Starting phenix.real_space_refine on Wed Jul 1 21:44:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qrv_18627/07_2026/8qrv_18627.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qrv_18627/07_2026/8qrv_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_18627/07_2026/8qrv_18627.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qrv_18627/07_2026/8qrv_18627.map" model { file = "/net/cci-nas-00/data/ceres_data/8qrv_18627/07_2026/8qrv_18627.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qrv_18627/07_2026/8qrv_18627.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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, 0 Ad-hoc single atom residues: {' NA': 1} Chain breaks: 1 Time building chain proxies: 0.81, per 1000 atoms: 0.26 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: 0.26 Conformation dependent library (CDL) restraints added in 119.0 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: 0.05 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: 0.37 Time building geometry restraints manager: 0.35 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 3.210 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: 1.310 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: 0.040 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 4.270 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 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= 0.160 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.001 0.000 ARG B 465 TYR 0.006 0.001 TYR B 334 PHE 0.009 0.001 PHE B 184 TRP 0.005 0.001 TRP B 275 HIS 0.001 0.001 HIS B 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 ( 3166) covalent geometry : angle 0.56956 / 0.30 ( 4313) hydrogen bonds : bond 0.13617 / 9.77 ( 260) hydrogen bonds : angle 6.53886 / 4.78 ( 774) *********************** 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 : 0.066 Fit side-chains REVERT: B 136 LEU cc_start: 0.8491 (mp) cc_final: 0.8004 (tp) outliers start: 2 outliers final: 1 residues processed: 43 average time/residue: 0.4121 time to fit residues: 18.2142 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 : 0.067 ------------------------------------------------------------------------------- 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 24 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 154 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.152746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.117088 restraints weight = 3715.469| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 1.90 r_work: 0.3311 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.1282 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= 0.182 Angle : 0.544 5.222 4313 Z= 0.279 Chirality : 0.040 0.136 541 Planarity : 0.004 0.033 533 Dihedral : 4.365 39.449 442 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.59 (0.43), residues: 413 helix: 2.17 (0.29), residues: 343 sheet: -1.72 (1.27), residues: 20 loop : 0.14 (0.92), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 301 TYR 0.010 0.001 TYR B 276 PHE 0.011 0.002 PHE B 184 TRP 0.007 0.001 TRP B 275 HIS 0.002 0.001 HIS B 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.18 ( 3166) covalent geometry : angle 0.54384 / 0.28 ( 4313) hydrogen bonds : bond 0.05178 / 3.65 ( 260) hydrogen bonds : angle 4.79482 / 3.51 ( 774) *********************** 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: 12 poor density : 34 time to evaluate : 0.077 Fit side-chains REVERT: B 136 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8200 (tp) outliers start: 12 outliers final: 4 residues processed: 43 average time/residue: 0.4920 time to fit residues: 21.7983 Evaluate side-chains 37 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.110 ------------------------------------------------------------------------------- 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 466 SER 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 10 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 13 optimal weight: 0.4980 chunk 25 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3894 r_free = 0.3894 target = 0.153680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.117821 restraints weight = 3654.679| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 1.90 r_work: 0.3321 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3166 Z= 0.154 Angle : 0.513 6.503 4313 Z= 0.261 Chirality : 0.039 0.178 541 Planarity : 0.004 0.032 533 Dihedral : 3.612 13.511 439 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 2.74 % Allowed : 15.55 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.73 (0.43), residues: 413 helix: 2.19 (0.28), residues: 347 sheet: -1.68 (1.29), residues: 20 loop : 0.62 (0.94), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 301 TYR 0.008 0.001 TYR B 334 PHE 0.009 0.001 PHE B 89 TRP 0.007 0.001 TRP B 275 HIS 0.001 0.000 HIS B 452 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.15 ( 3166) covalent geometry : angle 0.51313 / 0.26 ( 4313) hydrogen bonds : bond 0.04715 / 3.32 ( 260) hydrogen bonds : angle 4.55215 / 3.34 ( 774) *********************** 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 46 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 37 time to evaluate : 0.112 Fit side-chains REVERT: B 136 LEU cc_start: 0.8562 (mp) cc_final: 0.8175 (tp) outliers start: 9 outliers final: 4 residues processed: 44 average time/residue: 0.4866 time to fit residues: 22.1268 Evaluate side-chains 39 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.108 ------------------------------------------------------------------------------- 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 25 optimal weight: 0.9990 chunk 22 optimal weight: 0.3980 chunk 27 optimal weight: 0.0980 chunk 16 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 31 optimal weight: 0.2980 chunk 7 optimal weight: 0.8980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 154 GLN ** B 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.155847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.119836 restraints weight = 3624.394| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 1.91 r_work: 0.3351 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3166 Z= 0.127 Angle : 0.480 5.233 4313 Z= 0.243 Chirality : 0.038 0.189 541 Planarity : 0.004 0.031 533 Dihedral : 3.497 13.467 439 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.54 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.92 (0.43), residues: 413 helix: 2.36 (0.28), residues: 346 sheet: -1.64 (1.31), residues: 20 loop : 0.36 (0.91), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 301 TYR 0.007 0.001 TYR B 334 PHE 0.009 0.001 PHE B 89 TRP 0.006 0.001 TRP B 275 HIS 0.001 0.000 HIS B 452 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 ( 3166) covalent geometry : angle 0.47969 / 0.24 ( 4313) hydrogen bonds : bond 0.04126 / 2.90 ( 260) hydrogen bonds : angle 4.36200 / 3.21 ( 774) *********************** 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 53 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.117 Fit side-chains REVERT: B 136 LEU cc_start: 0.8595 (mp) cc_final: 0.8210 (tp) outliers start: 10 outliers final: 4 residues processed: 49 average time/residue: 0.4065 time to fit residues: 20.6646 Evaluate side-chains 43 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 0.7980 chunk 40 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3894 r_free = 0.3894 target = 0.153790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.117718 restraints weight = 3625.298| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 1.91 r_work: 0.3322 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3166 Z= 0.149 Angle : 0.497 5.304 4313 Z= 0.252 Chirality : 0.038 0.165 541 Planarity : 0.004 0.032 533 Dihedral : 3.502 13.099 439 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 3.96 % Allowed : 14.33 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.91 (0.43), residues: 413 helix: 2.37 (0.28), residues: 341 sheet: -1.53 (1.32), residues: 20 loop : 0.40 (0.89), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 301 TYR 0.011 0.001 TYR B 334 PHE 0.009 0.001 PHE B 184 TRP 0.006 0.001 TRP B 275 HIS 0.001 0.000 HIS B 452 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 ( 3166) covalent geometry : angle 0.49683 / 0.25 ( 4313) hydrogen bonds : bond 0.04520 / 3.19 ( 260) hydrogen bonds : angle 4.41163 / 3.25 ( 774) *********************** 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 49 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 36 time to evaluate : 0.123 Fit side-chains REVERT: B 136 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8194 (tp) outliers start: 13 outliers final: 6 residues processed: 43 average time/residue: 0.4311 time to fit residues: 19.1287 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 : 0.093 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain B residue 482 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 19 optimal weight: 0.2980 chunk 10 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 29 optimal weight: 0.5980 chunk 40 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.154529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.118329 restraints weight = 3613.037| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 1.90 r_work: 0.3332 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.1888 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= 0.139 Angle : 0.512 7.830 4313 Z= 0.250 Chirality : 0.038 0.155 541 Planarity : 0.004 0.031 533 Dihedral : 3.469 12.825 439 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 3.35 % Allowed : 15.24 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.98 (0.43), residues: 413 helix: 2.42 (0.28), residues: 341 sheet: -1.46 (1.35), residues: 20 loop : 0.38 (0.89), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 301 TYR 0.010 0.001 TYR B 334 PHE 0.009 0.001 PHE B 89 TRP 0.006 0.001 TRP B 275 HIS 0.001 0.000 HIS B 452 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 ( 3166) covalent geometry : angle 0.51240 / 0.25 ( 4313) hydrogen bonds : bond 0.04321 / 3.05 ( 260) hydrogen bonds : angle 4.36826 / 3.22 ( 774) *********************** 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 48 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 37 time to evaluate : 0.136 Fit side-chains REVERT: B 136 LEU cc_start: 0.8568 (mp) cc_final: 0.8182 (tp) REVERT: B 444 GLU cc_start: 0.7053 (OUTLIER) cc_final: 0.6649 (mt-10) outliers start: 11 outliers final: 6 residues processed: 44 average time/residue: 0.4844 time to fit residues: 21.9829 Evaluate side-chains 43 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.069 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 39 optimal weight: 0.6980 chunk 36 optimal weight: 20.0000 chunk 24 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3889 r_free = 0.3889 target = 0.153383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.117119 restraints weight = 3686.606| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 1.92 r_work: 0.3314 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3166 Z= 0.153 Angle : 0.516 6.844 4313 Z= 0.255 Chirality : 0.039 0.166 541 Planarity : 0.004 0.031 533 Dihedral : 3.507 13.078 439 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.16 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.90 (0.43), residues: 413 helix: 2.38 (0.29), residues: 340 sheet: -1.42 (1.36), residues: 20 loop : 0.32 (0.90), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 301 TYR 0.011 0.001 TYR B 334 PHE 0.009 0.001 PHE B 184 TRP 0.005 0.001 TRP B 275 HIS 0.001 0.000 HIS B 452 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.15 ( 3166) covalent geometry : angle 0.51601 / 0.26 ( 4313) hydrogen bonds : bond 0.04563 / 3.22 ( 260) hydrogen bonds : angle 4.41445 / 3.25 ( 774) *********************** 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: 10 poor density : 35 time to evaluate : 0.111 Fit side-chains REVERT: B 136 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8147 (tp) outliers start: 10 outliers final: 6 residues processed: 40 average time/residue: 0.4241 time to fit residues: 17.5866 Evaluate side-chains 40 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 33 time to evaluate : 0.113 ------------------------------------------------------------------------------- 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 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 21 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 2 optimal weight: 0.3980 chunk 38 optimal weight: 0.2980 chunk 5 optimal weight: 0.0980 chunk 20 optimal weight: 0.4980 chunk 30 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3922 r_free = 0.3922 target = 0.156418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.120136 restraints weight = 3681.259| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 1.94 r_work: 0.3353 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.2061 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= 0.120 Angle : 0.492 7.047 4313 Z= 0.240 Chirality : 0.037 0.163 541 Planarity : 0.004 0.031 533 Dihedral : 3.394 13.066 439 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 2.44 % Allowed : 15.85 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.08 (0.43), residues: 413 helix: 2.50 (0.28), residues: 341 sheet: -1.45 (1.39), residues: 20 loop : 0.38 (0.87), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 301 TYR 0.008 0.001 TYR B 334 PHE 0.009 0.001 PHE B 89 TRP 0.005 0.001 TRP B 275 HIS 0.000 0.000 HIS B 452 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 ( 3166) covalent geometry : angle 0.49179 / 0.24 ( 4313) hydrogen bonds : bond 0.03952 / 2.79 ( 260) hydrogen bonds : angle 4.27642 / 3.16 ( 774) *********************** 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 45 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 37 time to evaluate : 0.106 Fit side-chains REVERT: B 136 LEU cc_start: 0.8561 (mp) cc_final: 0.8158 (tp) REVERT: B 444 GLU cc_start: 0.7066 (OUTLIER) cc_final: 0.6663 (mt-10) outliers start: 8 outliers final: 5 residues processed: 42 average time/residue: 0.4256 time to fit residues: 18.4673 Evaluate side-chains 40 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.082 ------------------------------------------------------------------------------- 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 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 34 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 10 optimal weight: 0.0970 chunk 19 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3898 r_free = 0.3898 target = 0.154259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.118009 restraints weight = 3666.505| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 1.94 r_work: 0.3329 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.2052 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= 0.144 Angle : 0.509 6.507 4313 Z= 0.251 Chirality : 0.038 0.169 541 Planarity : 0.004 0.031 533 Dihedral : 3.440 13.077 439 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.96 (0.43), residues: 413 helix: 2.42 (0.28), residues: 340 sheet: -1.49 (1.37), residues: 20 loop : 0.39 (0.90), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 301 TYR 0.011 0.001 TYR B 334 PHE 0.009 0.001 PHE B 89 TRP 0.006 0.001 TRP B 275 HIS 0.001 0.000 HIS B 452 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.14 ( 3166) covalent geometry : angle 0.50940 / 0.25 ( 4313) hydrogen bonds : bond 0.04391 / 3.10 ( 260) hydrogen bonds : angle 4.34230 / 3.20 ( 774) *********************** 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 43 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 33 time to evaluate : 0.091 Fit side-chains REVERT: B 136 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8181 (tp) REVERT: B 444 GLU cc_start: 0.7082 (OUTLIER) cc_final: 0.6682 (mt-10) outliers start: 10 outliers final: 6 residues processed: 38 average time/residue: 0.4589 time to fit residues: 17.9941 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 : 0.106 ------------------------------------------------------------------------------- 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 308 CYS Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 444 GLU Chi-restraints excluded: chain B residue 459 VAL 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 36 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 28 optimal weight: 0.2980 chunk 12 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.154028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.117878 restraints weight = 3612.956| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 1.91 r_work: 0.3320 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.2078 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= 0.144 Angle : 0.510 6.438 4313 Z= 0.252 Chirality : 0.038 0.171 541 Planarity : 0.004 0.031 533 Dihedral : 3.449 13.064 439 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 4.54 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.95 (0.43), residues: 413 helix: 2.41 (0.28), residues: 339 sheet: -1.49 (1.36), residues: 20 loop : 0.47 (0.88), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 301 TYR 0.011 0.001 TYR B 334 PHE 0.009 0.001 PHE B 89 TRP 0.005 0.001 TRP B 275 HIS 0.001 0.000 HIS B 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 ( 3166) covalent geometry : angle 0.50979 / 0.25 ( 4313) hydrogen bonds : bond 0.04412 / 3.11 ( 260) hydrogen bonds : angle 4.36178 / 3.22 ( 774) ********************** 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 44 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 34 time to evaluate : 0.113 Fit side-chains REVERT: B 136 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8146 (tp) REVERT: B 444 GLU cc_start: 0.7096 (OUTLIER) cc_final: 0.6713 (mt-10) outliers start: 10 outliers final: 7 residues processed: 39 average time/residue: 0.4669 time to fit residues: 18.8280 Evaluate side-chains 42 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 33 time to evaluate : 0.109 ------------------------------------------------------------------------------- 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 459 VAL 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 31 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 10 optimal weight: 0.0370 chunk 29 optimal weight: 0.3980 chunk 16 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3906 r_free = 0.3906 target = 0.154841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.118577 restraints weight = 3673.095| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 1.93 r_work: 0.3333 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 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 0.029 3166 Z= 0.135 Angle : 0.499 6.461 4313 Z= 0.246 Chirality : 0.038 0.172 541 Planarity : 0.004 0.031 533 Dihedral : 3.415 13.030 439 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 2.74 % Allowed : 15.55 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.01 (0.43), residues: 413 helix: 2.43 (0.28), residues: 340 sheet: -1.49 (1.37), residues: 20 loop : 0.59 (0.89), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 301 TYR 0.010 0.001 TYR B 334 PHE 0.009 0.001 PHE B 89 TRP 0.004 0.001 TRP B 275 HIS 0.001 0.000 HIS B 452 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 ( 3166) covalent geometry : angle 0.49938 / 0.25 ( 4313) hydrogen bonds : bond 0.04255 / 3.00 ( 260) hydrogen bonds : angle 4.32452 / 3.19 ( 774) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1053.54 seconds wall clock time: 18 minutes 43.22 seconds (1123.22 seconds total)