Starting phenix.real_space_refine on Fri May 9 16:09:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qrq_18623/05_2025/8qrq_18623.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qrq_18623/05_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_18623/05_2025/8qrq_18623.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qrq_18623/05_2025/8qrq_18623.map" model { file = "/net/cci-nas-00/data/ceres_data/8qrq_18623/05_2025/8qrq_18623.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qrq_18623/05_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-5687/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: 2.52, per 1000 atoms: 0.82 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: 0.81 Conformation dependent library (CDL) restraints added in 402.3 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: 0.31 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: 0.89 Time building geometry restraints manager: 0.94 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: 0.570 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.080 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.750 ------------------------------------------------------------------------------- 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= 0.130 Angle : 0.504 6.057 4282 Z= 0.263 Chirality : 0.037 0.123 537 Planarity : 0.005 0.033 529 Dihedral : 13.403 80.195 1093 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 0.91 % Allowed : 13.11 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 Details of bonding type rmsd hydrogen bonds : bond 0.11096 ( 257) hydrogen bonds : angle 5.84748 ( 768) covalent geometry : bond 0.00285 ( 3144) covalent geometry : angle 0.50370 ( 4282) *********************** 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 : 0.342 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 36 average time/residue: 0.9233 time to fit residues: 34.6479 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 : 0.328 ------------------------------------------------------------------------------- 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: 0.3444 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 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= 0.137 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 Details of bonding type rmsd hydrogen bonds : bond 0.04265 ( 257) hydrogen bonds : angle 4.59424 ( 768) covalent geometry : bond 0.00308 ( 3144) covalent geometry : angle 0.50712 ( 4282) *********************** 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 : 0.428 Fit side-chains outliers start: 10 outliers final: 2 residues processed: 40 average time/residue: 0.8740 time to fit residues: 36.4988 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 : 0.316 ------------------------------------------------------------------------------- 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: 0.9990 chunk 8 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4090 r_free = 0.4090 target = 0.171197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.126001 restraints weight = 3675.056| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 1.86 r_work: 0.3540 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3440 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1193 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= 0.124 Angle : 0.476 5.172 4282 Z= 0.240 Chirality : 0.037 0.122 537 Planarity : 0.005 0.031 529 Dihedral : 3.686 30.171 436 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 5.52 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: 2.76 (0.42), residues: 408 helix: 2.25 (0.27), residues: 346 sheet: -1.42 (1.26), residues: 20 loop : 0.04 (1.01), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 461 HIS 0.002 0.001 HIS B 313 PHE 0.010 0.001 PHE B 237 TYR 0.006 0.001 TYR B 334 ARG 0.005 0.000 ARG B 85 Details of bonding type rmsd hydrogen bonds : bond 0.03964 ( 257) hydrogen bonds : angle 4.44640 ( 768) covalent geometry : bond 0.00276 ( 3144) covalent geometry : angle 0.47573 ( 4282) *********************** 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 42 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 33 time to evaluate : 0.341 Fit side-chains REVERT: B 292 MET cc_start: 0.7191 (mpt) cc_final: 0.6890 (pp-130) outliers start: 9 outliers final: 3 residues processed: 39 average time/residue: 0.7849 time to fit residues: 32.1435 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 : 0.339 ------------------------------------------------------------------------------- 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: 0.9990 chunk 3 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 38 optimal weight: 7.9990 chunk 18 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 10 optimal weight: 0.0870 overall best weight: 0.6760 ------------------------------------------------------------------------------- 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 = 0.4093 r_free = 0.4093 target = 0.171740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.126506 restraints weight = 3711.294| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 1.87 r_work: 0.3557 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3457 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1306 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= 0.120 Angle : 0.476 5.222 4282 Z= 0.238 Chirality : 0.037 0.122 537 Planarity : 0.004 0.032 529 Dihedral : 3.653 29.873 436 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % 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: 2.87 (0.42), residues: 408 helix: 2.38 (0.28), residues: 341 sheet: -1.51 (1.24), residues: 20 loop : -0.19 (0.93), residues: 47 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 0.010 0.001 PHE B 237 TYR 0.006 0.001 TYR B 334 ARG 0.004 0.000 ARG B 85 Details of bonding type rmsd hydrogen bonds : bond 0.03825 ( 257) hydrogen bonds : angle 4.38162 ( 768) covalent geometry : bond 0.00265 ( 3144) covalent geometry : angle 0.47632 ( 4282) *********************** 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 : 0.377 Fit side-chains REVERT: B 292 MET cc_start: 0.7126 (mpt) cc_final: 0.6689 (pp-130) REVERT: B 485 TYR cc_start: 0.6813 (t80) cc_final: 0.6349 (t80) outliers start: 7 outliers final: 3 residues processed: 37 average time/residue: 0.8904 time to fit residues: 34.4456 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 : 0.339 ------------------------------------------------------------------------------- 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: 0.6980 chunk 10 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 29 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 chunk 6 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4096 r_free = 0.4096 target = 0.172060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.126816 restraints weight = 3718.401| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 1.87 r_work: 0.3566 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3466 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 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 : 0.003 0.027 3144 Z= 0.119 Angle : 0.471 5.237 4282 Z= 0.235 Chirality : 0.037 0.122 537 Planarity : 0.004 0.032 529 Dihedral : 3.641 29.605 436 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 3.35 % Allowed : 13.72 % 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: 2.98 (0.42), residues: 408 helix: 2.41 (0.28), residues: 345 sheet: -1.50 (1.24), residues: 20 loop : 0.08 (1.00), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 272 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 Details of bonding type rmsd hydrogen bonds : bond 0.03786 ( 257) hydrogen bonds : angle 4.35879 ( 768) covalent geometry : bond 0.00264 ( 3144) covalent geometry : angle 0.47149 ( 4282) *********************** 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 42 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 31 time to evaluate : 0.321 Fit side-chains REVERT: B 292 MET cc_start: 0.7117 (mpt) cc_final: 0.6556 (pp-130) REVERT: B 485 TYR cc_start: 0.6824 (t80) cc_final: 0.6362 (t80) outliers start: 11 outliers final: 4 residues processed: 41 average time/residue: 0.7045 time to fit residues: 30.3913 Evaluate side-chains 34 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 30 time to evaluate : 0.317 ------------------------------------------------------------------------------- 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: 0.7980 chunk 34 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 12 optimal weight: 0.0970 chunk 18 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 25 optimal weight: 8.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- 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 = 0.4060 r_free = 0.4060 target = 0.170499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.124274 restraints weight = 3771.653| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 1.84 r_work: 0.3501 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3401 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.1488 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= 0.107 Angle : 0.464 5.167 4282 Z= 0.230 Chirality : 0.036 0.118 537 Planarity : 0.004 0.032 529 Dihedral : 3.602 29.281 436 Min Nonbonded Distance : 2.271 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: 3.11 (0.42), residues: 408 helix: 2.53 (0.28), residues: 341 sheet: -1.43 (1.26), residues: 20 loop : 0.15 (0.96), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 130 HIS 0.001 0.000 HIS B 313 PHE 0.008 0.001 PHE B 237 TYR 0.006 0.001 TYR B 208 ARG 0.003 0.000 ARG B 85 Details of bonding type rmsd hydrogen bonds : bond 0.03575 ( 257) hydrogen bonds : angle 4.26756 ( 768) covalent geometry : bond 0.00227 ( 3144) covalent geometry : angle 0.46355 ( 4282) *********************** 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 : 0.366 Fit side-chains REVERT: B 224 GLN cc_start: 0.7357 (pm20) cc_final: 0.7143 (pm20) REVERT: B 292 MET cc_start: 0.6984 (mpt) cc_final: 0.6442 (pp-130) REVERT: B 388 ASP cc_start: 0.8044 (OUTLIER) cc_final: 0.7440 (m-30) REVERT: B 485 TYR cc_start: 0.6805 (t80) cc_final: 0.6317 (t80) outliers start: 10 outliers final: 5 residues processed: 40 average time/residue: 0.7458 time to fit residues: 31.3603 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 : 0.312 ------------------------------------------------------------------------------- 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: 0.8980 chunk 14 optimal weight: 6.9990 chunk 3 optimal weight: 0.6980 chunk 5 optimal weight: 0.2980 chunk 26 optimal weight: 0.0870 chunk 18 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 28 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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 = 0.170252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.124241 restraints weight = 3668.192| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 1.83 r_work: 0.3503 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3402 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 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= 0.110 Angle : 0.467 5.403 4282 Z= 0.232 Chirality : 0.037 0.119 537 Planarity : 0.004 0.032 529 Dihedral : 3.582 29.009 436 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.74 % Allowed : 14.02 % Favored : 83.23 % 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: 3.19 (0.43), residues: 408 helix: 2.53 (0.28), residues: 346 sheet: -1.44 (1.25), residues: 20 loop : 0.34 (1.02), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 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 0.003 0.000 ARG B 85 Details of bonding type rmsd hydrogen bonds : bond 0.03617 ( 257) hydrogen bonds : angle 4.25155 ( 768) covalent geometry : bond 0.00235 ( 3144) covalent geometry : angle 0.46717 ( 4282) *********************** 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 39 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 30 time to evaluate : 0.319 Fit side-chains REVERT: B 292 MET cc_start: 0.6964 (mpt) cc_final: 0.6345 (pp-130) REVERT: B 388 ASP cc_start: 0.8037 (OUTLIER) cc_final: 0.7428 (m-30) REVERT: B 485 TYR cc_start: 0.6818 (t80) cc_final: 0.6336 (t80) outliers start: 9 outliers final: 5 residues processed: 38 average time/residue: 0.7478 time to fit residues: 29.8219 Evaluate side-chains 35 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 29 time to evaluate : 0.309 ------------------------------------------------------------------------------- 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: 0.9990 chunk 24 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 4 optimal weight: 0.4980 chunk 22 optimal weight: 7.9990 chunk 12 optimal weight: 0.8980 chunk 31 optimal weight: 6.9990 chunk 33 optimal weight: 0.0670 chunk 15 optimal weight: 2.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- 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 = 0.170239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.123238 restraints weight = 3718.115| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 1.95 r_work: 0.3477 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3373 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.1533 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= 0.109 Angle : 0.473 6.892 4282 Z= 0.232 Chirality : 0.037 0.119 537 Planarity : 0.004 0.032 529 Dihedral : 3.584 28.402 436 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.44 % Allowed : 14.94 % 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: 3.21 (0.43), residues: 408 helix: 2.54 (0.28), residues: 346 sheet: -1.44 (1.27), residues: 20 loop : 0.34 (1.03), 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 0.009 0.001 PHE B 237 TYR 0.007 0.001 TYR B 208 ARG 0.003 0.000 ARG B 85 Details of bonding type rmsd hydrogen bonds : bond 0.03567 ( 257) hydrogen bonds : angle 4.24706 ( 768) covalent geometry : bond 0.00234 ( 3144) covalent geometry : angle 0.47250 ( 4282) *********************** 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: 8 poor density : 33 time to evaluate : 0.332 Fit side-chains REVERT: B 292 MET cc_start: 0.6947 (mpt) cc_final: 0.6370 (pp-130) REVERT: B 388 ASP cc_start: 0.8171 (OUTLIER) cc_final: 0.7580 (m-30) REVERT: B 485 TYR cc_start: 0.6842 (t80) cc_final: 0.6365 (t80) outliers start: 8 outliers final: 5 residues processed: 40 average time/residue: 0.7021 time to fit residues: 29.5728 Evaluate side-chains 38 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 32 time to evaluate : 0.308 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 14 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 31 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 33 optimal weight: 9.9990 chunk 32 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4051 r_free = 0.4051 target = 0.169415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.122878 restraints weight = 3681.066| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 1.83 r_work: 0.3485 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3385 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1490 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= 0.124 Angle : 0.495 7.311 4282 Z= 0.244 Chirality : 0.037 0.122 537 Planarity : 0.004 0.034 529 Dihedral : 3.620 27.991 436 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % 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: 3.07 (0.43), residues: 408 helix: 2.44 (0.28), residues: 347 sheet: -1.55 (1.25), residues: 20 loop : 0.36 (1.05), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 275 HIS 0.001 0.001 HIS B 313 PHE 0.011 0.001 PHE B 237 TYR 0.008 0.001 TYR B 334 ARG 0.003 0.000 ARG B 85 Details of bonding type rmsd hydrogen bonds : bond 0.03781 ( 257) hydrogen bonds : angle 4.32058 ( 768) covalent geometry : bond 0.00279 ( 3144) covalent geometry : angle 0.49493 ( 4282) *********************** 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 44 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 35 time to evaluate : 0.314 Fit side-chains REVERT: B 292 MET cc_start: 0.6948 (mpt) cc_final: 0.6335 (pp-130) REVERT: B 388 ASP cc_start: 0.8078 (OUTLIER) cc_final: 0.7451 (m-30) REVERT: B 485 TYR cc_start: 0.6848 (t80) cc_final: 0.6384 (t80) outliers start: 9 outliers final: 5 residues processed: 42 average time/residue: 0.6834 time to fit residues: 30.2310 Evaluate side-chains 41 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.319 ------------------------------------------------------------------------------- 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: 0.9980 chunk 40 optimal weight: 4.9990 chunk 30 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 37 optimal weight: 0.0870 chunk 9 optimal weight: 3.9990 chunk 27 optimal weight: 0.4980 chunk 7 optimal weight: 0.9980 chunk 31 optimal weight: 7.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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 = 0.4054 r_free = 0.4054 target = 0.169753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.123677 restraints weight = 3631.976| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 1.82 r_work: 0.3495 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3396 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3144 Z= 0.117 Angle : 0.490 7.664 4282 Z= 0.240 Chirality : 0.037 0.120 537 Planarity : 0.004 0.034 529 Dihedral : 3.606 27.607 436 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.83 % Allowed : 16.16 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.14 (0.42), residues: 408 helix: 2.49 (0.28), residues: 346 sheet: -1.51 (1.25), residues: 20 loop : 0.40 (1.03), residues: 42 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 0.002 0.000 ARG B 85 Details of bonding type rmsd hydrogen bonds : bond 0.03677 ( 257) hydrogen bonds : angle 4.28428 ( 768) covalent geometry : bond 0.00256 ( 3144) covalent geometry : angle 0.48952 ( 4282) ********************** 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 41 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.315 Fit side-chains REVERT: B 292 MET cc_start: 0.6921 (mpt) cc_final: 0.6311 (pp-130) REVERT: B 388 ASP cc_start: 0.8044 (OUTLIER) cc_final: 0.7452 (m-30) REVERT: B 485 TYR cc_start: 0.6871 (t80) cc_final: 0.6391 (t80) outliers start: 6 outliers final: 5 residues processed: 40 average time/residue: 0.7227 time to fit residues: 30.3391 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 : 0.306 ------------------------------------------------------------------------------- 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: 1.9990 chunk 28 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 2 optimal weight: 7.9990 chunk 15 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4048 r_free = 0.4048 target = 0.169189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.122628 restraints weight = 3720.925| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 1.85 r_work: 0.3479 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3378 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.1533 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= 0.125 Angle : 0.498 7.589 4282 Z= 0.245 Chirality : 0.037 0.122 537 Planarity : 0.004 0.035 529 Dihedral : 3.641 27.822 436 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.13 % Allowed : 16.16 % 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: 3.06 (0.43), residues: 408 helix: 2.43 (0.28), residues: 347 sheet: -1.58 (1.25), residues: 20 loop : 0.40 (1.06), 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 0.011 0.001 PHE B 237 TYR 0.008 0.001 TYR B 334 ARG 0.002 0.000 ARG B 85 Details of bonding type rmsd hydrogen bonds : bond 0.03783 ( 257) hydrogen bonds : angle 4.32796 ( 768) covalent geometry : bond 0.00280 ( 3144) covalent geometry : angle 0.49766 ( 4282) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2445.12 seconds wall clock time: 42 minutes 51.98 seconds (2571.98 seconds total)