Starting phenix.real_space_refine on Mon Jan 13 17:02:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ayb_43984/01_2025/9ayb_43984_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ayb_43984/01_2025/9ayb_43984.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ayb_43984/01_2025/9ayb_43984.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ayb_43984/01_2025/9ayb_43984.map" model { file = "/net/cci-nas-00/data/ceres_data/9ayb_43984/01_2025/9ayb_43984_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ayb_43984/01_2025/9ayb_43984_neut.cif" } resolution = 3.19 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= 0.025 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 16 5.16 5 C 2236 2.51 5 N 523 2.21 5 O 572 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 3347 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3347 Classifications: {'peptide': 428} Link IDs: {'PTRANS': 18, 'TRANS': 409} Chain breaks: 1 Time building chain proxies: 2.84, per 1000 atoms: 0.85 Number of scatterers: 3347 At special positions: 0 Unit cell: (61.254, 81.18, 66.42, 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 16 16.00 O 572 8.00 N 523 7.00 C 2236 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.78 Conformation dependent library (CDL) restraints added in 380.4 milliseconds 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 780 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 0 sheets defined 89.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 37 through 68 removed outlier: 3.993A pdb=" N LEU A 60 " --> pdb=" O LEU A 56 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ALA A 61 " --> pdb=" O ARG A 57 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL A 62 " --> pdb=" O VAL A 58 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N VAL A 65 " --> pdb=" O ALA A 61 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ASP A 66 " --> pdb=" O VAL A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 120 removed outlier: 4.833A pdb=" N PHE A 115 " --> pdb=" O ILE A 111 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N PHE A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N TYR A 117 " --> pdb=" O GLY A 113 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY A 118 " --> pdb=" O SER A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 134 Processing helix chain 'A' and resid 134 through 152 removed outlier: 4.596A pdb=" N LEU A 138 " --> pdb=" O GLY A 134 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE A 152 " --> pdb=" O VAL A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 160 Processing helix chain 'A' and resid 160 through 176 Processing helix chain 'A' and resid 177 through 187 Processing helix chain 'A' and resid 191 through 193 No H-bonds generated for 'chain 'A' and resid 191 through 193' Processing helix chain 'A' and resid 194 through 224 removed outlier: 4.321A pdb=" N GLY A 205 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N ALA A 206 " --> pdb=" O SER A 202 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N GLN A 207 " --> pdb=" O TYR A 203 " (cutoff:3.500A) Proline residue: A 215 - end of helix removed outlier: 3.863A pdb=" N GLY A 218 " --> pdb=" O LEU A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 248 removed outlier: 4.077A pdb=" N PHE A 230 " --> pdb=" O TRP A 226 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU A 243 " --> pdb=" O PHE A 239 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TRP A 246 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL A 248 " --> pdb=" O TRP A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 255 Processing helix chain 'A' and resid 259 through 270 Processing helix chain 'A' and resid 281 through 288 Processing helix chain 'A' and resid 288 through 319 removed outlier: 3.670A pdb=" N TRP A 292 " --> pdb=" O SER A 288 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LEU A 312 " --> pdb=" O LEU A 308 " (cutoff:3.500A) Proline residue: A 313 - end of helix Processing helix chain 'A' and resid 323 through 328 removed outlier: 3.684A pdb=" N ASN A 327 " --> pdb=" O ASN A 323 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY A 328 " --> pdb=" O VAL A 324 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 323 through 328' Processing helix chain 'A' and resid 328 through 355 Proline residue: A 334 - end of helix Processing helix chain 'A' and resid 359 through 382 Proline residue: A 375 - end of helix removed outlier: 3.594A pdb=" N PHE A 378 " --> pdb=" O GLY A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 403 removed outlier: 3.553A pdb=" N ALA A 392 " --> pdb=" O ASP A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 408 Processing helix chain 'A' and resid 409 through 411 No H-bonds generated for 'chain 'A' and resid 409 through 411' Processing helix chain 'A' and resid 412 through 418 removed outlier: 3.616A pdb=" N ASP A 416 " --> pdb=" O ILE A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 434 Processing helix chain 'A' and resid 435 through 448 Proline residue: A 441 - end of helix Processing helix chain 'A' and resid 452 through 478 Processing helix chain 'A' and resid 483 through 487 245 hydrogen bonds defined for protein. 717 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: 0.94 Time building geometry restraints manager: 0.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 986 1.34 - 1.46: 793 1.46 - 1.57: 1645 1.57 - 1.69: 0 1.69 - 1.81: 25 Bond restraints: 3449 Sorted by residual: bond pdb=" N VAL A 34 " pdb=" CA VAL A 34 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.70e+00 bond pdb=" C PRO A 191 " pdb=" O PRO A 191 " ideal model delta sigma weight residual 1.246 1.239 0.006 8.50e-03 1.38e+04 5.28e-01 bond pdb=" C TRP A 339 " pdb=" O TRP A 339 " ideal model delta sigma weight residual 1.236 1.245 -0.008 1.15e-02 7.56e+03 5.13e-01 bond pdb=" CA ILE A 435 " pdb=" C ILE A 435 " ideal model delta sigma weight residual 1.520 1.526 -0.006 8.80e-03 1.29e+04 4.73e-01 bond pdb=" N THR A 448 " pdb=" CA THR A 448 " ideal model delta sigma weight residual 1.464 1.457 0.007 1.05e-02 9.07e+03 4.40e-01 ... (remaining 3444 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.84: 4338 0.84 - 1.69: 305 1.69 - 2.53: 43 2.53 - 3.37: 9 3.37 - 4.21: 12 Bond angle restraints: 4707 Sorted by residual: angle pdb=" C THR A 434 " pdb=" N ILE A 435 " pdb=" CA ILE A 435 " ideal model delta sigma weight residual 120.24 122.57 -2.33 6.30e-01 2.52e+00 1.37e+01 angle pdb=" C ILE A 435 " pdb=" CA ILE A 435 " pdb=" CB ILE A 435 " ideal model delta sigma weight residual 114.35 111.13 3.22 1.06e+00 8.90e-01 9.25e+00 angle pdb=" N VAL A 283 " pdb=" CA VAL A 283 " pdb=" C VAL A 283 " ideal model delta sigma weight residual 112.35 109.91 2.44 1.20e+00 6.94e-01 4.15e+00 angle pdb=" C VAL A 283 " pdb=" CA VAL A 283 " pdb=" CB VAL A 283 " ideal model delta sigma weight residual 114.00 111.59 2.41 1.31e+00 5.83e-01 3.39e+00 angle pdb=" N SER A 408 " pdb=" CA SER A 408 " pdb=" C SER A 408 " ideal model delta sigma weight residual 113.72 111.56 2.16 1.30e+00 5.92e-01 2.75e+00 ... (remaining 4702 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.88: 1730 14.88 - 29.76: 159 29.76 - 44.64: 49 44.64 - 59.52: 5 59.52 - 74.39: 1 Dihedral angle restraints: 1944 sinusoidal: 718 harmonic: 1226 Sorted by residual: dihedral pdb=" CA TRP A 246 " pdb=" C TRP A 246 " pdb=" N LEU A 247 " pdb=" CA LEU A 247 " ideal model delta harmonic sigma weight residual -180.00 -164.00 -16.00 0 5.00e+00 4.00e-02 1.02e+01 dihedral pdb=" N LYS A 278 " pdb=" CA LYS A 278 " pdb=" CB LYS A 278 " pdb=" CG LYS A 278 " ideal model delta sinusoidal sigma weight residual -180.00 -121.39 -58.61 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CA PHE A 305 " pdb=" C PHE A 305 " pdb=" N TYR A 306 " pdb=" CA TYR A 306 " ideal model delta harmonic sigma weight residual 180.00 164.72 15.28 0 5.00e+00 4.00e-02 9.34e+00 ... (remaining 1941 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 316 0.027 - 0.054: 128 0.054 - 0.082: 66 0.082 - 0.109: 22 0.109 - 0.136: 3 Chirality restraints: 535 Sorted by residual: chirality pdb=" CA VAL A 280 " pdb=" N VAL A 280 " pdb=" C VAL A 280 " pdb=" CB VAL A 280 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.64e-01 chirality pdb=" CA VAL A 34 " pdb=" N VAL A 34 " pdb=" C VAL A 34 " pdb=" CB VAL A 34 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.33e-01 chirality pdb=" CA PHE A 305 " pdb=" N PHE A 305 " pdb=" C PHE A 305 " pdb=" CB PHE A 305 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.28e-01 ... (remaining 532 not shown) Planarity restraints: 571 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 162 " 0.024 5.00e-02 4.00e+02 3.71e-02 2.20e+00 pdb=" N PRO A 163 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 163 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 163 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A 307 " -0.007 2.00e-02 2.50e+03 1.44e-02 2.08e+00 pdb=" C THR A 307 " 0.025 2.00e-02 2.50e+03 pdb=" O THR A 307 " -0.009 2.00e-02 2.50e+03 pdb=" N LEU A 308 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 374 " -0.021 5.00e-02 4.00e+02 3.23e-02 1.66e+00 pdb=" N PRO A 375 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 375 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 375 " -0.018 5.00e-02 4.00e+02 ... (remaining 568 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 1064 2.83 - 3.35: 3452 3.35 - 3.87: 5641 3.87 - 4.38: 6447 4.38 - 4.90: 11290 Nonbonded interactions: 27894 Sorted by model distance: nonbonded pdb=" O MET A 372 " pdb=" ND2 ASN A 467 " model vdw 2.313 3.120 nonbonded pdb=" O ASN A 357 " pdb=" OD1 ASN A 357 " model vdw 2.317 3.040 nonbonded pdb=" O CYS A 406 " pdb=" OG SER A 411 " model vdw 2.358 3.040 nonbonded pdb=" O THR A 448 " pdb=" OG1 THR A 448 " model vdw 2.388 3.040 nonbonded pdb=" NZ LYS A 136 " pdb=" O VAL A 248 " model vdw 2.439 3.120 ... (remaining 27889 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: 1.170 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: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.640 Find NCS groups from input model: 0.030 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 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 0.031 3449 Z= 0.175 Angle : 0.518 4.214 4707 Z= 0.314 Chirality : 0.038 0.136 535 Planarity : 0.005 0.037 571 Dihedral : 12.732 74.394 1164 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 0.57 % Allowed : 7.93 % Favored : 91.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.41), residues: 424 helix: 1.15 (0.29), residues: 325 sheet: None (None), residues: 0 loop : -0.04 (0.61), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 292 HIS 0.003 0.001 HIS A 255 PHE 0.014 0.001 PHE A 232 TYR 0.009 0.001 TYR A 306 ARG 0.002 0.000 ARG A 353 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 35 time to evaluate : 0.300 Fit side-chains REVERT: A 137 MET cc_start: 0.7869 (mmt) cc_final: 0.7605 (mmt) REVERT: A 175 GLU cc_start: 0.7972 (tt0) cc_final: 0.7638 (tt0) REVERT: A 182 MET cc_start: 0.7843 (tpp) cc_final: 0.7459 (tpt) REVERT: A 273 GLN cc_start: 0.8055 (mt0) cc_final: 0.7837 (mt0) outliers start: 2 outliers final: 2 residues processed: 37 average time/residue: 0.1645 time to fit residues: 7.7233 Evaluate side-chains 35 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 33 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 183 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 8.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.138799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.096457 restraints weight = 3624.747| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 2.40 r_work: 0.3005 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.0761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3449 Z= 0.197 Angle : 0.525 4.910 4707 Z= 0.278 Chirality : 0.042 0.193 535 Planarity : 0.005 0.041 571 Dihedral : 5.342 49.437 459 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 3.12 % Allowed : 8.22 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.41), residues: 424 helix: 1.45 (0.29), residues: 330 sheet: None (None), residues: 0 loop : -0.22 (0.64), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 292 HIS 0.001 0.001 HIS A 298 PHE 0.016 0.002 PHE A 51 TYR 0.008 0.001 TYR A 119 ARG 0.002 0.000 ARG A 353 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 29 time to evaluate : 0.269 Fit side-chains REVERT: A 175 GLU cc_start: 0.7890 (tt0) cc_final: 0.7635 (tt0) outliers start: 11 outliers final: 6 residues processed: 37 average time/residue: 0.1876 time to fit residues: 8.4761 Evaluate side-chains 33 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 27 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 316 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 37 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.135960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.094738 restraints weight = 3596.196| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.26 r_work: 0.3001 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.1107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3449 Z= 0.205 Angle : 0.508 4.939 4707 Z= 0.268 Chirality : 0.041 0.129 535 Planarity : 0.005 0.043 571 Dihedral : 5.359 52.192 459 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 2.27 % Allowed : 8.78 % Favored : 88.95 % 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: 1.49 (0.41), residues: 424 helix: 1.47 (0.29), residues: 337 sheet: None (None), residues: 0 loop : -0.78 (0.60), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 485 HIS 0.001 0.001 HIS A 255 PHE 0.018 0.002 PHE A 51 TYR 0.008 0.001 TYR A 119 ARG 0.003 0.001 ARG A 168 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 28 time to evaluate : 0.359 Fit side-chains REVERT: A 175 GLU cc_start: 0.7846 (tt0) cc_final: 0.7590 (tt0) outliers start: 8 outliers final: 5 residues processed: 34 average time/residue: 0.1539 time to fit residues: 6.7325 Evaluate side-chains 31 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 26 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 256 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 0 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 13 optimal weight: 0.0970 chunk 36 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 21 optimal weight: 0.3980 chunk 24 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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 = 0.3577 r_free = 0.3577 target = 0.140097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.098953 restraints weight = 3609.638| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.29 r_work: 0.3032 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3449 Z= 0.164 Angle : 0.476 4.976 4707 Z= 0.250 Chirality : 0.039 0.120 535 Planarity : 0.005 0.042 571 Dihedral : 5.274 53.947 459 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.55 % Allowed : 9.92 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.41), residues: 424 helix: 1.61 (0.29), residues: 337 sheet: None (None), residues: 0 loop : -0.96 (0.57), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 485 HIS 0.001 0.000 HIS A 183 PHE 0.017 0.001 PHE A 51 TYR 0.008 0.001 TYR A 306 ARG 0.003 0.001 ARG A 168 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 27 time to evaluate : 0.314 Fit side-chains REVERT: A 175 GLU cc_start: 0.7806 (tt0) cc_final: 0.7587 (tt0) outliers start: 9 outliers final: 7 residues processed: 34 average time/residue: 0.1568 time to fit residues: 6.8309 Evaluate side-chains 32 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 25 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 256 LYS Chi-restraints excluded: chain A residue 316 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 34 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 32 optimal weight: 6.9990 chunk 0 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 31 optimal weight: 0.3980 chunk 12 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 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 = 0.3524 r_free = 0.3524 target = 0.136491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.095333 restraints weight = 3653.782| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 2.29 r_work: 0.2907 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6835 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3449 Z= 0.196 Angle : 0.486 5.205 4707 Z= 0.254 Chirality : 0.040 0.118 535 Planarity : 0.005 0.042 571 Dihedral : 5.226 52.876 459 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.83 % Allowed : 9.63 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.40), residues: 424 helix: 1.62 (0.29), residues: 337 sheet: None (None), residues: 0 loop : -0.96 (0.56), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 339 HIS 0.001 0.001 HIS A 183 PHE 0.018 0.001 PHE A 51 TYR 0.008 0.001 TYR A 306 ARG 0.002 0.000 ARG A 168 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 27 time to evaluate : 0.343 Fit side-chains REVERT: A 175 GLU cc_start: 0.7712 (tt0) cc_final: 0.7455 (tt0) outliers start: 10 outliers final: 7 residues processed: 34 average time/residue: 0.1772 time to fit residues: 7.7218 Evaluate side-chains 34 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 27 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 256 LYS Chi-restraints excluded: chain A residue 316 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 17 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.3495 r_free = 0.3495 target = 0.133824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.093034 restraints weight = 3713.287| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 2.28 r_work: 0.2978 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3449 Z= 0.253 Angle : 0.518 5.225 4707 Z= 0.270 Chirality : 0.041 0.122 535 Planarity : 0.005 0.042 571 Dihedral : 5.272 51.715 459 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.83 % Allowed : 10.76 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.40), residues: 424 helix: 1.51 (0.29), residues: 338 sheet: None (None), residues: 0 loop : -0.95 (0.55), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 339 HIS 0.002 0.001 HIS A 298 PHE 0.020 0.002 PHE A 51 TYR 0.009 0.001 TYR A 119 ARG 0.003 0.000 ARG A 168 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 25 time to evaluate : 0.349 Fit side-chains outliers start: 10 outliers final: 7 residues processed: 31 average time/residue: 0.1639 time to fit residues: 6.5729 Evaluate side-chains 32 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 25 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 256 LYS Chi-restraints excluded: chain A residue 316 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 0.0470 chunk 11 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 overall best weight: 0.6078 ------------------------------------------------------------------------------- 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 = 0.3559 r_free = 0.3559 target = 0.138717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.097593 restraints weight = 3576.003| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 2.35 r_work: 0.3010 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3449 Z= 0.171 Angle : 0.486 5.329 4707 Z= 0.251 Chirality : 0.039 0.117 535 Planarity : 0.005 0.041 571 Dihedral : 5.327 56.361 459 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.83 % Allowed : 11.33 % Favored : 85.84 % 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: 1.66 (0.41), residues: 424 helix: 1.67 (0.29), residues: 336 sheet: None (None), residues: 0 loop : -1.08 (0.57), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 485 HIS 0.001 0.000 HIS A 298 PHE 0.017 0.001 PHE A 51 TYR 0.009 0.001 TYR A 306 ARG 0.002 0.000 ARG A 168 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 26 time to evaluate : 0.332 Fit side-chains outliers start: 10 outliers final: 9 residues processed: 33 average time/residue: 0.1687 time to fit residues: 7.1250 Evaluate side-chains 34 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 25 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 256 LYS Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 481 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 17 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 overall best weight: 0.8986 ------------------------------------------------------------------------------- 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 = 0.3549 r_free = 0.3549 target = 0.137594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.096519 restraints weight = 3582.587| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 2.36 r_work: 0.2991 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3449 Z= 0.219 Angle : 0.502 5.226 4707 Z= 0.259 Chirality : 0.040 0.118 535 Planarity : 0.005 0.041 571 Dihedral : 5.317 55.399 459 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.55 % Allowed : 11.33 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.41), residues: 424 helix: 1.64 (0.29), residues: 336 sheet: None (None), residues: 0 loop : -1.10 (0.57), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 339 HIS 0.001 0.001 HIS A 298 PHE 0.020 0.001 PHE A 51 TYR 0.008 0.001 TYR A 119 ARG 0.002 0.000 ARG A 353 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 25 time to evaluate : 0.358 Fit side-chains outliers start: 9 outliers final: 8 residues processed: 31 average time/residue: 0.1774 time to fit residues: 6.9966 Evaluate side-chains 33 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 25 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 256 LYS Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 481 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3514 r_free = 0.3514 target = 0.135787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.095067 restraints weight = 3643.648| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 2.29 r_work: 0.3004 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3449 Z= 0.207 Angle : 0.495 5.153 4707 Z= 0.256 Chirality : 0.040 0.118 535 Planarity : 0.005 0.041 571 Dihedral : 4.672 53.183 458 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.27 % Allowed : 11.33 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.41), residues: 424 helix: 1.67 (0.29), residues: 336 sheet: None (None), residues: 0 loop : -1.09 (0.57), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 339 HIS 0.001 0.000 HIS A 298 PHE 0.018 0.001 PHE A 51 TYR 0.008 0.001 TYR A 306 ARG 0.002 0.000 ARG A 168 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 25 time to evaluate : 0.346 Fit side-chains REVERT: A 175 GLU cc_start: 0.7458 (tt0) cc_final: 0.7216 (tt0) outliers start: 8 outliers final: 8 residues processed: 30 average time/residue: 0.1714 time to fit residues: 6.5161 Evaluate side-chains 33 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 25 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 256 LYS Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 481 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 0 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 1 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3519 r_free = 0.3519 target = 0.136192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.095620 restraints weight = 3572.412| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 2.27 r_work: 0.2911 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6905 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3449 Z= 0.199 Angle : 0.489 5.089 4707 Z= 0.253 Chirality : 0.040 0.118 535 Planarity : 0.005 0.041 571 Dihedral : 4.658 53.612 458 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.55 % Allowed : 11.05 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.41), residues: 424 helix: 1.71 (0.29), residues: 336 sheet: None (None), residues: 0 loop : -1.05 (0.58), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 339 HIS 0.001 0.001 HIS A 298 PHE 0.018 0.001 PHE A 51 TYR 0.008 0.001 TYR A 306 ARG 0.002 0.000 ARG A 168 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 25 time to evaluate : 0.348 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 31 average time/residue: 0.1729 time to fit residues: 6.8358 Evaluate side-chains 32 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 25 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 256 LYS Chi-restraints excluded: chain A residue 481 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 32 optimal weight: 6.9990 chunk 8 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 21 optimal weight: 0.0070 chunk 39 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 6 optimal weight: 0.5980 chunk 37 optimal weight: 0.0060 overall best weight: 0.4014 ------------------------------------------------------------------------------- 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 = 0.3589 r_free = 0.3589 target = 0.141631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.100196 restraints weight = 3595.051| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 2.39 r_work: 0.3040 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3449 Z= 0.144 Angle : 0.463 5.194 4707 Z= 0.240 Chirality : 0.039 0.115 535 Planarity : 0.005 0.041 571 Dihedral : 4.602 54.699 458 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.70 % Allowed : 11.61 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.41), residues: 424 helix: 1.81 (0.29), residues: 337 sheet: None (None), residues: 0 loop : -0.97 (0.59), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 485 HIS 0.001 0.000 HIS A 183 PHE 0.016 0.001 PHE A 51 TYR 0.009 0.001 TYR A 306 ARG 0.002 0.000 ARG A 168 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1787.37 seconds wall clock time: 32 minutes 57.00 seconds (1977.00 seconds total)