Starting phenix.real_space_refine on Wed Oct 9 14:24:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qrq_18623/10_2024/8qrq_18623.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qrq_18623/10_2024/8qrq_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qrq_18623/10_2024/8qrq_18623.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qrq_18623/10_2024/8qrq_18623.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qrq_18623/10_2024/8qrq_18623.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qrq_18623/10_2024/8qrq_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-5477/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: 3.11, per 1000 atoms: 1.01 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: 0.93 Conformation dependent library (CDL) restraints added in 422.0 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: 0.33 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: 0.98 Time building geometry restraints manager: 1.00 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: 0.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.700 Find NCS groups from input model: 0.040 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:14.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.650 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 3 poor density : 33 time to evaluate : 0.470 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 36 average time/residue: 1.0591 time to fit residues: 39.6913 Evaluate side-chains 34 residues out of total 328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 31 time to evaluate : 0.403 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 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 fitting. rotamer outliers: 10 poor density : 31 time to evaluate : 0.431 Fit side-chains outliers start: 10 outliers final: 2 residues processed: 40 average time/residue: 0.9993 time to fit residues: 41.8243 Evaluate side-chains 30 residues out of total 328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 28 time to evaluate : 0.374 ------------------------------------------------------------------------------- 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 20 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 37 optimal weight: 10.0000 chunk 40 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.1225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3144 Z= 0.236 Angle : 0.505 5.622 4282 Z= 0.255 Chirality : 0.038 0.128 537 Planarity : 0.005 0.031 529 Dihedral : 3.747 30.380 436 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % 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: 2.55 (0.42), residues: 408 helix: 2.09 (0.27), residues: 347 sheet: -1.54 (1.24), residues: 20 loop : 0.15 (1.03), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 272 HIS 0.002 0.001 HIS B 313 PHE 0.012 0.001 PHE B 237 TYR 0.009 0.002 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 41 residues out of total 328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 32 time to evaluate : 0.368 Fit side-chains REVERT: B 292 MET cc_start: 0.6915 (mpt) cc_final: 0.6510 (pp-130) outliers start: 9 outliers final: 4 residues processed: 38 average time/residue: 0.9669 time to fit residues: 38.4535 Evaluate side-chains 32 residues out of total 328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 28 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 331 LYS 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: 10.0000 chunk 28 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 37 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 chunk 35 optimal weight: 0.0370 chunk 10 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 overall best weight: 1.5464 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3144 Z= 0.291 Angle : 0.533 5.701 4282 Z= 0.269 Chirality : 0.039 0.133 537 Planarity : 0.005 0.032 529 Dihedral : 3.819 30.087 436 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.74 % Allowed : 15.24 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.42), residues: 408 helix: 1.99 (0.28), residues: 347 sheet: -1.74 (1.20), residues: 20 loop : 0.17 (1.05), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 272 HIS 0.002 0.001 HIS B 313 PHE 0.013 0.002 PHE B 237 TYR 0.011 0.002 TYR B 334 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 40 residues out of total 328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 31 time to evaluate : 0.348 Fit side-chains REVERT: B 292 MET cc_start: 0.6942 (mpt) cc_final: 0.6206 (ppp) REVERT: B 485 TYR cc_start: 0.6672 (t80) cc_final: 0.6180 (t80) outliers start: 9 outliers final: 3 residues processed: 38 average time/residue: 0.8828 time to fit residues: 35.1907 Evaluate side-chains 32 residues out of total 328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 29 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 331 LYS 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 22 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 29 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 13 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.1417 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= 0.209 Angle : 0.493 5.276 4282 Z= 0.248 Chirality : 0.038 0.127 537 Planarity : 0.005 0.032 529 Dihedral : 3.353 15.588 434 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 3.96 % Allowed : 13.11 % 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: 2.59 (0.43), residues: 408 helix: 2.11 (0.28), residues: 347 sheet: -1.66 (1.19), residues: 20 loop : 0.21 (1.06), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 275 HIS 0.002 0.000 HIS B 313 PHE 0.011 0.001 PHE B 237 TYR 0.006 0.001 TYR B 276 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 44 residues out of total 328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 31 time to evaluate : 0.566 Fit side-chains REVERT: B 292 MET cc_start: 0.6924 (mpt) cc_final: 0.6315 (pp-130) REVERT: B 388 ASP cc_start: 0.7915 (OUTLIER) cc_final: 0.7329 (m-30) REVERT: B 485 TYR cc_start: 0.6647 (t80) cc_final: 0.6154 (t80) outliers start: 13 outliers final: 5 residues processed: 41 average time/residue: 0.8444 time to fit residues: 36.4541 Evaluate side-chains 35 residues out of total 328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 29 time to evaluate : 0.390 ------------------------------------------------------------------------------- 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 388 ASP Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 441 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 23 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 chunk 13 optimal weight: 0.2980 chunk 20 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.1437 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= 0.167 Angle : 0.475 5.250 4282 Z= 0.239 Chirality : 0.037 0.122 537 Planarity : 0.004 0.032 529 Dihedral : 3.270 14.825 434 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 6.15 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.83 (0.43), residues: 408 helix: 2.28 (0.28), residues: 346 sheet: -1.59 (1.21), residues: 20 loop : 0.29 (1.08), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 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 208 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 42 residues out of total 328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 31 time to evaluate : 0.379 Fit side-chains REVERT: B 292 MET cc_start: 0.6891 (mpt) cc_final: 0.6242 (pp-130) REVERT: B 388 ASP cc_start: 0.7876 (OUTLIER) cc_final: 0.7313 (m-30) REVERT: B 485 TYR cc_start: 0.6680 (t80) cc_final: 0.6188 (t80) outliers start: 11 outliers final: 5 residues processed: 40 average time/residue: 0.9010 time to fit residues: 37.7303 Evaluate side-chains 35 residues out of total 328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 29 time to evaluate : 0.384 ------------------------------------------------------------------------------- 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 28 optimal weight: 0.5980 chunk 22 optimal weight: 7.9990 chunk 33 optimal weight: 7.9990 chunk 39 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 25 optimal weight: 7.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.1494 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= 0.198 Angle : 0.496 5.284 4282 Z= 0.248 Chirality : 0.038 0.126 537 Planarity : 0.005 0.032 529 Dihedral : 3.297 15.392 434 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 3.66 % Allowed : 14.63 % 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: 2.78 (0.43), residues: 408 helix: 2.19 (0.28), residues: 349 sheet: -1.63 (1.21), residues: 20 loop : 0.71 (1.11), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 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 0.007 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 43 residues out of total 328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 31 time to evaluate : 0.448 Fit side-chains REVERT: B 292 MET cc_start: 0.6765 (mpt) cc_final: 0.6247 (pp-130) REVERT: B 388 ASP cc_start: 0.7923 (OUTLIER) cc_final: 0.7332 (m-30) REVERT: B 485 TYR cc_start: 0.6682 (t80) cc_final: 0.6185 (t80) outliers start: 12 outliers final: 5 residues processed: 40 average time/residue: 0.9209 time to fit residues: 38.5426 Evaluate side-chains 36 residues out of total 328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 30 time to evaluate : 0.424 ------------------------------------------------------------------------------- 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 26 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 31 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 chunk 37 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 22 optimal weight: 10.0000 chunk 16 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.1507 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= 0.220 Angle : 0.508 6.066 4282 Z= 0.254 Chirality : 0.038 0.127 537 Planarity : 0.005 0.032 529 Dihedral : 3.318 15.652 434 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.74 % Allowed : 15.55 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.72 (0.43), residues: 408 helix: 2.15 (0.28), residues: 349 sheet: -1.65 (1.21), residues: 20 loop : 0.67 (1.11), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 275 HIS 0.001 0.001 HIS B 313 PHE 0.012 0.001 PHE B 237 TYR 0.009 0.002 TYR B 334 ARG 0.006 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 40 residues out of total 328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 31 time to evaluate : 0.343 Fit side-chains REVERT: B 292 MET cc_start: 0.6759 (mpt) cc_final: 0.6238 (pp-130) REVERT: B 388 ASP cc_start: 0.7948 (OUTLIER) cc_final: 0.7355 (m-30) REVERT: B 485 TYR cc_start: 0.6693 (t80) cc_final: 0.6191 (t80) outliers start: 9 outliers final: 5 residues processed: 38 average time/residue: 0.8869 time to fit residues: 35.2954 Evaluate side-chains 35 residues out of total 328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 29 time to evaluate : 0.488 ------------------------------------------------------------------------------- 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 11 optimal weight: 0.8980 chunk 33 optimal weight: 0.0470 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 38 optimal weight: 6.9990 chunk 23 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 37 optimal weight: 7.9990 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 GLN B 263 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.1562 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= 0.165 Angle : 0.488 6.624 4282 Z= 0.242 Chirality : 0.037 0.122 537 Planarity : 0.005 0.032 529 Dihedral : 3.265 14.575 434 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 3.05 % Allowed : 15.24 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.93 (0.42), residues: 408 helix: 2.32 (0.28), residues: 347 sheet: -1.49 (1.24), residues: 20 loop : 0.55 (1.05), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 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 208 ARG 0.006 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 43 residues out of total 328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 33 time to evaluate : 0.331 Fit side-chains REVERT: B 292 MET cc_start: 0.6710 (mpt) cc_final: 0.6209 (pp-130) REVERT: B 388 ASP cc_start: 0.7896 (OUTLIER) cc_final: 0.7307 (m-30) REVERT: B 485 TYR cc_start: 0.6687 (t80) cc_final: 0.6199 (t80) outliers start: 10 outliers final: 5 residues processed: 41 average time/residue: 0.9514 time to fit residues: 40.6779 Evaluate side-chains 37 residues out of total 328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 31 time to evaluate : 0.345 ------------------------------------------------------------------------------- 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 32 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 25 optimal weight: 0.0010 chunk 19 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.1538 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= 0.165 Angle : 0.494 7.339 4282 Z= 0.244 Chirality : 0.037 0.121 537 Planarity : 0.005 0.032 529 Dihedral : 3.267 14.582 434 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.83 % Allowed : 17.07 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.96 (0.43), residues: 408 helix: 2.33 (0.28), residues: 348 sheet: -1.43 (1.25), residues: 20 loop : 0.50 (1.07), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 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 0.006 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 37 residues out of total 328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 31 time to evaluate : 0.496 Fit side-chains REVERT: B 292 MET cc_start: 0.6700 (mpt) cc_final: 0.6195 (pp-130) REVERT: B 388 ASP cc_start: 0.7896 (OUTLIER) cc_final: 0.7302 (m-30) REVERT: B 485 TYR cc_start: 0.6722 (t80) cc_final: 0.6234 (t80) outliers start: 6 outliers final: 5 residues processed: 36 average time/residue: 0.9066 time to fit residues: 34.1471 Evaluate side-chains 36 residues out of total 328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 30 time to evaluate : 0.349 ------------------------------------------------------------------------------- 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 28 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 24 optimal weight: 0.3980 chunk 16 optimal weight: 0.7980 chunk 15 optimal weight: 0.2980 chunk 40 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.4059 r_free = 0.4059 target = 0.170091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.124076 restraints weight = 3693.619| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 1.82 r_work: 0.3496 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3393 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3144 Z= 0.148 Angle : 0.485 7.519 4282 Z= 0.238 Chirality : 0.037 0.119 537 Planarity : 0.004 0.032 529 Dihedral : 3.228 13.842 434 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.83 % Allowed : 17.38 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.09 (0.43), residues: 408 helix: 2.44 (0.28), residues: 347 sheet: -1.40 (1.26), residues: 20 loop : 0.48 (1.03), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 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 0.006 0.000 ARG B 85 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1327.61 seconds wall clock time: 26 minutes 42.35 seconds (1602.35 seconds total)