Starting phenix.real_space_refine on Wed Jul 1 21:41:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qrq_18623/07_2026/8qrq_18623.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qrq_18623/07_2026/8qrq_18623.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qrq_18623/07_2026/8qrq_18623.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qrq_18623/07_2026/8qrq_18623.map" model { file = "/net/cci-nas-00/data/ceres_data/8qrq_18623/07_2026/8qrq_18623.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qrq_18623/07_2026/8qrq_18623.cif" } resolution = 2.74 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 16 5.16 5 Na 3 4.78 5 C 2031 2.51 5 N 503 2.21 5 O 539 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 3092 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 3079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3079 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 16, 'TRANS': 397} Chain breaks: 2 Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 10 Ad-hoc single atom residues: {' NA': 3} Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain breaks: 3 Time building chain proxies: 0.81, per 1000 atoms: 0.26 Number of scatterers: 3092 At special positions: 0 Unit cell: (60.192, 71.06, 70.224, 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 16 16.00 Na 3 11.00 O 539 8.00 N 503 7.00 C 2031 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 116.5 milliseconds 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 750 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 1 sheets defined 87.2% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'B' and resid 51 through 75 removed outlier: 3.626A pdb=" N VAL B 55 " --> pdb=" O ALA B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 82 Processing helix chain 'B' and resid 82 through 103 removed outlier: 4.031A pdb=" N ALA B 88 " --> pdb=" O GLU B 84 " (cutoff:3.500A) Proline residue: B 92 - end of helix removed outlier: 3.744A 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 179 through 192 Processing helix chain 'B' and resid 195 through 200 Processing helix chain 'B' and resid 230 through 249 removed outlier: 3.570A pdb=" N GLY B 249 " --> pdb=" O LEU B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 292 removed outlier: 3.920A pdb=" N TRP B 275 " --> pdb=" O SER B 271 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N TYR B 276 " --> pdb=" O TRP B 272 " (cutoff:3.500A) Proline residue: B 278 - end of helix removed outlier: 3.621A pdb=" N MET B 292 " --> pdb=" O LYS B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 319 removed outlier: 6.981A pdb=" N LYS B 304 " --> pdb=" O ALA B 300 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N TYR B 305 " --> pdb=" O ARG B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 330 Processing helix chain 'B' and resid 332 through 340 removed outlier: 3.724A pdb=" N PHE B 336 " --> pdb=" O ASN B 332 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY B 339 " --> pdb=" O ARG B 335 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE B 340 " --> pdb=" O PHE B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 351 Processing helix chain 'B' and resid 352 through 367 Proline residue: B 358 - end of helix Processing helix chain 'B' and resid 371 through 385 Proline residue: B 380 - end of helix Processing helix chain 'B' and resid 387 through 405 Processing helix chain 'B' and resid 410 through 428 removed outlier: 3.534A pdb=" N VAL B 426 " --> pdb=" O THR B 422 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY B 427 " --> pdb=" O ALA B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 446 removed outlier: 4.084A pdb=" N THR B 438 " --> pdb=" O GLY B 434 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ILE B 441 " --> pdb=" O LEU B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 487 removed outlier: 3.749A pdb=" N ILE B 456 " --> pdb=" O HIS B 452 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA B 458 " --> pdb=" O SER B 454 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL B 459 " --> pdb=" O LEU B 455 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N TRP B 461 " --> pdb=" O LEU B 457 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N LEU B 462 " --> pdb=" O ALA B 458 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ARG B 465 " --> pdb=" O TRP B 461 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU B 470 " --> pdb=" O SER B 466 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ASP B 475 " --> pdb=" O ASN B 471 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN B 484 " --> pdb=" O GLY B 480 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 202 through 209 257 hydrogen bonds defined for protein. 768 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: 0.58 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: 976 1.34 - 1.46: 535 1.46 - 1.58: 1608 1.58 - 1.69: 0 1.69 - 1.81: 25 Bond restraints: 3144 Sorted by residual: bond pdb=" CG LEU B 112 " pdb=" CD1 LEU B 112 " ideal model delta sigma weight residual 1.521 1.495 0.026 3.30e-02 9.18e+02 6.30e-01 bond pdb=" CB VAL B 226 " pdb=" CG1 VAL B 226 " ideal model delta sigma weight residual 1.521 1.502 0.019 3.30e-02 9.18e+02 3.33e-01 bond pdb=" CG LEU B 107 " pdb=" CD2 LEU B 107 " ideal model delta sigma weight residual 1.521 1.502 0.019 3.30e-02 9.18e+02 3.30e-01 bond pdb=" C ALA B 64 " pdb=" O ALA B 64 " ideal model delta sigma weight residual 1.236 1.229 0.007 1.26e-02 6.30e+03 2.96e-01 bond pdb=" CB THR B 416 " pdb=" CG2 THR B 416 " ideal model delta sigma weight residual 1.521 1.504 0.017 3.30e-02 9.18e+02 2.74e-01 ... (remaining 3139 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.21: 4162 1.21 - 2.42: 92 2.42 - 3.63: 17 3.63 - 4.85: 8 4.85 - 6.06: 3 Bond angle restraints: 4282 Sorted by residual: angle pdb=" N ILE B 453 " pdb=" CA ILE B 453 " pdb=" C ILE B 453 " ideal model delta sigma weight residual 111.05 108.81 2.24 1.25e+00 6.40e-01 3.21e+00 angle pdb=" CB MET B 267 " pdb=" CG MET B 267 " pdb=" SD MET B 267 " ideal model delta sigma weight residual 112.70 117.96 -5.26 3.00e+00 1.11e-01 3.08e+00 angle pdb=" CA LEU B 457 " pdb=" CB LEU B 457 " pdb=" CG LEU B 457 " ideal model delta sigma weight residual 116.30 122.36 -6.06 3.50e+00 8.16e-02 3.00e+00 angle pdb=" C ASN B 471 " pdb=" N VAL B 472 " pdb=" CA VAL B 472 " ideal model delta sigma weight residual 121.97 119.17 2.80 1.80e+00 3.09e-01 2.42e+00 angle pdb=" N PHE B 91 " pdb=" CA PHE B 91 " pdb=" C PHE B 91 " ideal model delta sigma weight residual 113.16 115.19 -2.03 1.42e+00 4.96e-01 2.03e+00 ... (remaining 4277 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.04: 1642 16.04 - 32.08: 160 32.08 - 48.12: 31 48.12 - 64.16: 7 64.16 - 80.20: 3 Dihedral angle restraints: 1843 sinusoidal: 675 harmonic: 1168 Sorted by residual: dihedral pdb=" CA ASP B 120 " pdb=" CB ASP B 120 " pdb=" CG ASP B 120 " pdb=" OD1 ASP B 120 " ideal model delta sinusoidal sigma weight residual -30.00 -88.40 58.40 1 2.00e+01 2.50e-03 1.14e+01 dihedral pdb=" CA ASP B 294 " pdb=" CB ASP B 294 " pdb=" CG ASP B 294 " pdb=" OD1 ASP B 294 " ideal model delta sinusoidal sigma weight residual -30.00 -86.50 56.50 1 2.00e+01 2.50e-03 1.08e+01 dihedral pdb=" CG LYS B 247 " pdb=" CD LYS B 247 " pdb=" CE LYS B 247 " pdb=" NZ LYS B 247 " ideal model delta sinusoidal sigma weight residual 180.00 122.49 57.51 3 1.50e+01 4.44e-03 9.44e+00 ... (remaining 1840 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 322 0.025 - 0.049: 115 0.049 - 0.074: 65 0.074 - 0.098: 22 0.098 - 0.123: 13 Chirality restraints: 537 Sorted by residual: 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 3.77e-01 chirality pdb=" CA LEU B 379 " pdb=" N LEU B 379 " pdb=" C LEU B 379 " pdb=" CB LEU B 379 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.48e-01 chirality pdb=" CA PRO B 343 " pdb=" N PRO B 343 " pdb=" C PRO B 343 " pdb=" CB PRO B 343 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.33e-01 ... (remaining 534 not shown) Planarity restraints: 529 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 220 " 0.022 5.00e-02 4.00e+02 3.28e-02 1.72e+00 pdb=" N PRO B 221 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO B 221 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 221 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 357 " -0.020 5.00e-02 4.00e+02 3.07e-02 1.50e+00 pdb=" N PRO B 358 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO B 358 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 358 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 321 " -0.019 5.00e-02 4.00e+02 2.82e-02 1.28e+00 pdb=" N PRO B 322 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO B 322 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 322 " -0.016 5.00e-02 4.00e+02 ... (remaining 526 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 660 2.78 - 3.31: 3227 3.31 - 3.84: 5465 3.84 - 4.37: 6058 4.37 - 4.90: 10956 Nonbonded interactions: 26366 Sorted by model distance: nonbonded pdb=" O SER B 351 " pdb=" OG SER B 351 " model vdw 2.246 3.040 nonbonded pdb=" OG1 THR B 139 " pdb="NA NA B 603 " model vdw 2.250 3.210 nonbonded pdb=" O GLY B 349 " pdb=" NH2 ARG B 465 " model vdw 2.273 3.120 nonbonded pdb=" OG SER B 111 " pdb=" OD1 ASN B 263 " model vdw 2.309 3.040 nonbonded pdb=" O SER B 425 " pdb="NA NA B 602 " model vdw 2.318 3.210 ... (remaining 26361 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: 1.280 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: 0.050 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 4.910 Find NCS groups from input model: 0.010 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:6.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3144 Z= 0.130 Angle : 0.504 6.057 4282 Z= 0.263 Chirality : 0.037 0.123 537 Planarity : 0.005 0.033 529 Dihedral : 13.403 80.195 1093 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 0.91 % Allowed : 13.11 % Favored : 85.98 % 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: 2.09 (0.41), residues: 408 helix: 1.90 (0.29), residues: 330 sheet: -1.21 (1.28), residues: 20 loop : -0.52 (0.65), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 376 TYR 0.008 0.001 TYR B 208 PHE 0.010 0.001 PHE B 299 TRP 0.003 0.001 TRP B 272 HIS 0.001 0.001 HIS B 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 ( 3144) covalent geometry : angle 0.50370 / 0.26 ( 4282) hydrogen bonds : bond 0.11096 / 7.21 ( 257) hydrogen bonds : angle 5.84748 / 4.11 ( 768) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 0.114 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 36 average time/residue: 0.3288 time to fit residues: 12.2932 Evaluate side-chains 34 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 31 time to evaluate : 0.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 466 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 37 optimal weight: 9.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.170495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.125029 restraints weight = 3723.048| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 1.85 r_work: 0.3539 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3437 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3144 Z= 0.147 Angle : 0.518 5.677 4282 Z= 0.262 Chirality : 0.038 0.127 537 Planarity : 0.005 0.030 529 Dihedral : 3.898 29.836 438 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.44 % Allowed : 13.72 % 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: 2.53 (0.42), residues: 408 helix: 2.08 (0.27), residues: 347 sheet: -1.35 (1.26), residues: 20 loop : -0.08 (0.98), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 376 TYR 0.008 0.002 TYR B 208 PHE 0.012 0.001 PHE B 237 TRP 0.006 0.001 TRP B 461 HIS 0.002 0.001 HIS B 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 ( 3144) covalent geometry : angle 0.51836 / 0.26 ( 4282) hydrogen bonds : bond 0.04344 / 3.00 ( 257) hydrogen bonds : angle 4.62530 / 3.32 ( 768) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 32 time to evaluate : 0.102 Fit side-chains outliers start: 8 outliers final: 2 residues processed: 39 average time/residue: 0.2893 time to fit residues: 11.7762 Evaluate side-chains 30 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 28 time to evaluate : 0.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 431 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 25 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 34 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 37 optimal weight: 0.4980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.171462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.126145 restraints weight = 3730.248| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 1.88 r_work: 0.3539 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3438 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3144 Z= 0.126 Angle : 0.477 5.220 4282 Z= 0.242 Chirality : 0.037 0.122 537 Planarity : 0.004 0.031 529 Dihedral : 3.642 28.276 436 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 3.35 % Allowed : 13.11 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.66 (0.42), residues: 408 helix: 2.19 (0.27), residues: 346 sheet: -1.40 (1.25), residues: 20 loop : -0.15 (0.97), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 376 TYR 0.006 0.001 TYR B 334 PHE 0.010 0.001 PHE B 237 TRP 0.004 0.001 TRP B 461 HIS 0.002 0.001 HIS B 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 ( 3144) covalent geometry : angle 0.47714 / 0.24 ( 4282) hydrogen bonds : bond 0.03983 / 2.75 ( 257) hydrogen bonds : angle 4.47381 / 3.24 ( 768) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 34 time to evaluate : 0.066 Fit side-chains REVERT: B 292 MET cc_start: 0.7139 (mpt) cc_final: 0.6863 (pp-130) REVERT: B 485 TYR cc_start: 0.6863 (t80) cc_final: 0.6399 (t80) outliers start: 11 outliers final: 3 residues processed: 42 average time/residue: 0.2913 time to fit residues: 12.7839 Evaluate side-chains 33 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 30 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 446 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 9.9990 chunk 3 optimal weight: 0.6980 chunk 29 optimal weight: 5.9990 chunk 30 optimal weight: 0.6980 chunk 35 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 39 optimal weight: 0.1980 chunk 6 optimal weight: 0.6980 chunk 21 optimal weight: 0.1980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 316 HIS B 367 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.173026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.127772 restraints weight = 3695.159| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 1.88 r_work: 0.3586 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3486 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3144 Z= 0.110 Angle : 0.469 5.139 4282 Z= 0.234 Chirality : 0.036 0.118 537 Planarity : 0.004 0.032 529 Dihedral : 3.594 27.364 436 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.13 % Allowed : 15.55 % 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 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: 2.88 (0.42), residues: 408 helix: 2.42 (0.28), residues: 340 sheet: -1.44 (1.25), residues: 20 loop : -0.36 (0.88), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 85 TYR 0.006 0.001 TYR B 208 PHE 0.008 0.001 PHE B 237 TRP 0.002 0.000 TRP B 275 HIS 0.001 0.000 HIS B 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 ( 3144) covalent geometry : angle 0.46901 / 0.23 ( 4282) hydrogen bonds : bond 0.03706 / 2.56 ( 257) hydrogen bonds : angle 4.35447 / 3.15 ( 768) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.098 Fit side-chains REVERT: B 140 LEU cc_start: 0.7922 (mp) cc_final: 0.7617 (mp) REVERT: B 292 MET cc_start: 0.7098 (mpt) cc_final: 0.6766 (pp-130) REVERT: B 485 TYR cc_start: 0.6824 (t80) cc_final: 0.6362 (t80) outliers start: 7 outliers final: 3 residues processed: 41 average time/residue: 0.3066 time to fit residues: 13.1554 Evaluate side-chains 35 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 32 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 446 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 27 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 37 optimal weight: 0.1980 chunk 8 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 35 optimal weight: 0.0060 chunk 0 optimal weight: 10.0000 chunk 32 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.172955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.127637 restraints weight = 3672.979| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 1.87 r_work: 0.3597 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3496 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3144 Z= 0.112 Angle : 0.466 5.242 4282 Z= 0.233 Chirality : 0.036 0.121 537 Planarity : 0.004 0.032 529 Dihedral : 3.574 26.583 436 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % 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 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 (0.42), residues: 408 helix: 2.48 (0.28), residues: 340 sheet: -1.44 (1.26), residues: 20 loop : -0.47 (0.87), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 85 TYR 0.006 0.001 TYR B 208 PHE 0.009 0.001 PHE B 237 TRP 0.002 0.000 TRP B 275 HIS 0.001 0.000 HIS B 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 ( 3144) covalent geometry : angle 0.46592 / 0.23 ( 4282) hydrogen bonds : bond 0.03685 / 2.56 ( 257) hydrogen bonds : angle 4.32259 / 3.14 ( 768) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 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 : 0.077 Fit side-chains REVERT: B 140 LEU cc_start: 0.7858 (mp) cc_final: 0.7560 (mp) REVERT: B 292 MET cc_start: 0.7136 (mpt) cc_final: 0.6577 (pp-130) REVERT: B 331 LYS cc_start: 0.8229 (tptt) cc_final: 0.7270 (ttmm) REVERT: B 485 TYR cc_start: 0.6813 (t80) cc_final: 0.6352 (t80) outliers start: 10 outliers final: 4 residues processed: 43 average time/residue: 0.3151 time to fit residues: 14.1263 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 : 0.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 446 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 9.9990 chunk 27 optimal weight: 0.2980 chunk 24 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 367 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.172101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.126843 restraints weight = 3710.397| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 1.88 r_work: 0.3571 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3469 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3144 Z= 0.123 Angle : 0.482 5.487 4282 Z= 0.242 Chirality : 0.037 0.123 537 Planarity : 0.004 0.032 529 Dihedral : 3.593 26.199 436 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 3.35 % Allowed : 14.63 % 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: 2.93 (0.42), residues: 408 helix: 2.41 (0.28), residues: 342 sheet: -1.50 (1.26), residues: 20 loop : -0.13 (0.96), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 85 TYR 0.007 0.001 TYR B 334 PHE 0.011 0.001 PHE B 237 TRP 0.003 0.001 TRP B 272 HIS 0.001 0.000 HIS B 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 ( 3144) covalent geometry : angle 0.48227 / 0.24 ( 4282) hydrogen bonds : bond 0.03814 / 2.65 ( 257) hydrogen bonds : angle 4.35452 / 3.16 ( 768) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 31 time to evaluate : 0.069 Fit side-chains REVERT: B 292 MET cc_start: 0.7061 (mpt) cc_final: 0.6537 (pp-130) REVERT: B 485 TYR cc_start: 0.6855 (t80) cc_final: 0.6377 (t80) outliers start: 11 outliers final: 5 residues processed: 41 average time/residue: 0.3092 time to fit residues: 13.2214 Evaluate side-chains 36 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 31 time to evaluate : 0.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 446 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 32 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.168004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.120552 restraints weight = 3724.871| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 1.95 r_work: 0.3453 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3351 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3144 Z= 0.148 Angle : 0.506 5.675 4282 Z= 0.254 Chirality : 0.038 0.127 537 Planarity : 0.005 0.032 529 Dihedral : 3.657 26.316 436 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % 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: 2.77 (0.43), residues: 408 helix: 2.23 (0.28), residues: 348 sheet: -1.61 (1.22), residues: 20 loop : 0.19 (1.06), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 85 TYR 0.010 0.001 TYR B 334 PHE 0.012 0.001 PHE B 237 TRP 0.007 0.001 TRP B 272 HIS 0.001 0.001 HIS B 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 ( 3144) covalent geometry : angle 0.50554 / 0.25 ( 4282) hydrogen bonds : bond 0.04089 / 2.85 ( 257) hydrogen bonds : angle 4.45753 / 3.24 ( 768) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 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: 8 poor density : 33 time to evaluate : 0.085 Fit side-chains REVERT: B 224 GLN cc_start: 0.7472 (pm20) cc_final: 0.7243 (pm20) REVERT: B 292 MET cc_start: 0.6886 (mpt) cc_final: 0.6312 (pp-130) REVERT: B 388 ASP cc_start: 0.8174 (OUTLIER) cc_final: 0.7405 (m-30) REVERT: B 485 TYR cc_start: 0.6789 (t80) cc_final: 0.6305 (t80) outliers start: 8 outliers final: 5 residues processed: 40 average time/residue: 0.3331 time to fit residues: 13.9469 Evaluate side-chains 38 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 32 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 446 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 17 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 28 optimal weight: 0.2980 chunk 32 optimal weight: 5.9990 chunk 1 optimal weight: 0.5980 chunk 21 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 367 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.169406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.122304 restraints weight = 3735.627| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 1.95 r_work: 0.3479 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3377 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3144 Z= 0.122 Angle : 0.485 6.457 4282 Z= 0.241 Chirality : 0.037 0.122 537 Planarity : 0.004 0.032 529 Dihedral : 3.591 25.443 436 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.83 % Allowed : 16.16 % 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: 2.90 (0.42), residues: 408 helix: 2.36 (0.28), residues: 346 sheet: -1.55 (1.23), residues: 20 loop : 0.04 (1.01), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 85 TYR 0.006 0.001 TYR B 208 PHE 0.010 0.001 PHE B 237 TRP 0.003 0.001 TRP B 275 HIS 0.001 0.000 HIS B 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 ( 3144) covalent geometry : angle 0.48464 / 0.24 ( 4282) hydrogen bonds : bond 0.03801 / 2.64 ( 257) hydrogen bonds : angle 4.38146 / 3.18 ( 768) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 31 time to evaluate : 0.122 Fit side-chains REVERT: B 292 MET cc_start: 0.6982 (mpt) cc_final: 0.6329 (pp-130) REVERT: B 485 TYR cc_start: 0.6829 (t80) cc_final: 0.6343 (t80) outliers start: 6 outliers final: 5 residues processed: 36 average time/residue: 0.4249 time to fit residues: 15.9378 Evaluate side-chains 34 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 29 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 446 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 10 optimal weight: 0.6980 chunk 23 optimal weight: 4.9990 chunk 35 optimal weight: 7.9990 chunk 29 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 26 optimal weight: 0.1980 chunk 31 optimal weight: 6.9990 chunk 39 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 316 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.169936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.122823 restraints weight = 3776.252| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 1.97 r_work: 0.3453 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3144 Z= 0.117 Angle : 0.486 6.919 4282 Z= 0.241 Chirality : 0.037 0.121 537 Planarity : 0.004 0.032 529 Dihedral : 3.593 24.536 436 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.13 % Allowed : 15.55 % 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 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: 2.94 (0.43), residues: 408 helix: 2.36 (0.28), residues: 348 sheet: -1.54 (1.24), residues: 20 loop : 0.11 (1.06), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 85 TYR 0.007 0.001 TYR B 208 PHE 0.010 0.001 PHE B 237 TRP 0.003 0.001 TRP B 275 HIS 0.001 0.000 HIS B 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 ( 3144) covalent geometry : angle 0.48554 / 0.24 ( 4282) hydrogen bonds : bond 0.03736 / 2.59 ( 257) hydrogen bonds : angle 4.33655 / 3.15 ( 768) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 30 time to evaluate : 0.112 Fit side-chains REVERT: B 292 MET cc_start: 0.6951 (mpt) cc_final: 0.6342 (pp-130) REVERT: B 485 TYR cc_start: 0.6832 (t80) cc_final: 0.6376 (t80) outliers start: 7 outliers final: 5 residues processed: 35 average time/residue: 0.3426 time to fit residues: 12.5140 Evaluate side-chains 36 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 31 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 446 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 0 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 38 optimal weight: 7.9990 chunk 33 optimal weight: 0.0010 chunk 24 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 overall best weight: 0.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 367 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.169677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.122586 restraints weight = 3640.176| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 1.93 r_work: 0.3472 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3371 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3144 Z= 0.123 Angle : 0.496 7.632 4282 Z= 0.245 Chirality : 0.037 0.122 537 Planarity : 0.004 0.032 529 Dihedral : 3.600 24.133 436 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.44 % Allowed : 15.55 % 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: 2.92 (0.43), residues: 408 helix: 2.35 (0.28), residues: 348 sheet: -1.63 (1.23), residues: 20 loop : 0.12 (1.05), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 85 TYR 0.007 0.001 TYR B 208 PHE 0.011 0.001 PHE B 237 TRP 0.006 0.001 TRP B 275 HIS 0.001 0.001 HIS B 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 ( 3144) covalent geometry : angle 0.49623 / 0.25 ( 4282) hydrogen bonds : bond 0.03800 / 2.64 ( 257) hydrogen bonds : angle 4.35953 / 3.16 ( 768) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 30 time to evaluate : 0.125 Fit side-chains REVERT: B 292 MET cc_start: 0.6947 (mpt) cc_final: 0.6320 (pp-130) REVERT: B 485 TYR cc_start: 0.6851 (t80) cc_final: 0.6383 (t80) outliers start: 8 outliers final: 5 residues processed: 37 average time/residue: 0.3802 time to fit residues: 14.7448 Evaluate side-chains 34 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 29 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 446 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 17 optimal weight: 0.9990 chunk 33 optimal weight: 0.0030 chunk 13 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 14 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.169699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.122063 restraints weight = 3723.254| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 1.98 r_work: 0.3467 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3365 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3144 Z= 0.117 Angle : 0.492 7.815 4282 Z= 0.243 Chirality : 0.037 0.121 537 Planarity : 0.004 0.032 529 Dihedral : 3.591 23.681 436 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.52 % Allowed : 16.46 % 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: 408 helix: 2.38 (0.28), residues: 348 sheet: -1.62 (1.23), residues: 20 loop : 0.13 (1.06), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 85 TYR 0.007 0.001 TYR B 208 PHE 0.010 0.001 PHE B 237 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 0.00257 / 0.12 ( 3144) covalent geometry : angle 0.49242 / 0.24 ( 4282) hydrogen bonds : bond 0.03710 / 2.57 ( 257) hydrogen bonds : angle 4.32788 / 3.14 ( 768) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1135.50 seconds wall clock time: 20 minutes 5.68 seconds (1205.68 seconds total)