Starting phenix.real_space_refine on Wed Mar 5 19:05:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ayb_43984/03_2025/9ayb_43984_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ayb_43984/03_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_43984/03_2025/9ayb_43984.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ayb_43984/03_2025/9ayb_43984.map" model { file = "/net/cci-nas-00/data/ceres_data/9ayb_43984/03_2025/9ayb_43984_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ayb_43984/03_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-5624/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: 2.95, per 1000 atoms: 0.88 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: 0.83 Conformation dependent library (CDL) restraints added in 410.3 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: 0.33 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: 0.90 Time building geometry restraints manager: 1.00 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: 3.080 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: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.290 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.570 ------------------------------------------------------------------------------- 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 : 0.323 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: 0.1654 time to fit residues: 7.7260 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 : 0.314 ------------------------------------------------------------------------------- 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 = 0.138811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.096446 restraints weight = 3624.367| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 2.41 r_work: 0.3007 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 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 4.911 4707 Z= 0.278 Chirality : 0.042 0.193 535 Planarity : 0.005 0.041 571 Dihedral : 5.342 49.449 459 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 : 0.322 Fit side-chains REVERT: A 175 GLU cc_start: 0.7891 (tt0) cc_final: 0.7637 (tt0) outliers start: 11 outliers final: 6 residues processed: 37 average time/residue: 0.1711 time to fit residues: 7.8976 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 : 0.332 ------------------------------------------------------------------------------- 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: 2.9990 chunk 40 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 21 optimal weight: 0.0970 chunk 1 optimal weight: 0.9980 overall best weight: 0.6778 ------------------------------------------------------------------------------- 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 = 0.3527 r_free = 0.3527 target = 0.136996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.095732 restraints weight = 3581.995| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 2.26 r_work: 0.3010 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.1124 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= 0.186 Angle : 0.497 4.910 4707 Z= 0.262 Chirality : 0.040 0.125 535 Planarity : 0.005 0.043 571 Dihedral : 5.331 52.104 459 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 2.27 % Allowed : 9.07 % 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: 1.54 (0.41), residues: 424 helix: 1.50 (0.29), residues: 337 sheet: None (None), residues: 0 loop : -0.77 (0.60), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 189 HIS 0.001 0.001 HIS A 255 PHE 0.017 0.001 PHE A 51 TYR 0.008 0.001 TYR A 306 ARG 0.002 0.000 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 : 0.344 Fit side-chains REVERT: A 175 GLU cc_start: 0.7777 (tt0) cc_final: 0.7527 (tt0) outliers start: 8 outliers final: 5 residues processed: 34 average time/residue: 0.1559 time to fit residues: 6.8407 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 : 0.330 ------------------------------------------------------------------------------- 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: 0.7980 chunk 25 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 13 optimal weight: 0.0970 chunk 36 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 21 optimal weight: 0.0870 chunk 24 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 overall best weight: 0.4356 ------------------------------------------------------------------------------- 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 = 0.3586 r_free = 0.3586 target = 0.141063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.099284 restraints weight = 3611.837| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 2.37 r_work: 0.3017 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3449 Z= 0.150 Angle : 0.473 5.009 4707 Z= 0.248 Chirality : 0.039 0.116 535 Planarity : 0.005 0.042 571 Dihedral : 5.205 52.111 459 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.98 % Allowed : 10.76 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.41), residues: 424 helix: 1.64 (0.29), residues: 337 sheet: None (None), residues: 0 loop : -0.89 (0.57), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 485 HIS 0.000 0.000 HIS A 414 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 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 33 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 26 time to evaluate : 0.336 Fit side-chains REVERT: A 175 GLU cc_start: 0.7839 (tt0) cc_final: 0.7607 (tt0) REVERT: A 257 ARG cc_start: 0.8263 (mtm110) cc_final: 0.7957 (mtm110) outliers start: 7 outliers final: 4 residues processed: 31 average time/residue: 0.1644 time to fit residues: 6.5074 Evaluate side-chains 31 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 27 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 183 HIS 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: 0.0570 chunk 36 optimal weight: 0.6980 chunk 32 optimal weight: 6.9990 chunk 0 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 21 optimal weight: 5.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- 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 = 0.3536 r_free = 0.3536 target = 0.137895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.096624 restraints weight = 3637.796| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.32 r_work: 0.3026 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3449 Z= 0.176 Angle : 0.479 5.015 4707 Z= 0.251 Chirality : 0.039 0.118 535 Planarity : 0.005 0.042 571 Dihedral : 5.165 52.875 459 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 3.27 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: 1.69 (0.41), residues: 424 helix: 1.66 (0.29), residues: 337 sheet: None (None), residues: 0 loop : -0.94 (0.57), 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 0.009 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 38 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 28 time to evaluate : 0.350 Fit side-chains REVERT: A 175 GLU cc_start: 0.7876 (tt0) cc_final: 0.7669 (tt0) outliers start: 10 outliers final: 7 residues processed: 35 average time/residue: 0.1571 time to fit residues: 7.0452 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 : 0.297 ------------------------------------------------------------------------------- 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: 0.9990 chunk 4 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 37 optimal weight: 0.2980 chunk 30 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.139567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.098130 restraints weight = 3635.722| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 2.38 r_work: 0.3004 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3449 Z= 0.173 Angle : 0.478 5.054 4707 Z= 0.248 Chirality : 0.039 0.120 535 Planarity : 0.005 0.042 571 Dihedral : 5.153 52.517 459 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.83 % Allowed : 10.20 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.41), residues: 424 helix: 1.69 (0.29), residues: 337 sheet: None (None), residues: 0 loop : -0.90 (0.58), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 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 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 38 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 28 time to evaluate : 0.291 Fit side-chains outliers start: 10 outliers final: 7 residues processed: 35 average time/residue: 0.1563 time to fit residues: 7.0324 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 : 0.332 ------------------------------------------------------------------------------- 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 481 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 0.3980 chunk 11 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 2 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.137829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.097073 restraints weight = 3595.124| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.27 r_work: 0.3036 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3449 Z= 0.179 Angle : 0.477 5.045 4707 Z= 0.248 Chirality : 0.039 0.117 535 Planarity : 0.005 0.041 571 Dihedral : 5.288 56.301 459 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 3.68 % Allowed : 10.76 % Favored : 85.55 % 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: 1.73 (0.41), residues: 424 helix: 1.68 (0.29), residues: 337 sheet: None (None), residues: 0 loop : -0.94 (0.58), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 339 HIS 0.001 0.000 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 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 40 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 27 time to evaluate : 0.374 Fit side-chains outliers start: 13 outliers final: 9 residues processed: 36 average time/residue: 0.1526 time to fit residues: 7.0911 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 : 0.305 ------------------------------------------------------------------------------- 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 476 LEU 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: 0.6980 chunk 36 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 23 optimal weight: 0.6980 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 = 0.3523 r_free = 0.3523 target = 0.136755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.095995 restraints weight = 3598.726| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.28 r_work: 0.3025 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.1703 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= 0.202 Angle : 0.492 5.055 4707 Z= 0.253 Chirality : 0.040 0.118 535 Planarity : 0.005 0.041 571 Dihedral : 5.309 56.201 459 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 3.72 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: 1.72 (0.41), residues: 424 helix: 1.68 (0.29), residues: 337 sheet: None (None), residues: 0 loop : -0.95 (0.58), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 339 HIS 0.002 0.001 HIS A 183 PHE 0.019 0.001 PHE A 51 TYR 0.008 0.001 TYR A 119 ARG 0.002 0.000 ARG A 168 *********************** 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 35 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 26 time to evaluate : 0.362 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 33 average time/residue: 0.1675 time to fit residues: 7.1240 Evaluate side-chains 33 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 26 time to evaluate : 0.312 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 4 optimal weight: 0.2980 chunk 28 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.137151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.096430 restraints weight = 3634.903| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 2.30 r_work: 0.3014 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3449 Z= 0.188 Angle : 0.486 5.048 4707 Z= 0.249 Chirality : 0.039 0.117 535 Planarity : 0.005 0.041 571 Dihedral : 4.614 53.318 458 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 3.87 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: 1.82 (0.41), residues: 424 helix: 1.75 (0.29), residues: 337 sheet: None (None), residues: 0 loop : -0.91 (0.59), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 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 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 35 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 26 time to evaluate : 0.443 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 32 average time/residue: 0.1655 time to fit residues: 6.8502 Evaluate side-chains 33 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 26 time to evaluate : 0.328 ------------------------------------------------------------------------------- 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 0 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 13 optimal weight: 0.0170 chunk 20 optimal weight: 0.6980 overall best weight: 0.5418 ------------------------------------------------------------------------------- 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 = 0.3587 r_free = 0.3587 target = 0.141504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.100487 restraints weight = 3525.617| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 2.36 r_work: 0.3047 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3449 Z= 0.157 Angle : 0.473 5.454 4707 Z= 0.242 Chirality : 0.039 0.116 535 Planarity : 0.005 0.041 571 Dihedral : 4.594 55.316 458 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.70 % Allowed : 12.46 % 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: 1.95 (0.41), residues: 424 helix: 1.86 (0.29), residues: 336 sheet: None (None), residues: 0 loop : -0.89 (0.59), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 240 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 0.002 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 31 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 25 time to evaluate : 0.308 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 29 average time/residue: 0.1654 time to fit residues: 6.1074 Evaluate side-chains 30 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 24 time to evaluate : 0.307 ------------------------------------------------------------------------------- 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 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: 5.9990 chunk 8 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 37 optimal weight: 0.1980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.3571 r_free = 0.3571 target = 0.139771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.098588 restraints weight = 3633.117| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 2.39 r_work: 0.3020 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.1864 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= 0.194 Angle : 0.492 6.663 4707 Z= 0.250 Chirality : 0.040 0.117 535 Planarity : 0.005 0.041 571 Dihedral : 4.590 54.566 458 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.98 % Allowed : 12.18 % 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: 1.88 (0.41), residues: 424 helix: 1.79 (0.29), residues: 337 sheet: None (None), residues: 0 loop : -0.87 (0.59), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 339 HIS 0.002 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 353 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1761.15 seconds wall clock time: 31 minutes 13.46 seconds (1873.46 seconds total)