Starting phenix.real_space_refine on Mon Jan 13 15:39:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qrv_18627/01_2025/8qrv_18627.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qrv_18627/01_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_18627/01_2025/8qrv_18627.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qrv_18627/01_2025/8qrv_18627.map" model { file = "/net/cci-nas-00/data/ceres_data/8qrv_18627/01_2025/8qrv_18627.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qrv_18627/01_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-5571/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: 2.61, per 1000 atoms: 0.84 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: 0.77 Conformation dependent library (CDL) restraints added in 416.9 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: 0.30 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: 0.84 Time building geometry restraints manager: 0.91 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.300 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:10.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.390 ------------------------------------------------------------------------------- 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 : 0.342 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: 1.1431 time to fit residues: 50.8689 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 : 0.380 ------------------------------------------------------------------------------- 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 = 0.153539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.117916 restraints weight = 3656.069| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 1.88 r_work: 0.3324 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 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 5.316 4313 Z= 0.271 Chirality : 0.039 0.133 541 Planarity : 0.004 0.032 533 Dihedral : 4.309 39.235 442 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 : 0.327 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: 1.0235 time to fit residues: 45.5883 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 : 0.362 ------------------------------------------------------------------------------- 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: 0.9990 chunk 6 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 27 optimal weight: 0.0980 chunk 3 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3897 r_free = 0.3897 target = 0.153888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.118158 restraints weight = 3624.783| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.88 r_work: 0.3327 rms_B_bonded: 2.64 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: 0.8335 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3166 Z= 0.234 Angle : 0.511 6.469 4313 Z= 0.260 Chirality : 0.039 0.172 541 Planarity : 0.004 0.032 533 Dihedral : 3.592 13.346 439 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.54 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: 2.80 (0.43), residues: 413 helix: 2.26 (0.28), residues: 346 sheet: -1.70 (1.29), residues: 20 loop : 0.53 (0.92), 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 0.009 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 : 0.306 Fit side-chains REVERT: B 136 LEU cc_start: 0.8587 (mp) cc_final: 0.8201 (tp) outliers start: 11 outliers final: 4 residues processed: 46 average time/residue: 0.9916 time to fit residues: 47.2861 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 : 0.335 ------------------------------------------------------------------------------- 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: 0.8980 chunk 25 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 28 optimal weight: 0.2980 chunk 16 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3890 r_free = 0.3890 target = 0.153380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.117332 restraints weight = 3702.114| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.91 r_work: 0.3318 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 3166 Z= 0.241 Angle : 0.503 5.272 4313 Z= 0.257 Chirality : 0.039 0.192 541 Planarity : 0.004 0.032 533 Dihedral : 3.568 13.095 439 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.54 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: 2.80 (0.43), residues: 413 helix: 2.27 (0.28), residues: 346 sheet: -1.66 (1.30), residues: 20 loop : 0.41 (0.94), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 275 HIS 0.001 0.000 HIS B 452 PHE 0.009 0.001 PHE B 89 TYR 0.009 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 : 0.337 Fit side-chains REVERT: B 136 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8187 (tp) outliers start: 12 outliers final: 5 residues processed: 43 average time/residue: 0.9932 time to fit residues: 44.3021 Evaluate side-chains 41 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.263 ------------------------------------------------------------------------------- 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 481 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 3 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 31 optimal weight: 0.1980 chunk 0 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 10 optimal weight: 0.0970 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3892 r_free = 0.3892 target = 0.153646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.117685 restraints weight = 3647.688| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 1.90 r_work: 0.3323 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.1772 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 : 0.499 5.315 4313 Z= 0.253 Chirality : 0.039 0.200 541 Planarity : 0.004 0.032 533 Dihedral : 3.508 12.911 439 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 3.96 % Allowed : 13.72 % Favored : 82.32 % 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: 2.30 (0.28), residues: 346 sheet: -1.55 (1.32), residues: 20 loop : 0.30 (0.93), residues: 47 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 0.009 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: 13 poor density : 37 time to evaluate : 0.319 Fit side-chains REVERT: B 136 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8181 (tp) outliers start: 13 outliers final: 4 residues processed: 44 average time/residue: 0.9816 time to fit residues: 44.8350 Evaluate side-chains 38 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 33 time to evaluate : 0.344 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 0.9980 chunk 13 optimal weight: 0.0870 chunk 1 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 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 = 0.3895 r_free = 0.3895 target = 0.153875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.117507 restraints weight = 3704.505| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 1.93 r_work: 0.3300 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1889 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= 0.220 Angle : 0.518 7.607 4313 Z= 0.254 Chirality : 0.038 0.163 541 Planarity : 0.004 0.032 533 Dihedral : 3.498 12.858 439 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.22 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: 2.88 (0.43), residues: 413 helix: 2.37 (0.29), residues: 340 sheet: -1.43 (1.36), residues: 20 loop : 0.24 (0.87), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 275 HIS 0.000 0.000 HIS B 452 PHE 0.009 0.001 PHE B 89 TYR 0.009 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 47 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 37 time to evaluate : 0.306 Fit side-chains REVERT: B 136 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8160 (tp) outliers start: 10 outliers final: 5 residues processed: 42 average time/residue: 1.0176 time to fit residues: 44.3369 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 : 0.337 ------------------------------------------------------------------------------- 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 406 GLN Chi-restraints excluded: chain B residue 481 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: 0.5980 chunk 28 optimal weight: 0.0030 chunk 30 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 35 optimal weight: 0.9980 chunk 31 optimal weight: 0.0060 chunk 29 optimal weight: 0.6980 overall best weight: 0.3806 ------------------------------------------------------------------------------- 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 = 0.3926 r_free = 0.3926 target = 0.156532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.120301 restraints weight = 3608.413| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 1.93 r_work: 0.3358 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3166 Z= 0.168 Angle : 0.487 7.209 4313 Z= 0.238 Chirality : 0.037 0.158 541 Planarity : 0.004 0.031 533 Dihedral : 3.397 12.864 439 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.52 % Allowed : 17.68 % 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: 3.07 (0.43), residues: 413 helix: 2.50 (0.28), residues: 341 sheet: -1.44 (1.38), residues: 20 loop : 0.30 (0.86), 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 0.007 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 43 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.314 Fit side-chains REVERT: B 136 LEU cc_start: 0.8564 (mp) cc_final: 0.8159 (tp) REVERT: B 362 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8374 (tttm) outliers start: 5 outliers final: 2 residues processed: 40 average time/residue: 1.0925 time to fit residues: 45.2313 Evaluate side-chains 39 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 36 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 362 LYS Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 481 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 37 optimal weight: 0.7980 chunk 36 optimal weight: 0.2980 chunk 20 optimal weight: 0.9980 chunk 38 optimal weight: 0.3980 chunk 13 optimal weight: 0.0670 chunk 32 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 overall best weight: 0.3918 ------------------------------------------------------------------------------- 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 = 0.3924 r_free = 0.3924 target = 0.156376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.120228 restraints weight = 3629.604| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 1.92 r_work: 0.3353 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3166 Z= 0.182 Angle : 0.498 6.964 4313 Z= 0.243 Chirality : 0.038 0.167 541 Planarity : 0.004 0.031 533 Dihedral : 3.373 12.599 439 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 3.05 % Allowed : 15.55 % 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: 3.09 (0.43), residues: 413 helix: 2.51 (0.28), residues: 341 sheet: -1.49 (1.37), residues: 20 loop : 0.38 (0.87), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 275 HIS 0.000 0.000 HIS B 452 PHE 0.008 0.001 PHE B 89 TYR 0.009 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 48 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 38 time to evaluate : 0.330 Fit side-chains REVERT: B 136 LEU cc_start: 0.8528 (mp) cc_final: 0.8115 (tp) REVERT: B 209 GLU cc_start: 0.7419 (mt-10) cc_final: 0.6476 (tm-30) REVERT: B 362 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8446 (tttm) REVERT: B 444 GLU cc_start: 0.7052 (OUTLIER) cc_final: 0.6677 (mt-10) outliers start: 10 outliers final: 4 residues processed: 45 average time/residue: 1.1178 time to fit residues: 52.1263 Evaluate side-chains 43 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 37 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 1.9990 chunk 15 optimal weight: 0.9980 chunk 36 optimal weight: 0.3980 chunk 1 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 21 optimal weight: 0.0070 chunk 32 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 10 optimal weight: 0.0970 chunk 7 optimal weight: 0.3980 chunk 22 optimal weight: 1.9990 overall best weight: 0.3596 ------------------------------------------------------------------------------- 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 = 0.3931 r_free = 0.3931 target = 0.157116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.120894 restraints weight = 3651.717| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 1.93 r_work: 0.3357 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2110 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= 0.173 Angle : 0.492 6.839 4313 Z= 0.240 Chirality : 0.038 0.172 541 Planarity : 0.004 0.031 533 Dihedral : 3.342 12.525 439 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 2.74 % Allowed : 15.85 % 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: 3.16 (0.43), residues: 413 helix: 2.56 (0.28), residues: 341 sheet: -1.52 (1.37), residues: 20 loop : 0.41 (0.87), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 275 HIS 0.000 0.000 HIS B 313 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 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 46 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 37 time to evaluate : 0.313 Fit side-chains REVERT: B 136 LEU cc_start: 0.8524 (mp) cc_final: 0.8100 (tp) REVERT: B 209 GLU cc_start: 0.7395 (mt-10) cc_final: 0.6479 (tm-30) REVERT: B 362 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.8388 (tttm) outliers start: 9 outliers final: 5 residues processed: 42 average time/residue: 1.1083 time to fit residues: 48.1412 Evaluate side-chains 42 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.293 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 16 optimal weight: 0.3980 chunk 27 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 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 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 = 0.154126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.117782 restraints weight = 3563.677| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 1.91 r_work: 0.3300 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3166 Z= 0.244 Angle : 0.526 6.392 4313 Z= 0.260 Chirality : 0.039 0.163 541 Planarity : 0.004 0.031 533 Dihedral : 3.450 12.268 439 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 2.13 % Allowed : 17.38 % 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: 2.95 (0.43), residues: 413 helix: 2.41 (0.29), residues: 340 sheet: -1.53 (1.35), residues: 20 loop : 0.41 (0.90), 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 316 PHE 0.009 0.001 PHE B 184 TYR 0.013 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 41 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 34 time to evaluate : 0.333 Fit side-chains REVERT: B 136 LEU cc_start: 0.8473 (mp) cc_final: 0.8077 (tp) REVERT: B 362 LYS cc_start: 0.8718 (OUTLIER) cc_final: 0.8438 (tttm) outliers start: 7 outliers final: 3 residues processed: 38 average time/residue: 1.0226 time to fit residues: 40.3558 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 : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 362 LYS Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 481 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.0886 > 50: distance: 22 - 27: 34.184 distance: 28 - 29: 40.404 distance: 29 - 33: 27.914 distance: 33 - 34: 18.079 distance: 34 - 35: 50.145 distance: 34 - 37: 28.465 distance: 35 - 41: 53.614 distance: 41 - 42: 30.178 distance: 42 - 43: 34.144 distance: 42 - 45: 34.944 distance: 44 - 76: 41.592 distance: 45 - 46: 3.930 distance: 46 - 48: 4.523 distance: 50 - 53: 50.329 distance: 51 - 60: 39.262 distance: 52 - 84: 54.086 distance: 53 - 54: 40.680 distance: 54 - 55: 55.594 distance: 55 - 57: 22.224 distance: 57 - 59: 44.218 distance: 60 - 61: 40.978 distance: 62 - 67: 40.109 distance: 63 - 92: 56.988 distance: 64 - 66: 41.322 distance: 67 - 68: 11.843 distance: 68 - 69: 25.970 distance: 68 - 71: 17.238 distance: 69 - 70: 40.976 distance: 69 - 76: 42.491 distance: 70 - 99: 14.946 distance: 71 - 72: 6.458 distance: 72 - 73: 39.372 distance: 73 - 74: 20.938 distance: 78 - 84: 37.580 distance: 79 - 107: 32.581 distance: 80 - 82: 47.364 distance: 81 - 83: 55.972 distance: 84 - 85: 38.453 distance: 85 - 86: 19.557 distance: 86 - 87: 21.978 distance: 86 - 92: 18.452 distance: 87 - 115: 31.310 distance: 88 - 90: 39.220 distance: 89 - 91: 3.958 distance: 92 - 93: 39.826 distance: 93 - 94: 43.499 distance: 94 - 95: 16.185 distance: 94 - 99: 22.995 distance: 95 - 122: 35.377 distance: 99 - 100: 37.673 distance: 100 - 101: 10.158 distance: 101 - 102: 26.728 distance: 101 - 107: 30.855 distance: 102 - 128: 21.568 distance: 104 - 106: 12.474