Starting phenix.real_space_refine on Wed Mar 5 17:37:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qrv_18627/03_2025/8qrv_18627.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qrv_18627/03_2025/8qrv_18627.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qrv_18627/03_2025/8qrv_18627.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qrv_18627/03_2025/8qrv_18627.map" model { file = "/net/cci-nas-00/data/ceres_data/8qrv_18627/03_2025/8qrv_18627.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qrv_18627/03_2025/8qrv_18627.cif" } resolution = 2.9 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= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 15 5.16 5 Na 1 4.78 5 C 2044 2.51 5 N 509 2.21 5 O 542 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 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: 3111 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 3110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3110 Classifications: {'peptide': 419} Link IDs: {'PTRANS': 16, 'TRANS': 402} Chain breaks: 2 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.74, per 1000 atoms: 0.88 Number of scatterers: 3111 At special positions: 0 Unit cell: (65.408, 62.342, 76.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 15 16.00 Na 1 11.00 O 542 8.00 N 509 7.00 C 2044 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: 0.90 Conformation dependent library (CDL) restraints added in 350.4 milliseconds 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 758 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 2 sheets defined 88.1% alpha, 1.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'B' and resid 49 through 75 removed outlier: 3.639A pdb=" N VAL B 55 " --> pdb=" O ALA B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 103 Proline residue: B 83 - end of helix Proline residue: B 92 - end of helix removed outlier: 3.877A pdb=" N ILE B 103 " --> pdb=" O LEU B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 118 Processing helix chain 'B' and resid 120 through 154 Processing helix chain 'B' and resid 155 through 158 removed outlier: 4.104A pdb=" N ALA B 158 " --> pdb=" O PRO B 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 155 through 158' Processing helix chain 'B' and resid 179 through 192 Processing helix chain 'B' and resid 195 through 200 Processing helix chain 'B' and resid 230 through 249 removed outlier: 3.723A pdb=" N GLY B 249 " --> pdb=" O LEU B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 292 removed outlier: 3.510A pdb=" N GLU B 253 " --> pdb=" O GLY B 249 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LEU B 254 " --> pdb=" O PRO B 250 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N LEU B 255 " --> pdb=" O GLU B 251 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N TRP B 275 " --> pdb=" O SER B 271 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR B 276 " --> pdb=" O TRP B 272 " (cutoff:3.500A) Proline residue: B 278 - end of helix removed outlier: 3.753A pdb=" N PHE B 283 " --> pdb=" O VAL B 279 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LYS B 288 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N MET B 292 " --> pdb=" O LYS B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 319 removed outlier: 6.401A pdb=" N LYS B 304 " --> pdb=" O ALA B 300 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N TYR B 305 " --> pdb=" O ARG B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 329 Processing helix chain 'B' and resid 332 through 339 removed outlier: 3.517A pdb=" N PHE B 336 " --> pdb=" O ASN B 332 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY B 339 " --> pdb=" O ARG B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 351 Processing helix chain 'B' and resid 352 through 367 removed outlier: 3.506A pdb=" N THR B 356 " --> pdb=" O SER B 352 " (cutoff:3.500A) Proline residue: B 358 - end of helix Processing helix chain 'B' and resid 371 through 386 Proline residue: B 380 - end of helix removed outlier: 3.766A pdb=" N THR B 384 " --> pdb=" O PRO B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 405 Processing helix chain 'B' and resid 410 through 426 removed outlier: 3.903A pdb=" N VAL B 426 " --> pdb=" O THR B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 446 Processing helix chain 'B' and resid 452 through 458 removed outlier: 3.572A pdb=" N ILE B 456 " --> pdb=" O HIS B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 487 removed outlier: 3.907A pdb=" N ARG B 465 " --> pdb=" O TRP B 461 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 202 through 205 Processing sheet with id=AA2, first strand: chain 'B' and resid 208 through 209 260 hydrogen bonds defined for protein. 774 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: 0.78 Time building geometry restraints manager: 1.04 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: 985 1.34 - 1.46: 475 1.46 - 1.57: 1682 1.57 - 1.69: 0 1.69 - 1.80: 24 Bond restraints: 3166 Sorted by residual: bond pdb=" CG1 ILE B 417 " pdb=" CD1 ILE B 417 " ideal model delta sigma weight residual 1.513 1.468 0.045 3.90e-02 6.57e+02 1.32e+00 bond pdb=" CB ILE B 442 " pdb=" CG2 ILE B 442 " ideal model delta sigma weight residual 1.521 1.489 0.032 3.30e-02 9.18e+02 9.64e-01 bond pdb=" CG LYS B 288 " pdb=" CD LYS B 288 " ideal model delta sigma weight residual 1.520 1.544 -0.024 3.00e-02 1.11e+03 6.42e-01 bond pdb=" CB ILE B 417 " pdb=" CG2 ILE B 417 " ideal model delta sigma weight residual 1.521 1.495 0.026 3.30e-02 9.18e+02 6.07e-01 bond pdb=" CG1 ILE B 441 " pdb=" CD1 ILE B 441 " ideal model delta sigma weight residual 1.513 1.483 0.030 3.90e-02 6.57e+02 5.79e-01 ... (remaining 3161 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 4257 1.96 - 3.93: 40 3.93 - 5.89: 15 5.89 - 7.85: 0 7.85 - 9.82: 1 Bond angle restraints: 4313 Sorted by residual: angle pdb=" C LEU B 284 " pdb=" N VAL B 285 " pdb=" CA VAL B 285 " ideal model delta sigma weight residual 122.35 117.81 4.54 1.18e+00 7.18e-01 1.48e+01 angle pdb=" CA LEU B 455 " pdb=" CB LEU B 455 " pdb=" CG LEU B 455 " ideal model delta sigma weight residual 116.30 126.12 -9.82 3.50e+00 8.16e-02 7.87e+00 angle pdb=" N ASN B 447 " pdb=" CA ASN B 447 " pdb=" C ASN B 447 " ideal model delta sigma weight residual 108.63 112.35 -3.72 1.60e+00 3.91e-01 5.42e+00 angle pdb=" CA VAL B 459 " pdb=" CB VAL B 459 " pdb=" CG2 VAL B 459 " ideal model delta sigma weight residual 110.40 113.98 -3.58 1.70e+00 3.46e-01 4.43e+00 angle pdb=" N PHE B 91 " pdb=" CA PHE B 91 " pdb=" C PHE B 91 " ideal model delta sigma weight residual 113.45 116.28 -2.83 1.39e+00 5.18e-01 4.14e+00 ... (remaining 4308 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 1676 17.75 - 35.50: 134 35.50 - 53.25: 41 53.25 - 71.01: 4 71.01 - 88.76: 2 Dihedral angle restraints: 1857 sinusoidal: 676 harmonic: 1181 Sorted by residual: dihedral pdb=" CB GLU B 366 " pdb=" CG GLU B 366 " pdb=" CD GLU B 366 " pdb=" OE1 GLU B 366 " ideal model delta sinusoidal sigma weight residual 0.00 88.76 -88.76 1 3.00e+01 1.11e-03 1.04e+01 dihedral pdb=" CG ARG B 101 " pdb=" CD ARG B 101 " pdb=" NE ARG B 101 " pdb=" CZ ARG B 101 " ideal model delta sinusoidal sigma weight residual -180.00 -135.85 -44.15 2 1.50e+01 4.44e-03 1.03e+01 dihedral pdb=" CA GLU B 225 " pdb=" CB GLU B 225 " pdb=" CG GLU B 225 " pdb=" CD GLU B 225 " ideal model delta sinusoidal sigma weight residual -180.00 -122.41 -57.59 3 1.50e+01 4.44e-03 9.44e+00 ... (remaining 1854 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 452 0.056 - 0.111: 86 0.111 - 0.167: 2 0.167 - 0.222: 0 0.222 - 0.278: 1 Chirality restraints: 541 Sorted by residual: chirality pdb=" CB VAL B 459 " pdb=" CA VAL B 459 " pdb=" CG1 VAL B 459 " pdb=" CG2 VAL B 459 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CA PHE B 91 " pdb=" N PHE B 91 " pdb=" C PHE B 91 " pdb=" CB PHE B 91 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.80e-01 chirality pdb=" CA PRO B 322 " pdb=" N PRO B 322 " pdb=" C PRO B 322 " pdb=" CB PRO B 322 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.11 2.00e-01 2.50e+01 3.23e-01 ... (remaining 538 not shown) Planarity restraints: 533 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 258 " -0.010 2.00e-02 2.50e+03 1.93e-02 3.73e+00 pdb=" C PHE B 258 " 0.033 2.00e-02 2.50e+03 pdb=" O PHE B 258 " -0.013 2.00e-02 2.50e+03 pdb=" N PHE B 259 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 256 " 0.008 2.00e-02 2.50e+03 1.60e-02 2.57e+00 pdb=" C ILE B 256 " -0.028 2.00e-02 2.50e+03 pdb=" O ILE B 256 " 0.010 2.00e-02 2.50e+03 pdb=" N ARG B 257 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 257 " 0.008 2.00e-02 2.50e+03 1.53e-02 2.35e+00 pdb=" C ARG B 257 " -0.027 2.00e-02 2.50e+03 pdb=" O ARG B 257 " 0.010 2.00e-02 2.50e+03 pdb=" N PHE B 258 " 0.009 2.00e-02 2.50e+03 ... (remaining 530 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.88: 1187 2.88 - 3.38: 3314 3.38 - 3.89: 5192 3.89 - 4.39: 5622 4.39 - 4.90: 9812 Nonbonded interactions: 25127 Sorted by model distance: nonbonded pdb=" O ASN B 386 " pdb="NA NA B 601 " model vdw 2.373 2.470 nonbonded pdb=" O GLY B 434 " pdb=" OG1 THR B 438 " model vdw 2.416 3.040 nonbonded pdb=" O THR B 350 " pdb=" OG SER B 351 " model vdw 2.428 3.040 nonbonded pdb=" O THR B 416 " pdb=" OG1 THR B 420 " model vdw 2.431 3.040 nonbonded pdb=" OE1 GLU B 179 " pdb=" OH TYR B 208 " model vdw 2.439 3.040 ... (remaining 25122 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: 1.130 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.310 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:11.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 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 : 0.004 0.045 3166 Z= 0.239 Angle : 0.570 9.816 4313 Z= 0.296 Chirality : 0.040 0.278 541 Planarity : 0.005 0.030 533 Dihedral : 14.311 88.757 1099 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.61 % Allowed : 15.55 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.43), residues: 413 helix: 1.72 (0.29), residues: 340 sheet: -1.51 (1.25), residues: 20 loop : 0.67 (0.87), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 275 HIS 0.001 0.001 HIS B 313 PHE 0.009 0.001 PHE B 184 TYR 0.006 0.001 TYR B 334 ARG 0.001 0.000 ARG B 465 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 41 time to evaluate : 0.372 Fit side-chains REVERT: B 136 LEU cc_start: 0.8492 (mp) cc_final: 0.8004 (tp) outliers start: 2 outliers final: 1 residues processed: 43 average time/residue: 1.2018 time to fit residues: 53.4266 Evaluate side-chains 38 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 37 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 406 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 154 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.153538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.117916 restraints weight = 3656.082| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 1.88 r_work: 0.3326 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3166 Z= 0.261 Angle : 0.532 5.313 4313 Z= 0.271 Chirality : 0.039 0.133 541 Planarity : 0.004 0.032 533 Dihedral : 4.309 39.234 442 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 3.05 % Allowed : 15.24 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.66 (0.43), residues: 413 helix: 2.22 (0.29), residues: 343 sheet: -1.66 (1.28), residues: 20 loop : 0.09 (0.91), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 275 HIS 0.002 0.001 HIS B 313 PHE 0.010 0.001 PHE B 184 TYR 0.009 0.001 TYR B 276 ARG 0.002 0.000 ARG B 301 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 36 time to evaluate : 0.320 Fit side-chains REVERT: B 136 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8217 (tp) outliers start: 10 outliers final: 3 residues processed: 43 average time/residue: 1.0404 time to fit residues: 46.3653 Evaluate side-chains 37 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 481 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 chunk 27 optimal weight: 0.0980 chunk 3 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 154 GLN ** B 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 484 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.154357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.118539 restraints weight = 3624.082| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 1.89 r_work: 0.3330 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3166 Z= 0.225 Angle : 0.507 6.502 4313 Z= 0.257 Chirality : 0.038 0.171 541 Planarity : 0.004 0.032 533 Dihedral : 3.576 13.401 439 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 3.35 % Allowed : 14.94 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.83 (0.43), residues: 413 helix: 2.28 (0.28), residues: 346 sheet: -1.67 (1.30), residues: 20 loop : 0.51 (0.91), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 275 HIS 0.001 0.001 HIS B 452 PHE 0.009 0.001 PHE B 89 TYR 0.008 0.001 TYR B 334 ARG 0.002 0.000 ARG B 301 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 38 time to evaluate : 0.328 Fit side-chains REVERT: B 136 LEU cc_start: 0.8591 (mp) cc_final: 0.8192 (tp) outliers start: 11 outliers final: 4 residues processed: 46 average time/residue: 0.9935 time to fit residues: 47.4221 Evaluate side-chains 40 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 308 CYS Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 481 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 9 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 154 GLN B 263 ASN B 403 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.153175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.117126 restraints weight = 3701.855| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 1.90 r_work: 0.3314 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 3166 Z= 0.251 Angle : 0.507 5.286 4313 Z= 0.259 Chirality : 0.039 0.191 541 Planarity : 0.004 0.033 533 Dihedral : 3.579 13.111 439 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 3.66 % Allowed : 14.94 % Favored : 81.40 % 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: 2.79 (0.43), residues: 413 helix: 2.28 (0.28), residues: 345 sheet: -1.59 (1.31), residues: 20 loop : 0.31 (0.93), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 275 HIS 0.002 0.001 HIS B 452 PHE 0.009 0.001 PHE B 89 TYR 0.010 0.001 TYR B 334 ARG 0.002 0.000 ARG B 301 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 37 time to evaluate : 0.353 Fit side-chains REVERT: B 136 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8180 (tp) REVERT: B 475 ASP cc_start: 0.7498 (m-30) cc_final: 0.7261 (m-30) outliers start: 12 outliers final: 4 residues processed: 44 average time/residue: 0.9325 time to fit residues: 42.6969 Evaluate side-chains 40 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 481 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 3 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 15 optimal weight: 0.0970 chunk 2 optimal weight: 0.9990 chunk 31 optimal weight: 0.3980 chunk 0 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 10 optimal weight: 0.3980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 154 GLN B 403 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.154501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.118488 restraints weight = 3641.192| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 1.91 r_work: 0.3333 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3166 Z= 0.195 Angle : 0.507 7.500 4313 Z= 0.251 Chirality : 0.039 0.199 541 Planarity : 0.004 0.031 533 Dihedral : 3.483 12.912 439 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 3.05 % Allowed : 14.94 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.92 (0.43), residues: 413 helix: 2.39 (0.28), residues: 341 sheet: -1.52 (1.34), residues: 20 loop : 0.32 (0.86), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 275 HIS 0.001 0.000 HIS B 452 PHE 0.009 0.001 PHE B 89 TYR 0.008 0.001 TYR B 334 ARG 0.002 0.000 ARG B 301 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.355 Fit side-chains REVERT: B 136 LEU cc_start: 0.8574 (mp) cc_final: 0.8184 (tp) outliers start: 10 outliers final: 4 residues processed: 46 average time/residue: 0.9429 time to fit residues: 45.1044 Evaluate side-chains 38 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 481 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 0.7980 chunk 13 optimal weight: 0.0270 chunk 1 optimal weight: 2.9990 chunk 10 optimal weight: 0.0970 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 overall best weight: 0.3836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 154 GLN B 403 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.156360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.119979 restraints weight = 3698.766| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 1.94 r_work: 0.3352 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3166 Z= 0.168 Angle : 0.492 7.011 4313 Z= 0.240 Chirality : 0.038 0.157 541 Planarity : 0.004 0.031 533 Dihedral : 3.404 12.700 439 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 2.44 % Allowed : 16.77 % Favored : 80.79 % 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: 3.05 (0.43), residues: 413 helix: 2.49 (0.28), residues: 341 sheet: -1.44 (1.37), residues: 20 loop : 0.27 (0.85), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 275 HIS 0.001 0.000 HIS B 452 PHE 0.008 0.001 PHE B 89 TYR 0.008 0.001 TYR B 334 ARG 0.002 0.000 ARG B 301 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.342 Fit side-chains REVERT: B 136 LEU cc_start: 0.8557 (mp) cc_final: 0.8149 (tp) outliers start: 8 outliers final: 5 residues processed: 42 average time/residue: 1.0433 time to fit residues: 45.4175 Evaluate side-chains 40 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 308 CYS Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 482 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 29 optimal weight: 0.0870 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 154 GLN B 403 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.154401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.118090 restraints weight = 3599.117| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.91 r_work: 0.3325 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3166 Z= 0.214 Angle : 0.504 6.168 4313 Z= 0.250 Chirality : 0.038 0.167 541 Planarity : 0.004 0.031 533 Dihedral : 3.439 12.826 439 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 3.35 % Allowed : 14.94 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.96 (0.43), residues: 413 helix: 2.40 (0.28), residues: 341 sheet: -1.38 (1.38), residues: 20 loop : 0.44 (0.90), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 275 HIS 0.001 0.000 HIS B 452 PHE 0.009 0.001 PHE B 89 TYR 0.011 0.001 TYR B 334 ARG 0.002 0.000 ARG B 301 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 34 time to evaluate : 0.360 Fit side-chains REVERT: B 136 LEU cc_start: 0.8568 (mp) cc_final: 0.8178 (tp) REVERT: B 362 LYS cc_start: 0.8709 (OUTLIER) cc_final: 0.8454 (tttm) outliers start: 11 outliers final: 5 residues processed: 42 average time/residue: 0.9922 time to fit residues: 43.3202 Evaluate side-chains 39 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 308 CYS Chi-restraints excluded: chain B residue 362 LYS Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 482 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 37 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 38 optimal weight: 0.0000 chunk 13 optimal weight: 0.8980 chunk 32 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 154 GLN B 403 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.154340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.118059 restraints weight = 3635.758| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 1.92 r_work: 0.3325 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 3166 Z= 0.233 Angle : 0.513 5.906 4313 Z= 0.254 Chirality : 0.039 0.165 541 Planarity : 0.004 0.031 533 Dihedral : 3.475 12.568 439 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 3.05 % Allowed : 16.16 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.91 (0.43), residues: 413 helix: 2.36 (0.29), residues: 341 sheet: -1.39 (1.38), residues: 20 loop : 0.46 (0.89), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 275 HIS 0.001 0.000 HIS B 452 PHE 0.009 0.001 PHE B 89 TYR 0.011 0.001 TYR B 334 ARG 0.002 0.000 ARG B 301 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 33 time to evaluate : 0.316 Fit side-chains REVERT: B 136 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8076 (tp) REVERT: B 444 GLU cc_start: 0.7120 (OUTLIER) cc_final: 0.6705 (mt-10) outliers start: 10 outliers final: 6 residues processed: 38 average time/residue: 1.0855 time to fit residues: 42.7679 Evaluate side-chains 41 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 33 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 308 CYS Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 444 GLU Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 482 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 14 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 36 optimal weight: 0.0970 chunk 1 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 154 GLN B 403 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.153441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.117036 restraints weight = 3663.821| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 1.94 r_work: 0.3312 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3166 Z= 0.246 Angle : 0.522 5.798 4313 Z= 0.259 Chirality : 0.039 0.168 541 Planarity : 0.004 0.031 533 Dihedral : 3.503 12.736 439 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 3.05 % Allowed : 16.46 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.85 (0.43), residues: 413 helix: 2.33 (0.29), residues: 340 sheet: -1.42 (1.38), residues: 20 loop : 0.38 (0.89), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 275 HIS 0.001 0.000 HIS B 452 PHE 0.009 0.001 PHE B 184 TYR 0.011 0.001 TYR B 334 ARG 0.002 0.000 ARG B 301 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 32 time to evaluate : 0.342 Fit side-chains REVERT: B 136 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8083 (tp) REVERT: B 362 LYS cc_start: 0.8684 (OUTLIER) cc_final: 0.8422 (tttm) REVERT: B 444 GLU cc_start: 0.7158 (OUTLIER) cc_final: 0.6758 (mt-10) outliers start: 10 outliers final: 5 residues processed: 37 average time/residue: 1.0871 time to fit residues: 41.7031 Evaluate side-chains 40 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 32 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 362 LYS Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 444 GLU Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 482 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 chunk 0 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 27 optimal weight: 0.5980 chunk 38 optimal weight: 0.0970 chunk 18 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 154 GLN B 403 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.154951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.118850 restraints weight = 3559.401| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 1.90 r_work: 0.3335 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3166 Z= 0.206 Angle : 0.503 5.790 4313 Z= 0.249 Chirality : 0.038 0.170 541 Planarity : 0.004 0.031 533 Dihedral : 3.451 12.991 439 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 2.44 % Allowed : 16.46 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.91 (0.43), residues: 413 helix: 2.36 (0.29), residues: 341 sheet: -1.50 (1.37), residues: 20 loop : 0.47 (0.90), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 275 HIS 0.001 0.000 HIS B 316 PHE 0.009 0.001 PHE B 89 TYR 0.010 0.001 TYR B 334 ARG 0.002 0.000 ARG B 301 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 0.355 Fit side-chains REVERT: B 136 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8141 (tp) REVERT: B 444 GLU cc_start: 0.7134 (OUTLIER) cc_final: 0.6735 (mt-10) outliers start: 8 outliers final: 5 residues processed: 39 average time/residue: 1.1096 time to fit residues: 44.7831 Evaluate side-chains 41 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 34 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 444 GLU Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 482 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 12 optimal weight: 0.6980 chunk 5 optimal weight: 0.0870 chunk 34 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 154 GLN B 403 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.153996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.117756 restraints weight = 3622.402| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 1.91 r_work: 0.3318 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3166 Z= 0.230 Angle : 0.513 5.534 4313 Z= 0.255 Chirality : 0.039 0.170 541 Planarity : 0.004 0.031 533 Dihedral : 3.475 12.947 439 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 2.74 % Allowed : 16.77 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.86 (0.43), residues: 413 helix: 2.33 (0.29), residues: 340 sheet: -1.49 (1.37), residues: 20 loop : 0.43 (0.90), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 275 HIS 0.001 0.000 HIS B 452 PHE 0.009 0.001 PHE B 184 TYR 0.011 0.001 TYR B 334 ARG 0.002 0.000 ARG B 301 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2436.10 seconds wall clock time: 42 minutes 16.91 seconds (2536.91 seconds total)