Starting phenix.real_space_refine on Fri Aug 22 13:14:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qrq_18623/08_2025/8qrq_18623.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qrq_18623/08_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_18623/08_2025/8qrq_18623.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qrq_18623/08_2025/8qrq_18623.map" model { file = "/net/cci-nas-00/data/ceres_data/8qrq_18623/08_2025/8qrq_18623.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qrq_18623/08_2025/8qrq_18623.cif" } resolution = 2.74 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 16 5.16 5 Na 3 4.78 5 C 2031 2.51 5 N 503 2.21 5 O 539 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3092 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 3079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3079 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 16, 'TRANS': 397} Chain breaks: 2 Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 13 Unusual residues: {' NA': 3} Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1} Link IDs: {None: 3} Time building chain proxies: 1.27, per 1000 atoms: 0.41 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: 0.29 Conformation dependent library (CDL) restraints added in 142.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.07 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: 0.36 Time building geometry restraints manager: 0.37 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: 0.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.030 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 4.720 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.140 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.09 (0.41), residues: 408 helix: 1.90 (0.29), residues: 330 sheet: -1.21 (1.28), residues: 20 loop : -0.52 (0.65), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 376 TYR 0.008 0.001 TYR B 208 PHE 0.010 0.001 PHE B 299 TRP 0.003 0.001 TRP B 272 HIS 0.001 0.001 HIS B 316 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 3144) covalent geometry : angle 0.50370 ( 4282) hydrogen bonds : bond 0.11096 ( 257) hydrogen bonds : angle 5.84748 ( 768) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 0.073 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 36 average time/residue: 0.4775 time to fit residues: 17.7544 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 : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 466 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 37 optimal weight: 9.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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 = 0.4079 r_free = 0.4079 target = 0.169654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.124177 restraints weight = 3724.356| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 1.85 r_work: 0.3519 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3416 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3144 Z= 0.164 Angle : 0.529 5.895 4282 Z= 0.266 Chirality : 0.039 0.129 537 Planarity : 0.005 0.031 529 Dihedral : 3.959 30.628 438 Min Nonbonded Distance : 2.221 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.48 (0.42), residues: 408 helix: 2.03 (0.27), residues: 347 sheet: -1.41 (1.25), residues: 20 loop : 0.10 (1.02), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 376 TYR 0.008 0.002 TYR B 208 PHE 0.012 0.001 PHE B 237 TRP 0.005 0.001 TRP B 461 HIS 0.002 0.001 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 3144) covalent geometry : angle 0.52867 ( 4282) hydrogen bonds : bond 0.04427 ( 257) hydrogen bonds : angle 4.65725 ( 768) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 31 time to evaluate : 0.082 Fit side-chains outliers start: 9 outliers final: 2 residues processed: 39 average time/residue: 0.4318 time to fit residues: 17.4662 Evaluate side-chains 29 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 27 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 431 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 25 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 35 optimal weight: 0.0170 chunk 19 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.7218 ------------------------------------------------------------------------------- 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 = 0.171298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.125936 restraints weight = 3732.503| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 1.88 r_work: 0.3534 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3434 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.1222 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 : 0.477 5.206 4282 Z= 0.241 Chirality : 0.037 0.123 537 Planarity : 0.005 0.031 529 Dihedral : 3.703 29.997 436 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 3.05 % Allowed : 13.11 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.67 (0.42), residues: 408 helix: 2.16 (0.27), residues: 347 sheet: -1.45 (1.25), residues: 20 loop : 0.15 (1.04), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 85 TYR 0.006 0.001 TYR B 276 PHE 0.010 0.001 PHE B 237 TRP 0.004 0.001 TRP B 461 HIS 0.002 0.001 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 3144) covalent geometry : angle 0.47698 ( 4282) hydrogen bonds : bond 0.03965 ( 257) hydrogen bonds : angle 4.46922 ( 768) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 31 time to evaluate : 0.100 Fit side-chains REVERT: B 292 MET cc_start: 0.7106 (mpt) cc_final: 0.6808 (pp-130) outliers start: 10 outliers final: 3 residues processed: 38 average time/residue: 0.3604 time to fit residues: 14.2040 Evaluate side-chains 31 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 28 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 446 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 9.9990 chunk 3 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 chunk 30 optimal weight: 0.7980 chunk 35 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 39 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.4087 r_free = 0.4087 target = 0.171237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.125714 restraints weight = 3701.991| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 1.88 r_work: 0.3536 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3435 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1289 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= 0.126 Angle : 0.481 5.275 4282 Z= 0.240 Chirality : 0.037 0.123 537 Planarity : 0.004 0.032 529 Dihedral : 3.687 29.931 436 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.79 (0.42), residues: 408 helix: 2.27 (0.28), residues: 346 sheet: -1.58 (1.23), residues: 20 loop : 0.06 (1.02), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 85 TYR 0.006 0.001 TYR B 334 PHE 0.010 0.001 PHE B 237 TRP 0.003 0.001 TRP B 275 HIS 0.001 0.000 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 3144) covalent geometry : angle 0.48084 ( 4282) hydrogen bonds : bond 0.03908 ( 257) hydrogen bonds : angle 4.42821 ( 768) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 29 time to evaluate : 0.174 Fit side-chains REVERT: B 292 MET cc_start: 0.7161 (mpt) cc_final: 0.6758 (pp-130) REVERT: B 485 TYR cc_start: 0.6827 (t80) cc_final: 0.6374 (t80) outliers start: 9 outliers final: 3 residues processed: 37 average time/residue: 0.3606 time to fit residues: 13.9868 Evaluate side-chains 31 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 28 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 446 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 27 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 35 optimal weight: 0.4980 chunk 0 optimal weight: 8.9990 chunk 32 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 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 = 0.4087 r_free = 0.4087 target = 0.171261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.125830 restraints weight = 3679.228| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 1.87 r_work: 0.3567 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3468 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1375 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 5.252 4282 Z= 0.238 Chirality : 0.037 0.124 537 Planarity : 0.004 0.032 529 Dihedral : 3.657 29.512 436 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 3.05 % Allowed : 13.41 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.85 (0.42), residues: 408 helix: 2.32 (0.28), residues: 346 sheet: -1.58 (1.21), residues: 20 loop : 0.02 (1.03), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 85 TYR 0.007 0.001 TYR B 334 PHE 0.011 0.001 PHE B 237 TRP 0.003 0.001 TRP B 275 HIS 0.001 0.000 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 3144) covalent geometry : angle 0.47643 ( 4282) hydrogen bonds : bond 0.03852 ( 257) hydrogen bonds : angle 4.40452 ( 768) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 31 time to evaluate : 0.137 Fit side-chains REVERT: B 292 MET cc_start: 0.7119 (mpt) cc_final: 0.6575 (pp-130) REVERT: B 388 ASP cc_start: 0.8195 (OUTLIER) cc_final: 0.7569 (m-30) REVERT: B 485 TYR cc_start: 0.6807 (t80) cc_final: 0.6338 (t80) outliers start: 10 outliers final: 4 residues processed: 40 average time/residue: 0.3481 time to fit residues: 14.5225 Evaluate side-chains 35 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 30 time to evaluate : 0.146 ------------------------------------------------------------------------------- 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 446 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 7.9990 chunk 27 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 12 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.171239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.125965 restraints weight = 3719.712| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 1.88 r_work: 0.3528 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3428 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3144 Z= 0.123 Angle : 0.478 5.223 4282 Z= 0.239 Chirality : 0.037 0.123 537 Planarity : 0.004 0.032 529 Dihedral : 3.638 29.409 436 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 3.05 % Allowed : 14.02 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.95 (0.43), residues: 408 helix: 2.37 (0.28), residues: 346 sheet: -1.55 (1.21), residues: 20 loop : 0.26 (1.09), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 85 TYR 0.007 0.001 TYR B 334 PHE 0.010 0.001 PHE B 237 TRP 0.003 0.001 TRP B 275 HIS 0.001 0.000 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 3144) covalent geometry : angle 0.47761 ( 4282) hydrogen bonds : bond 0.03808 ( 257) hydrogen bonds : angle 4.38418 ( 768) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 30 time to evaluate : 0.123 Fit side-chains REVERT: B 292 MET cc_start: 0.7188 (mpt) cc_final: 0.6639 (pp-130) REVERT: B 388 ASP cc_start: 0.8397 (OUTLIER) cc_final: 0.7819 (m-30) REVERT: B 485 TYR cc_start: 0.6899 (t80) cc_final: 0.6430 (t80) outliers start: 10 outliers final: 4 residues processed: 38 average time/residue: 0.3777 time to fit residues: 14.9819 Evaluate side-chains 34 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 29 time to evaluate : 0.090 ------------------------------------------------------------------------------- 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 446 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.8980 chunk 22 optimal weight: 6.9990 chunk 36 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 32 optimal weight: 0.8980 chunk 38 optimal weight: 8.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.168324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.121892 restraints weight = 3722.995| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 1.83 r_work: 0.3463 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3362 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.1464 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= 0.134 Angle : 0.489 5.519 4282 Z= 0.245 Chirality : 0.038 0.125 537 Planarity : 0.004 0.032 529 Dihedral : 3.658 29.291 436 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 3.96 % Allowed : 13.72 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.92 (0.43), residues: 408 helix: 2.31 (0.28), residues: 348 sheet: -1.60 (1.21), residues: 20 loop : 0.52 (1.10), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 85 TYR 0.008 0.001 TYR B 334 PHE 0.012 0.001 PHE B 237 TRP 0.004 0.001 TRP B 272 HIS 0.001 0.001 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 3144) covalent geometry : angle 0.48939 ( 4282) hydrogen bonds : bond 0.03935 ( 257) hydrogen bonds : angle 4.41017 ( 768) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 30 time to evaluate : 0.117 Fit side-chains REVERT: B 292 MET cc_start: 0.6996 (mpt) cc_final: 0.6361 (pp-130) REVERT: B 388 ASP cc_start: 0.8154 (OUTLIER) cc_final: 0.7575 (m-30) REVERT: B 485 TYR cc_start: 0.6814 (t80) cc_final: 0.6338 (t80) outliers start: 13 outliers final: 5 residues processed: 40 average time/residue: 0.3683 time to fit residues: 15.3996 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 : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 446 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 17 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.168937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.122596 restraints weight = 3734.977| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 1.83 r_work: 0.3476 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3372 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.1457 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 : 0.486 6.199 4282 Z= 0.241 Chirality : 0.037 0.123 537 Planarity : 0.004 0.032 529 Dihedral : 3.643 29.139 436 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.13 % Allowed : 15.55 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.95 (0.42), residues: 408 helix: 2.35 (0.28), residues: 347 sheet: -1.54 (1.22), residues: 20 loop : 0.38 (1.07), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 85 TYR 0.007 0.001 TYR B 334 PHE 0.011 0.001 PHE B 237 TRP 0.004 0.001 TRP B 275 HIS 0.001 0.000 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 3144) covalent geometry : angle 0.48605 ( 4282) hydrogen bonds : bond 0.03820 ( 257) hydrogen bonds : angle 4.37834 ( 768) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 31 time to evaluate : 0.082 Fit side-chains REVERT: B 292 MET cc_start: 0.6956 (mpt) cc_final: 0.6312 (pp-130) REVERT: B 388 ASP cc_start: 0.8140 (OUTLIER) cc_final: 0.7559 (m-30) REVERT: B 485 TYR cc_start: 0.6816 (t80) cc_final: 0.6332 (t80) outliers start: 7 outliers final: 5 residues processed: 36 average time/residue: 0.4511 time to fit residues: 16.8653 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 : 0.131 ------------------------------------------------------------------------------- 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 10 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 35 optimal weight: 0.0000 chunk 29 optimal weight: 0.0770 chunk 11 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 31 optimal weight: 5.9990 chunk 39 optimal weight: 6.9990 chunk 18 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 overall best weight: 0.4744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.170163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.124092 restraints weight = 3767.032| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 1.85 r_work: 0.3499 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3399 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.1550 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= 0.107 Angle : 0.475 7.014 4282 Z= 0.234 Chirality : 0.037 0.119 537 Planarity : 0.004 0.032 529 Dihedral : 3.600 28.680 436 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 2.13 % Allowed : 15.85 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.15 (0.43), residues: 408 helix: 2.50 (0.28), residues: 346 sheet: -1.40 (1.25), residues: 20 loop : 0.38 (1.04), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 85 TYR 0.007 0.001 TYR B 208 PHE 0.009 0.001 PHE B 237 TRP 0.004 0.001 TRP B 275 HIS 0.001 0.000 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00228 ( 3144) covalent geometry : angle 0.47502 ( 4282) hydrogen bonds : bond 0.03573 ( 257) hydrogen bonds : angle 4.29748 ( 768) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 31 time to evaluate : 0.123 Fit side-chains REVERT: B 292 MET cc_start: 0.6865 (mpt) cc_final: 0.6285 (pp-130) REVERT: B 388 ASP cc_start: 0.8032 (OUTLIER) cc_final: 0.7410 (m-30) REVERT: B 485 TYR cc_start: 0.6834 (t80) cc_final: 0.6378 (t80) outliers start: 7 outliers final: 5 residues processed: 36 average time/residue: 0.4626 time to fit residues: 17.2664 Evaluate side-chains 33 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 27 time to evaluate : 0.115 ------------------------------------------------------------------------------- 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 0 optimal weight: 9.9990 chunk 32 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3959 r_free = 0.3959 target = 0.163975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.118274 restraints weight = 3628.095| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 1.85 r_work: 0.3329 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.1527 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= 0.132 Angle : 0.503 7.398 4282 Z= 0.249 Chirality : 0.038 0.124 537 Planarity : 0.005 0.032 529 Dihedral : 3.651 28.672 436 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.13 % Allowed : 15.85 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.02 (0.42), residues: 408 helix: 2.40 (0.28), residues: 347 sheet: -1.51 (1.24), residues: 20 loop : 0.38 (1.06), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 85 TYR 0.008 0.001 TYR B 334 PHE 0.011 0.001 PHE B 237 TRP 0.004 0.001 TRP B 272 HIS 0.001 0.000 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 3144) covalent geometry : angle 0.50300 ( 4282) hydrogen bonds : bond 0.03864 ( 257) hydrogen bonds : angle 4.37921 ( 768) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 29 time to evaluate : 0.124 Fit side-chains REVERT: B 292 MET cc_start: 0.6698 (mpt) cc_final: 0.6287 (pp-130) REVERT: B 388 ASP cc_start: 0.8129 (OUTLIER) cc_final: 0.7503 (m-30) REVERT: B 485 TYR cc_start: 0.6834 (t80) cc_final: 0.6336 (t80) outliers start: 7 outliers final: 5 residues processed: 35 average time/residue: 0.3262 time to fit residues: 11.9900 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 : 0.084 ------------------------------------------------------------------------------- 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 17 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 14 optimal weight: 0.1980 chunk 24 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 367 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.164755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.118967 restraints weight = 3728.719| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 1.88 r_work: 0.3345 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3144 Z= 0.117 Angle : 0.492 7.645 4282 Z= 0.242 Chirality : 0.037 0.121 537 Planarity : 0.005 0.032 529 Dihedral : 3.630 28.453 436 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 2.13 % Allowed : 15.85 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.09 (0.42), residues: 408 helix: 2.45 (0.28), residues: 346 sheet: -1.48 (1.25), residues: 20 loop : 0.39 (1.04), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 85 TYR 0.007 0.001 TYR B 334 PHE 0.010 0.001 PHE B 237 TRP 0.003 0.001 TRP B 275 HIS 0.001 0.000 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 3144) covalent geometry : angle 0.49239 ( 4282) hydrogen bonds : bond 0.03717 ( 257) hydrogen bonds : angle 4.34073 ( 768) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1275.50 seconds wall clock time: 22 minutes 28.74 seconds (1348.74 seconds total)