Starting phenix.real_space_refine on Wed Mar 5 17:25:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qrq_18623/03_2025/8qrq_18623.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qrq_18623/03_2025/8qrq_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_18623/03_2025/8qrq_18623.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qrq_18623/03_2025/8qrq_18623.map" model { file = "/net/cci-nas-00/data/ceres_data/8qrq_18623/03_2025/8qrq_18623.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qrq_18623/03_2025/8qrq_18623.cif" } resolution = 2.74 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 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-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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, 13 Unusual residues: {' NA': 3} Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1} Link IDs: {None: 3} Time building chain proxies: 2.58, per 1000 atoms: 0.83 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: 0.74 Conformation dependent library (CDL) restraints added in 355.4 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: 0.26 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: 0.83 Time building geometry restraints manager: 0.86 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 2.470 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 2.470 ... (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: 0.630 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.330 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 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= 0.180 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (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 TRP 0.003 0.001 TRP B 272 HIS 0.001 0.001 HIS B 316 PHE 0.010 0.001 PHE B 299 TYR 0.008 0.001 TYR B 208 ARG 0.002 0.000 ARG B 376 *********************** 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 : 0.316 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 36 average time/residue: 0.9729 time to fit residues: 36.4663 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 : 0.317 ------------------------------------------------------------------------------- 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 34 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 0.3980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 10.0000 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 316 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.170940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.125553 restraints weight = 3701.783| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 1.85 r_work: 0.3545 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3446 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.0994 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= 0.195 Angle : 0.507 5.695 4282 Z= 0.255 Chirality : 0.038 0.125 537 Planarity : 0.005 0.030 529 Dihedral : 3.914 30.687 438 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 3.05 % Allowed : 12.50 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.63 (0.42), residues: 408 helix: 2.14 (0.27), residues: 347 sheet: -1.31 (1.26), residues: 20 loop : 0.04 (1.01), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 461 HIS 0.001 0.001 HIS B 313 PHE 0.011 0.001 PHE B 237 TYR 0.008 0.001 TYR B 208 ARG 0.001 0.000 ARG B 465 *********************** 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 41 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 31 time to evaluate : 0.336 Fit side-chains outliers start: 10 outliers final: 2 residues processed: 40 average time/residue: 0.8741 time to fit residues: 36.4780 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 : 0.313 ------------------------------------------------------------------------------- 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 2 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 30 optimal weight: 0.4980 chunk 12 optimal weight: 0.4980 chunk 33 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.171785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.126617 restraints weight = 3675.308| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 1.87 r_work: 0.3554 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3453 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.1196 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= 0.163 Angle : 0.471 5.208 4282 Z= 0.238 Chirality : 0.037 0.121 537 Planarity : 0.005 0.031 529 Dihedral : 3.674 30.140 436 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.74 % Allowed : 13.11 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.83 (0.42), residues: 408 helix: 2.30 (0.27), residues: 345 sheet: -1.39 (1.26), residues: 20 loop : 0.05 (0.98), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 461 HIS 0.001 0.001 HIS B 313 PHE 0.010 0.001 PHE B 393 TYR 0.006 0.001 TYR B 334 ARG 0.005 0.000 ARG B 85 *********************** 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 43 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 34 time to evaluate : 0.336 Fit side-chains REVERT: B 292 MET cc_start: 0.7151 (mpt) cc_final: 0.6817 (pp-130) outliers start: 9 outliers final: 3 residues processed: 40 average time/residue: 0.8157 time to fit residues: 34.2789 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 : 0.313 ------------------------------------------------------------------------------- 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 39 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 38 optimal weight: 8.9990 chunk 18 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 24 optimal weight: 0.0010 chunk 10 optimal weight: 0.0170 overall best weight: 0.4824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 367 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.172787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.127790 restraints weight = 3696.155| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 1.87 r_work: 0.3592 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3491 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.1332 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= 0.142 Angle : 0.467 5.195 4282 Z= 0.232 Chirality : 0.036 0.119 537 Planarity : 0.004 0.032 529 Dihedral : 3.628 29.843 436 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.13 % Allowed : 15.24 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.00 (0.42), residues: 408 helix: 2.49 (0.28), residues: 340 sheet: -1.46 (1.26), residues: 20 loop : -0.15 (0.91), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 461 HIS 0.001 0.000 HIS B 313 PHE 0.009 0.001 PHE B 237 TYR 0.005 0.001 TYR B 208 ARG 0.004 0.000 ARG B 85 *********************** 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 38 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 31 time to evaluate : 0.338 Fit side-chains REVERT: B 292 MET cc_start: 0.7095 (mpt) cc_final: 0.6759 (pp-130) REVERT: B 485 TYR cc_start: 0.6825 (t80) cc_final: 0.6364 (t80) outliers start: 7 outliers final: 3 residues processed: 37 average time/residue: 0.8341 time to fit residues: 32.4035 Evaluate side-chains 32 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 29 time to evaluate : 0.319 ------------------------------------------------------------------------------- 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 31 optimal weight: 8.9990 chunk 28 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 35 optimal weight: 7.9990 chunk 6 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.167094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.121646 restraints weight = 3570.358| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 1.83 r_work: 0.3557 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3456 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.1327 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= 0.180 Angle : 0.478 5.384 4282 Z= 0.238 Chirality : 0.037 0.123 537 Planarity : 0.004 0.032 529 Dihedral : 3.638 29.758 436 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 3.66 % Allowed : 13.41 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.95 (0.43), residues: 408 helix: 2.39 (0.28), residues: 346 sheet: -1.53 (1.22), residues: 20 loop : 0.04 (1.02), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 272 HIS 0.001 0.000 HIS B 313 PHE 0.011 0.001 PHE B 237 TYR 0.007 0.001 TYR B 334 ARG 0.004 0.000 ARG B 85 *********************** 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 43 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 31 time to evaluate : 0.337 Fit side-chains REVERT: B 292 MET cc_start: 0.7096 (mpt) cc_final: 0.6574 (pp-130) REVERT: B 485 TYR cc_start: 0.6819 (t80) cc_final: 0.6357 (t80) outliers start: 12 outliers final: 4 residues processed: 42 average time/residue: 0.7354 time to fit residues: 32.4892 Evaluate side-chains 35 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 31 time to evaluate : 0.311 ------------------------------------------------------------------------------- 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 30 optimal weight: 0.3980 chunk 11 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 1 optimal weight: 0.5980 chunk 38 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 25 optimal weight: 6.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.167305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.122030 restraints weight = 3669.910| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 1.85 r_work: 0.3572 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3474 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1418 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= 0.160 Angle : 0.472 5.516 4282 Z= 0.235 Chirality : 0.037 0.121 537 Planarity : 0.004 0.032 529 Dihedral : 3.616 29.569 436 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 3.05 % Allowed : 14.33 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.07 (0.43), residues: 408 helix: 2.43 (0.28), residues: 346 sheet: -1.44 (1.23), residues: 20 loop : 0.48 (1.06), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 275 HIS 0.001 0.000 HIS B 313 PHE 0.010 0.001 PHE B 237 TYR 0.006 0.001 TYR B 334 ARG 0.003 0.000 ARG B 85 *********************** 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 41 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 31 time to evaluate : 0.320 Fit side-chains REVERT: B 292 MET cc_start: 0.7106 (mpt) cc_final: 0.6596 (pp-130) REVERT: B 388 ASP cc_start: 0.8189 (OUTLIER) cc_final: 0.7579 (m-30) REVERT: B 485 TYR cc_start: 0.6846 (t80) cc_final: 0.6378 (t80) outliers start: 10 outliers final: 5 residues processed: 39 average time/residue: 0.7931 time to fit residues: 32.4385 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 : 0.323 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 8 optimal weight: 0.7980 chunk 14 optimal weight: 7.9990 chunk 3 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 26 optimal weight: 0.1980 chunk 18 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 28 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.170058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.123985 restraints weight = 3671.343| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 1.82 r_work: 0.3494 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3395 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.1467 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= 0.152 Angle : 0.469 5.491 4282 Z= 0.233 Chirality : 0.037 0.120 537 Planarity : 0.004 0.032 529 Dihedral : 3.598 29.179 436 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 3.05 % Allowed : 14.33 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.12 (0.42), residues: 408 helix: 2.48 (0.28), residues: 346 sheet: -1.42 (1.24), residues: 20 loop : 0.35 (1.02), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 275 HIS 0.001 0.000 HIS B 313 PHE 0.010 0.001 PHE B 237 TYR 0.007 0.001 TYR B 208 ARG 0.003 0.000 ARG B 85 *********************** 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: 10 poor density : 31 time to evaluate : 0.335 Fit side-chains REVERT: B 292 MET cc_start: 0.6999 (mpt) cc_final: 0.6379 (pp-130) REVERT: B 388 ASP cc_start: 0.8078 (OUTLIER) cc_final: 0.7489 (m-30) REVERT: B 485 TYR cc_start: 0.6824 (t80) cc_final: 0.6332 (t80) outliers start: 10 outliers final: 5 residues processed: 39 average time/residue: 0.7697 time to fit residues: 31.5362 Evaluate side-chains 36 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 30 time to evaluate : 0.338 ------------------------------------------------------------------------------- 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 13 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 8 optimal weight: 0.8980 chunk 4 optimal weight: 0.3980 chunk 22 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 31 optimal weight: 6.9990 chunk 33 optimal weight: 0.0970 chunk 15 optimal weight: 0.8980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.170615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.124528 restraints weight = 3718.308| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 1.84 r_work: 0.3501 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3402 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.1539 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= 0.143 Angle : 0.472 6.716 4282 Z= 0.231 Chirality : 0.036 0.120 537 Planarity : 0.004 0.032 529 Dihedral : 3.571 28.728 436 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.13 % Allowed : 14.94 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.21 (0.42), residues: 408 helix: 2.54 (0.28), residues: 346 sheet: -1.36 (1.25), residues: 20 loop : 0.33 (1.03), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 275 HIS 0.001 0.000 HIS B 313 PHE 0.009 0.001 PHE B 237 TYR 0.007 0.001 TYR B 208 ARG 0.003 0.000 ARG B 85 *********************** 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 41 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 34 time to evaluate : 0.290 Fit side-chains REVERT: B 292 MET cc_start: 0.6883 (mpt) cc_final: 0.6291 (pp-130) REVERT: B 331 LYS cc_start: 0.8215 (tptt) cc_final: 0.7236 (ttmm) REVERT: B 388 ASP cc_start: 0.8008 (OUTLIER) cc_final: 0.7402 (m-30) REVERT: B 485 TYR cc_start: 0.6808 (t80) cc_final: 0.6326 (t80) outliers start: 7 outliers final: 5 residues processed: 39 average time/residue: 0.7946 time to fit residues: 32.5828 Evaluate side-chains 39 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.288 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 14 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 31 optimal weight: 8.9990 chunk 17 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 33 optimal weight: 10.0000 chunk 32 optimal weight: 3.9990 chunk 4 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.168942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.122447 restraints weight = 3676.720| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 1.83 r_work: 0.3481 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 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 0.027 3144 Z= 0.185 Angle : 0.495 7.309 4282 Z= 0.244 Chirality : 0.037 0.123 537 Planarity : 0.004 0.035 529 Dihedral : 3.622 28.400 436 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.74 % Allowed : 14.94 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.08 (0.43), residues: 408 helix: 2.44 (0.28), residues: 347 sheet: -1.45 (1.24), residues: 20 loop : 0.38 (1.06), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 275 HIS 0.001 0.000 HIS B 313 PHE 0.011 0.001 PHE B 237 TYR 0.008 0.001 TYR B 334 ARG 0.003 0.000 ARG B 85 *********************** 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 46 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 37 time to evaluate : 0.317 Fit side-chains REVERT: B 292 MET cc_start: 0.6921 (mpt) cc_final: 0.6324 (pp-130) REVERT: B 388 ASP cc_start: 0.8112 (OUTLIER) cc_final: 0.7489 (m-30) REVERT: B 485 TYR cc_start: 0.6868 (t80) cc_final: 0.6403 (t80) outliers start: 9 outliers final: 5 residues processed: 43 average time/residue: 0.7328 time to fit residues: 33.1599 Evaluate side-chains 42 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.308 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 37 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 27 optimal weight: 0.1980 chunk 7 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.168381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.122016 restraints weight = 3632.057| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 1.80 r_work: 0.3465 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3363 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.1540 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= 0.201 Angle : 0.506 7.662 4282 Z= 0.250 Chirality : 0.038 0.125 537 Planarity : 0.004 0.034 529 Dihedral : 3.659 28.163 436 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 5.36 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.98 (0.43), residues: 408 helix: 2.36 (0.28), residues: 347 sheet: -1.54 (1.24), residues: 20 loop : 0.46 (1.07), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 275 HIS 0.001 0.001 HIS B 313 PHE 0.012 0.001 PHE B 237 TYR 0.009 0.001 TYR B 334 ARG 0.002 0.000 ARG B 85 ********************** 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 44 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.348 Fit side-chains REVERT: B 292 MET cc_start: 0.6969 (mpt) cc_final: 0.6359 (pp-130) REVERT: B 388 ASP cc_start: 0.8195 (OUTLIER) cc_final: 0.7619 (m-30) REVERT: B 485 TYR cc_start: 0.6902 (t80) cc_final: 0.6421 (t80) outliers start: 8 outliers final: 5 residues processed: 43 average time/residue: 0.6602 time to fit residues: 29.9824 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 : 0.317 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 30 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.169249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.122840 restraints weight = 3724.765| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 1.82 r_work: 0.3473 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3370 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.1531 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= 0.175 Angle : 0.496 7.679 4282 Z= 0.245 Chirality : 0.037 0.122 537 Planarity : 0.004 0.035 529 Dihedral : 3.648 28.319 436 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.83 % Allowed : 16.46 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.05 (0.42), residues: 408 helix: 2.42 (0.28), residues: 346 sheet: -1.55 (1.24), residues: 20 loop : 0.45 (1.04), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 275 HIS 0.001 0.000 HIS B 313 PHE 0.011 0.001 PHE B 237 TYR 0.007 0.001 TYR B 334 ARG 0.002 0.000 ARG B 85 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2403.34 seconds wall clock time: 41 minutes 38.96 seconds (2498.96 seconds total)