Starting phenix.real_space_refine on Fri Dec 27 06:10:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qrr_18624/12_2024/8qrr_18624.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qrr_18624/12_2024/8qrr_18624.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qrr_18624/12_2024/8qrr_18624.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qrr_18624/12_2024/8qrr_18624.map" model { file = "/net/cci-nas-00/data/ceres_data/8qrr_18624/12_2024/8qrr_18624.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qrr_18624/12_2024/8qrr_18624.cif" } resolution = 2.78 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 2052 2.51 5 N 512 2.21 5 O 546 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 3129 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 3116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3116 Classifications: {'peptide': 420} Link IDs: {'PTRANS': 16, 'TRANS': 403} 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: 2.80, per 1000 atoms: 0.89 Number of scatterers: 3129 At special positions: 0 Unit cell: (60.192, 70.224, 75.24, 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 546 8.00 N 512 7.00 C 2052 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: 0.88 Conformation dependent library (CDL) restraints added in 408.1 milliseconds 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 762 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 1 sheets defined 85.3% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'B' and resid 52 through 75 Processing helix chain 'B' and resid 77 through 82 Processing helix chain 'B' and resid 82 through 103 removed outlier: 3.687A pdb=" N ALA B 88 " --> pdb=" O GLU B 84 " (cutoff:3.500A) Proline residue: B 92 - end of helix removed outlier: 3.795A 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 Processing helix chain 'B' and resid 249 through 292 removed outlier: 4.530A pdb=" N LEU B 254 " --> pdb=" O PRO B 250 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N LEU B 255 " --> pdb=" O GLU B 251 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N TRP B 275 " --> pdb=" O SER B 271 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N TYR B 276 " --> pdb=" O TRP B 272 " (cutoff:3.500A) Proline residue: B 278 - end of helix Processing helix chain 'B' and resid 294 through 302 Processing helix chain 'B' and resid 302 through 319 Processing helix chain 'B' and resid 319 through 329 Processing helix chain 'B' and resid 332 through 340 removed outlier: 3.731A pdb=" N PHE B 336 " --> pdb=" O ASN B 332 " (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 383 Proline residue: B 380 - end of helix Processing helix chain 'B' and resid 387 through 405 Processing helix chain 'B' and resid 410 through 426 removed outlier: 4.110A pdb=" N VAL B 426 " --> pdb=" O THR B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 446 removed outlier: 3.522A pdb=" N ALA B 440 " --> pdb=" O VAL B 436 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ILE B 441 " --> pdb=" O LEU B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 487 removed outlier: 3.640A pdb=" N ILE B 456 " --> pdb=" O HIS B 452 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N VAL B 459 " --> pdb=" O LEU B 455 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N TRP B 461 " --> pdb=" O LEU B 457 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU B 462 " --> pdb=" O ALA B 458 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ARG B 465 " --> pdb=" O TRP B 461 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 202 through 210 260 hydrogen bonds defined for protein. 780 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: 0.88 Time building geometry restraints manager: 1.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 988 1.34 - 1.46: 426 1.46 - 1.57: 1742 1.57 - 1.69: 0 1.69 - 1.81: 25 Bond restraints: 3181 Sorted by residual: bond pdb=" CG ARG B 301 " pdb=" CD ARG B 301 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.19e-01 bond pdb=" CG LEU B 112 " pdb=" CD1 LEU B 112 " ideal model delta sigma weight residual 1.521 1.499 0.022 3.30e-02 9.18e+02 4.51e-01 bond pdb=" CG LEU B 107 " pdb=" CD1 LEU B 107 " ideal model delta sigma weight residual 1.521 1.500 0.021 3.30e-02 9.18e+02 4.02e-01 bond pdb=" CG1 ILE B 104 " pdb=" CD1 ILE B 104 " ideal model delta sigma weight residual 1.513 1.490 0.023 3.90e-02 6.57e+02 3.35e-01 bond pdb=" CA VAL B 472 " pdb=" C VAL B 472 " ideal model delta sigma weight residual 1.523 1.516 0.007 1.27e-02 6.20e+03 3.31e-01 ... (remaining 3176 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.12: 4214 1.12 - 2.23: 80 2.23 - 3.35: 23 3.35 - 4.47: 8 4.47 - 5.58: 7 Bond angle restraints: 4332 Sorted by residual: angle pdb=" CB ARG B 301 " pdb=" CG ARG B 301 " pdb=" CD ARG B 301 " ideal model delta sigma weight residual 111.30 116.88 -5.58 2.30e+00 1.89e-01 5.89e+00 angle pdb=" CG ARG B 301 " pdb=" CD ARG B 301 " pdb=" NE ARG B 301 " ideal model delta sigma weight residual 112.00 117.10 -5.10 2.20e+00 2.07e-01 5.37e+00 angle pdb=" CA VAL B 459 " pdb=" CB VAL B 459 " pdb=" CG2 VAL B 459 " ideal model delta sigma weight residual 110.40 114.29 -3.89 1.70e+00 3.46e-01 5.25e+00 angle pdb=" N ILE B 103 " pdb=" CA ILE B 103 " pdb=" C ILE B 103 " ideal model delta sigma weight residual 109.34 113.04 -3.70 2.08e+00 2.31e-01 3.16e+00 angle pdb=" N VAL B 459 " pdb=" CA VAL B 459 " pdb=" CB VAL B 459 " ideal model delta sigma weight residual 112.16 110.10 2.06 1.30e+00 5.92e-01 2.51e+00 ... (remaining 4327 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 1669 17.95 - 35.89: 166 35.89 - 53.83: 28 53.83 - 71.78: 1 71.78 - 89.72: 3 Dihedral angle restraints: 1867 sinusoidal: 681 harmonic: 1186 Sorted by residual: 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 -86.47 56.47 1 2.00e+01 2.50e-03 1.07e+01 dihedral pdb=" CB GLU B 251 " pdb=" CG GLU B 251 " pdb=" CD GLU B 251 " pdb=" OE1 GLU B 251 " ideal model delta sinusoidal sigma weight residual 0.00 85.67 -85.67 1 3.00e+01 1.11e-03 9.86e+00 dihedral pdb=" CA GLU B 225 " pdb=" CB GLU B 225 " pdb=" CG GLU B 225 " pdb=" CD GLU B 225 " ideal model delta sinusoidal sigma weight residual -180.00 -130.28 -49.72 3 1.50e+01 4.44e-03 8.81e+00 ... (remaining 1864 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 468 0.059 - 0.118: 73 0.118 - 0.177: 1 0.177 - 0.235: 0 0.235 - 0.294: 1 Chirality restraints: 543 Sorted by residual: chirality pdb=" CB VAL B 459 " pdb=" CA VAL B 459 " pdb=" CG1 VAL B 459 " pdb=" CG2 VAL B 459 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.16e+00 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 3.75e-01 chirality pdb=" CA ILE B 431 " pdb=" N ILE B 431 " pdb=" C ILE B 431 " pdb=" CB ILE B 431 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.41e-01 ... (remaining 540 not shown) Planarity restraints: 536 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 474 " -0.009 2.00e-02 2.50e+03 1.78e-02 3.16e+00 pdb=" C GLY B 474 " 0.031 2.00e-02 2.50e+03 pdb=" O GLY B 474 " -0.012 2.00e-02 2.50e+03 pdb=" N ASP B 475 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 471 " 0.009 2.00e-02 2.50e+03 1.76e-02 3.11e+00 pdb=" C ASN B 471 " -0.031 2.00e-02 2.50e+03 pdb=" O ASN B 471 " 0.011 2.00e-02 2.50e+03 pdb=" N VAL B 472 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 469 " -0.008 2.00e-02 2.50e+03 1.59e-02 2.53e+00 pdb=" C VAL B 469 " 0.028 2.00e-02 2.50e+03 pdb=" O VAL B 469 " -0.010 2.00e-02 2.50e+03 pdb=" N LEU B 470 " -0.009 2.00e-02 2.50e+03 ... (remaining 533 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 617 2.77 - 3.30: 3207 3.30 - 3.83: 5511 3.83 - 4.37: 6085 4.37 - 4.90: 11075 Nonbonded interactions: 26495 Sorted by model distance: nonbonded pdb=" OD1 ASP B 388 " pdb="NA NA B 603 " model vdw 2.234 2.470 nonbonded pdb=" O PHE B 135 " pdb="NA NA B 603 " model vdw 2.255 2.470 nonbonded pdb=" OG1 THR B 139 " pdb="NA NA B 603 " model vdw 2.278 2.470 nonbonded pdb=" OD1 ASN B 386 " pdb="NA NA B 603 " model vdw 2.288 2.470 nonbonded pdb=" OG1 THR B 138 " pdb="NA NA B 603 " model vdw 2.310 2.470 ... (remaining 26490 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: 0.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.820 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:13.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.010 Internal consistency checks: 0.000 Total: 27.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 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 0.029 3181 Z= 0.174 Angle : 0.491 5.583 4332 Z= 0.255 Chirality : 0.039 0.294 543 Planarity : 0.005 0.055 536 Dihedral : 14.324 89.721 1105 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.21 % Allowed : 18.48 % Favored : 80.30 % 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: 2.25 (0.43), residues: 414 helix: 1.96 (0.29), residues: 340 sheet: -1.40 (1.27), residues: 20 loop : -0.25 (0.91), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 338 HIS 0.001 0.001 HIS B 452 PHE 0.008 0.001 PHE B 237 TYR 0.009 0.001 TYR B 334 ARG 0.014 0.001 ARG B 301 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.344 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 45 average time/residue: 0.9722 time to fit residues: 45.4109 Evaluate side-chains 43 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 40 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 410 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.0809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3181 Z= 0.206 Angle : 0.510 6.133 4332 Z= 0.255 Chirality : 0.039 0.199 543 Planarity : 0.004 0.030 536 Dihedral : 3.771 29.938 446 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 3.03 % Allowed : 17.27 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.93 (0.43), residues: 414 helix: 2.43 (0.28), residues: 341 sheet: -1.37 (1.28), residues: 20 loop : 0.01 (0.94), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 275 HIS 0.001 0.001 HIS B 316 PHE 0.011 0.001 PHE B 237 TYR 0.009 0.001 TYR B 334 ARG 0.008 0.000 ARG B 301 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 0.313 Fit side-chains outliers start: 10 outliers final: 3 residues processed: 51 average time/residue: 0.8972 time to fit residues: 47.7267 Evaluate side-chains 43 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 40 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 486 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3181 Z= 0.205 Angle : 0.498 5.141 4332 Z= 0.249 Chirality : 0.039 0.245 543 Planarity : 0.004 0.031 536 Dihedral : 3.229 13.296 441 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 4.85 % Allowed : 15.76 % Favored : 79.39 % 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: 2.90 (0.42), residues: 414 helix: 2.48 (0.28), residues: 341 sheet: None (None), residues: 0 loop : -0.90 (0.70), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 275 HIS 0.001 0.001 HIS B 316 PHE 0.011 0.001 PHE B 237 TYR 0.010 0.001 TYR B 334 ARG 0.008 0.000 ARG B 301 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 42 time to evaluate : 0.358 Fit side-chains outliers start: 16 outliers final: 4 residues processed: 52 average time/residue: 0.9203 time to fit residues: 49.8344 Evaluate side-chains 44 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 486 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 38 optimal weight: 5.9990 chunk 40 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 36 optimal weight: 7.9990 chunk 10 optimal weight: 0.5980 chunk 33 optimal weight: 0.0170 chunk 23 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.1143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3181 Z= 0.182 Angle : 0.489 5.088 4332 Z= 0.244 Chirality : 0.039 0.255 543 Planarity : 0.004 0.031 536 Dihedral : 3.211 13.412 441 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 3.33 % Allowed : 16.36 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.95 (0.42), residues: 414 helix: 2.53 (0.28), residues: 341 sheet: None (None), residues: 0 loop : -0.95 (0.67), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 275 HIS 0.001 0.000 HIS B 316 PHE 0.009 0.001 PHE B 237 TYR 0.009 0.001 TYR B 334 ARG 0.010 0.000 ARG B 301 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.378 Fit side-chains outliers start: 11 outliers final: 3 residues processed: 51 average time/residue: 0.8624 time to fit residues: 45.8444 Evaluate side-chains 43 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 40 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 486 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 3181 Z= 0.343 Angle : 0.557 5.508 4332 Z= 0.279 Chirality : 0.042 0.273 543 Planarity : 0.004 0.033 536 Dihedral : 3.362 13.019 441 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 5.15 % Allowed : 14.85 % Favored : 80.00 % 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: 2.60 (0.42), residues: 414 helix: 2.24 (0.28), residues: 343 sheet: None (None), residues: 0 loop : -0.96 (0.70), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 272 HIS 0.002 0.001 HIS B 316 PHE 0.013 0.002 PHE B 237 TYR 0.018 0.002 TYR B 334 ARG 0.011 0.001 ARG B 301 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 39 time to evaluate : 0.340 Fit side-chains REVERT: B 104 ILE cc_start: 0.8747 (mm) cc_final: 0.8521 (mt) outliers start: 17 outliers final: 6 residues processed: 51 average time/residue: 0.9359 time to fit residues: 49.6217 Evaluate side-chains 44 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 486 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 3 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 21 optimal weight: 0.4980 chunk 39 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 GLN B 484 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.1324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3181 Z= 0.206 Angle : 0.508 5.526 4332 Z= 0.255 Chirality : 0.040 0.288 543 Planarity : 0.004 0.037 536 Dihedral : 3.308 13.371 441 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 3.03 % Allowed : 16.97 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.78 (0.42), residues: 414 helix: 2.40 (0.28), residues: 341 sheet: None (None), residues: 0 loop : -0.97 (0.68), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 338 HIS 0.001 0.000 HIS B 316 PHE 0.010 0.001 PHE B 237 TYR 0.011 0.001 TYR B 334 ARG 0.012 0.001 ARG B 301 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 38 time to evaluate : 0.363 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 44 average time/residue: 0.9427 time to fit residues: 43.2006 Evaluate side-chains 44 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 486 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 0.0870 chunk 34 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3181 Z= 0.197 Angle : 0.507 5.538 4332 Z= 0.254 Chirality : 0.040 0.299 543 Planarity : 0.004 0.041 536 Dihedral : 3.278 12.481 441 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 3.33 % Allowed : 16.36 % Favored : 80.30 % 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: 2.86 (0.42), residues: 414 helix: 2.47 (0.28), residues: 341 sheet: None (None), residues: 0 loop : -1.03 (0.67), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 338 HIS 0.001 0.000 HIS B 316 PHE 0.010 0.001 PHE B 237 TYR 0.010 0.001 TYR B 334 ARG 0.013 0.001 ARG B 301 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.361 Fit side-chains outliers start: 11 outliers final: 4 residues processed: 45 average time/residue: 0.9809 time to fit residues: 45.9303 Evaluate side-chains 43 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 486 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 7.9990 chunk 31 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3181 Z= 0.229 Angle : 0.528 6.085 4332 Z= 0.261 Chirality : 0.041 0.308 543 Planarity : 0.004 0.044 536 Dihedral : 3.281 11.916 441 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 2.12 % Allowed : 17.58 % Favored : 80.30 % 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: 2.80 (0.42), residues: 414 helix: 2.42 (0.28), residues: 341 sheet: None (None), residues: 0 loop : -0.98 (0.68), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 338 HIS 0.001 0.000 HIS B 316 PHE 0.011 0.001 PHE B 237 TYR 0.012 0.001 TYR B 334 ARG 0.013 0.001 ARG B 301 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.340 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 45 average time/residue: 0.9817 time to fit residues: 45.9185 Evaluate side-chains 45 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 486 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 24 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 chunk 38 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 25 optimal weight: 0.0060 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3181 Z= 0.196 Angle : 0.505 6.066 4332 Z= 0.252 Chirality : 0.040 0.305 543 Planarity : 0.004 0.048 536 Dihedral : 3.237 12.205 441 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.52 % Allowed : 18.18 % Favored : 80.30 % 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: 2.89 (0.42), residues: 414 helix: 2.49 (0.28), residues: 341 sheet: None (None), residues: 0 loop : -1.00 (0.67), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 338 HIS 0.001 0.000 HIS B 316 PHE 0.010 0.001 PHE B 237 TYR 0.011 0.001 TYR B 334 ARG 0.014 0.001 ARG B 301 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.376 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 46 average time/residue: 0.9879 time to fit residues: 47.2131 Evaluate side-chains 45 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 42 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 329 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3181 Z= 0.225 Angle : 0.524 6.459 4332 Z= 0.260 Chirality : 0.041 0.305 543 Planarity : 0.004 0.049 536 Dihedral : 3.261 12.446 441 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 0.91 % Allowed : 19.09 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.83 (0.42), residues: 414 helix: 2.45 (0.28), residues: 341 sheet: None (None), residues: 0 loop : -1.03 (0.67), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 338 HIS 0.001 0.000 HIS B 316 PHE 0.011 0.001 PHE B 237 TYR 0.013 0.002 TYR B 334 ARG 0.015 0.001 ARG B 301 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 41 time to evaluate : 0.365 Fit side-chains REVERT: B 292 MET cc_start: 0.7522 (mpt) cc_final: 0.7244 (mpt) outliers start: 3 outliers final: 3 residues processed: 43 average time/residue: 1.0465 time to fit residues: 46.6633 Evaluate side-chains 43 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 40 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 329 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 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 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.128628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.093066 restraints weight = 3626.467| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.01 r_work: 0.2934 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 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 0.032 3181 Z= 0.230 Angle : 0.526 6.476 4332 Z= 0.261 Chirality : 0.041 0.308 543 Planarity : 0.004 0.049 536 Dihedral : 3.285 12.883 441 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.52 % Allowed : 18.48 % Favored : 80.00 % 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: 2.82 (0.42), residues: 414 helix: 2.44 (0.28), residues: 341 sheet: None (None), residues: 0 loop : -1.03 (0.67), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 338 HIS 0.001 0.000 HIS B 316 PHE 0.011 0.001 PHE B 237 TYR 0.013 0.001 TYR B 334 ARG 0.015 0.001 ARG B 301 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1459.88 seconds wall clock time: 26 minutes 55.76 seconds (1615.76 seconds total)