. 258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.239 Fit side-chains REVERT: C 173 TYR cc_start: 0.7525 (m-10) cc_final: 0.7307 (m-10) REVERT: C 195 LYS cc_start: 0.4538 (mptt) cc_final: 0.3466 (tppt) outliers start: 7 outliers final: 5 residues processed: 58 average time/residue: 0.1558 time to fit residues: 10.5644 Evaluate side-chains 58 residues out of total 245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 53 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 136 MET Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 339 CYS Chi-restraints excluded: chain C residue 341 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 2 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 15 optimal weight: 7.9990 chunk 1 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.4126 r_free = 0.4126 target = 0.156701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.122868 restraints weight = 3672.706| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 2.78 r_work: 0.3521 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.4700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2260 Z= 0.235 Angle : 0.682 14.743 3058 Z= 0.323 Chirality : 0.040 0.157 363 Planarity : 0.004 0.040 353 Dihedral : 5.871 34.258 323 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.04 % Allowed : 25.31 % Favored : 72.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.88 (0.51), residues: 258 helix: 2.59 (0.33), residues: 222 sheet: None (None), residues: 0 loop : -2.82 (0.78), residues: 36 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 120 HIS 0.002 0.001 HIS C 114 PHE 0.011 0.001 PHE C 205 TYR 0.009 0.001 TYR C 139 ARG 0.002 0.000 ARG C 286 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1433.18 seconds wall clock time: 26 minutes 2.93 seconds (1562.93 seconds total)