Starting phenix.real_space_refine on Fri Dec 27 06:19:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cv3_27007/12_2024/8cv3_27007.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cv3_27007/12_2024/8cv3_27007.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8cv3_27007/12_2024/8cv3_27007.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cv3_27007/12_2024/8cv3_27007.map" model { file = "/net/cci-nas-00/data/ceres_data/8cv3_27007/12_2024/8cv3_27007.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cv3_27007/12_2024/8cv3_27007.cif" } resolution = 3.04 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= 0.004 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 21 5.16 5 Na 2 4.78 5 C 2076 2.51 5 N 504 2.21 5 O 565 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 3168 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3166 Classifications: {'peptide': 416} Link IDs: {'PTRANS': 11, 'TRANS': 404} Chain breaks: 2 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.34, per 1000 atoms: 1.05 Number of scatterers: 3168 At special positions: 0 Unit cell: (67.308, 61.344, 77.532, 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 21 16.00 Na 2 11.00 O 565 8.00 N 504 7.00 C 2076 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: 0.86 Conformation dependent library (CDL) restraints added in 393.1 milliseconds 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 770 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 1 sheets defined 85.3% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 18 through 42 removed outlier: 3.634A pdb=" N LEU A 22 " --> pdb=" O ASN A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.694A pdb=" N ALA A 53 " --> pdb=" O LYS A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 82 removed outlier: 4.403A pdb=" N LEU A 68 " --> pdb=" O LYS A 64 " (cutoff:3.500A) Proline residue: A 69 - end of helix removed outlier: 3.857A pdb=" N LEU A 82 " --> pdb=" O GLY A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 117 removed outlier: 3.594A pdb=" N ILE A 90 " --> pdb=" O VAL A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 148 Processing helix chain 'A' and resid 153 through 158 removed outlier: 3.533A pdb=" N ALA A 158 " --> pdb=" O LEU A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 230 removed outlier: 3.629A pdb=" N LEU A 215 " --> pdb=" O ASN A 211 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLY A 230 " --> pdb=" O ILE A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 273 removed outlier: 3.556A pdb=" N VAL A 237 " --> pdb=" O GLY A 233 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N TYR A 257 " --> pdb=" O ILE A 253 " (cutoff:3.500A) Proline residue: A 259 - end of helix removed outlier: 4.285A pdb=" N VAL A 273 " --> pdb=" O CYS A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 282 Processing helix chain 'A' and resid 282 through 299 removed outlier: 3.554A pdb=" N VAL A 289 " --> pdb=" O TYR A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 309 Processing helix chain 'A' and resid 312 through 320 removed outlier: 3.755A pdb=" N PHE A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA A 317 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 331 Processing helix chain 'A' and resid 333 through 335 No H-bonds generated for 'chain 'A' and resid 333 through 335' Processing helix chain 'A' and resid 336 through 347 Processing helix chain 'A' and resid 351 through 366 removed outlier: 3.794A pdb=" N PHE A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) Proline residue: A 360 - end of helix Processing helix chain 'A' and resid 367 through 385 Processing helix chain 'A' and resid 390 through 404 Processing helix chain 'A' and resid 416 through 427 removed outlier: 3.716A pdb=" N VAL A 422 " --> pdb=" O THR A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 431 No H-bonds generated for 'chain 'A' and resid 429 through 431' Processing helix chain 'A' and resid 432 through 437 removed outlier: 4.252A pdb=" N ILE A 436 " --> pdb=" O ASP A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 466 removed outlier: 4.717A pdb=" N ARG A 445 " --> pdb=" O CYS A 441 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N PHE A 446 " --> pdb=" O LEU A 442 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY A 460 " --> pdb=" O ALA A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 476 removed outlier: 3.782A pdb=" N VAL A 475 " --> pdb=" O GLU A 471 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N SER A 476 " --> pdb=" O GLN A 472 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 167 242 hydrogen bonds defined for protein. 723 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: 0.81 Time building geometry restraints manager: 0.97 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: 946 1.34 - 1.45: 356 1.45 - 1.57: 1872 1.57 - 1.69: 0 1.69 - 1.81: 39 Bond restraints: 3213 Sorted by residual: bond pdb=" N ILE A 421 " pdb=" CA ILE A 421 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.17e-02 7.31e+03 7.46e+00 bond pdb=" N VAL A 411 " pdb=" CA VAL A 411 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.23e-02 6.61e+03 7.18e+00 bond pdb=" N GLY A 410 " pdb=" CA GLY A 410 " ideal model delta sigma weight residual 1.447 1.476 -0.028 1.58e-02 4.01e+03 3.21e+00 bond pdb=" C GLN A 413 " pdb=" O GLN A 413 " ideal model delta sigma weight residual 1.234 1.255 -0.021 1.20e-02 6.94e+03 3.13e+00 bond pdb=" CB GLN A 413 " pdb=" CG GLN A 413 " ideal model delta sigma weight residual 1.520 1.570 -0.050 3.00e-02 1.11e+03 2.75e+00 ... (remaining 3208 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 4281 1.56 - 3.11: 57 3.11 - 4.67: 14 4.67 - 6.22: 4 6.22 - 7.78: 4 Bond angle restraints: 4360 Sorted by residual: angle pdb=" CA GLN A 413 " pdb=" CB GLN A 413 " pdb=" CG GLN A 413 " ideal model delta sigma weight residual 114.10 120.85 -6.75 2.00e+00 2.50e-01 1.14e+01 angle pdb=" CA PRO A 412 " pdb=" C PRO A 412 " pdb=" O PRO A 412 " ideal model delta sigma weight residual 121.77 118.13 3.64 1.14e+00 7.69e-01 1.02e+01 angle pdb=" CA ILE A 421 " pdb=" C ILE A 421 " pdb=" O ILE A 421 " ideal model delta sigma weight residual 121.17 118.11 3.06 1.06e+00 8.90e-01 8.35e+00 angle pdb=" CB LEU A 265 " pdb=" CG LEU A 265 " pdb=" CD1 LEU A 265 " ideal model delta sigma weight residual 110.70 103.30 7.40 3.00e+00 1.11e-01 6.08e+00 angle pdb=" O ILE A 421 " pdb=" C ILE A 421 " pdb=" N VAL A 422 " ideal model delta sigma weight residual 121.91 124.32 -2.41 9.80e-01 1.04e+00 6.06e+00 ... (remaining 4355 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.87: 1592 11.87 - 23.75: 209 23.75 - 35.62: 82 35.62 - 47.49: 23 47.49 - 59.36: 15 Dihedral angle restraints: 1921 sinusoidal: 728 harmonic: 1193 Sorted by residual: dihedral pdb=" CA ASP A 351 " pdb=" CB ASP A 351 " pdb=" CG ASP A 351 " pdb=" OD1 ASP A 351 " ideal model delta sinusoidal sigma weight residual -30.00 -83.34 53.34 1 2.00e+01 2.50e-03 9.67e+00 dihedral pdb=" CB ARG A 445 " pdb=" CG ARG A 445 " pdb=" CD ARG A 445 " pdb=" NE ARG A 445 " ideal model delta sinusoidal sigma weight residual 60.00 119.36 -59.36 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CG LYS A 201 " pdb=" CD LYS A 201 " pdb=" CE LYS A 201 " pdb=" NZ LYS A 201 " ideal model delta sinusoidal sigma weight residual 60.00 1.95 58.05 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 1918 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 403 0.038 - 0.076: 120 0.076 - 0.114: 26 0.114 - 0.152: 2 0.152 - 0.190: 2 Chirality restraints: 553 Sorted by residual: chirality pdb=" CA ILE A 421 " pdb=" N ILE A 421 " pdb=" C ILE A 421 " pdb=" CB ILE A 421 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 9.03e-01 chirality pdb=" CA VAL A 411 " pdb=" N VAL A 411 " pdb=" C VAL A 411 " pdb=" CB VAL A 411 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 6.82e-01 chirality pdb=" CA MET A 367 " pdb=" N MET A 367 " pdb=" C MET A 367 " pdb=" CB MET A 367 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 5.22e-01 ... (remaining 550 not shown) Planarity restraints: 531 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 417 " -0.026 2.00e-02 2.50e+03 5.13e-02 2.63e+01 pdb=" C VAL A 417 " 0.089 2.00e-02 2.50e+03 pdb=" O VAL A 417 " -0.033 2.00e-02 2.50e+03 pdb=" N THR A 418 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 326 " -0.008 2.00e-02 2.50e+03 1.61e-02 2.59e+00 pdb=" C THR A 326 " 0.028 2.00e-02 2.50e+03 pdb=" O THR A 326 " -0.010 2.00e-02 2.50e+03 pdb=" N ALA A 327 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A 258 " -0.026 5.00e-02 4.00e+02 3.86e-02 2.39e+00 pdb=" N PRO A 259 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 259 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 259 " -0.022 5.00e-02 4.00e+02 ... (remaining 528 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 933 2.83 - 3.35: 3144 3.35 - 3.86: 4984 3.86 - 4.38: 5450 4.38 - 4.90: 9882 Nonbonded interactions: 24393 Sorted by model distance: nonbonded pdb=" O THR A 336 " pdb=" OG1 THR A 340 " model vdw 2.310 3.040 nonbonded pdb=" O PRO A 69 " pdb=" OG SER A 73 " model vdw 2.323 3.040 nonbonded pdb=" OD1 ASP A 368 " pdb="NA NA A 602 " model vdw 2.366 2.470 nonbonded pdb=" OG1 THR A 101 " pdb="NA NA A 602 " model vdw 2.386 2.470 nonbonded pdb=" O THR A 396 " pdb=" OG1 THR A 400 " model vdw 2.396 3.040 ... (remaining 24388 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: 1.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.780 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 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 0.050 3213 Z= 0.198 Angle : 0.513 7.776 4360 Z= 0.277 Chirality : 0.038 0.190 553 Planarity : 0.004 0.051 531 Dihedral : 14.071 59.364 1151 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.00 % Allowed : 19.60 % Favored : 80.40 % 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: 1.93 (0.42), residues: 410 helix: 1.97 (0.29), residues: 325 sheet: 0.18 (1.38), residues: 18 loop : -1.91 (0.65), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 276 HIS 0.000 0.000 HIS A 296 PHE 0.003 0.000 PHE A 14 TYR 0.012 0.001 TYR A 200 ARG 0.001 0.000 ARG A 445 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.388 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.1353 time to fit residues: 8.5516 Evaluate side-chains 47 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 37 optimal weight: 0.0980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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: 0.8046 moved from start: 0.1062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3213 Z= 0.168 Angle : 0.467 7.096 4360 Z= 0.248 Chirality : 0.037 0.131 553 Planarity : 0.004 0.066 531 Dihedral : 3.636 15.460 436 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.02 % Allowed : 17.00 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.56 (0.42), residues: 410 helix: 2.39 (0.28), residues: 327 sheet: 0.37 (1.44), residues: 18 loop : -1.66 (0.66), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 19 HIS 0.001 0.000 HIS A 296 PHE 0.008 0.001 PHE A 240 TYR 0.007 0.001 TYR A 305 ARG 0.001 0.000 ARG A 447 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.376 Fit side-chains revert: symmetry clash REVERT: A 21 LEU cc_start: 0.5892 (OUTLIER) cc_final: 0.5424 (tp) REVERT: A 255 MET cc_start: 0.8460 (mmt) cc_final: 0.8040 (mmt) outliers start: 7 outliers final: 3 residues processed: 50 average time/residue: 0.1244 time to fit residues: 8.0724 Evaluate side-chains 48 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 265 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 25 optimal weight: 0.0030 chunk 10 optimal weight: 3.9990 chunk 37 optimal weight: 0.0570 chunk 40 optimal weight: 1.9990 chunk 33 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 overall best weight: 0.7912 ------------------------------------------------------------------------------- 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: 0.8064 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3213 Z= 0.184 Angle : 0.468 6.676 4360 Z= 0.249 Chirality : 0.037 0.134 553 Planarity : 0.004 0.069 531 Dihedral : 3.654 15.388 436 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.73 % Allowed : 18.16 % Favored : 80.12 % 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: 2.56 (0.41), residues: 410 helix: 2.38 (0.28), residues: 327 sheet: 1.31 (1.37), residues: 16 loop : -1.90 (0.63), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 276 HIS 0.001 0.000 HIS A 41 PHE 0.011 0.001 PHE A 240 TYR 0.005 0.001 TYR A 97 ARG 0.001 0.000 ARG A 447 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.385 Fit side-chains revert: symmetry clash REVERT: A 255 MET cc_start: 0.8439 (mmt) cc_final: 0.8143 (mmt) REVERT: A 373 TYR cc_start: 0.6455 (t80) cc_final: 0.5618 (t80) outliers start: 6 outliers final: 3 residues processed: 50 average time/residue: 0.1216 time to fit residues: 8.0305 Evaluate side-chains 47 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 44 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 265 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 7.9990 chunk 28 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 37 optimal weight: 0.0470 chunk 39 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 10 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 overall best weight: 1.0882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 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 0.036 3213 Z= 0.220 Angle : 0.489 6.818 4360 Z= 0.262 Chirality : 0.037 0.137 553 Planarity : 0.004 0.069 531 Dihedral : 3.731 16.127 436 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.59 % Allowed : 17.29 % Favored : 80.12 % 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: 2.42 (0.42), residues: 410 helix: 2.28 (0.28), residues: 327 sheet: 1.19 (1.35), residues: 16 loop : -1.89 (0.65), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 276 HIS 0.001 0.000 HIS A 41 PHE 0.014 0.001 PHE A 240 TYR 0.006 0.001 TYR A 97 ARG 0.001 0.000 ARG A 447 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.329 Fit side-chains revert: symmetry clash REVERT: A 255 MET cc_start: 0.8488 (mmt) cc_final: 0.8204 (mmt) REVERT: A 373 TYR cc_start: 0.6464 (t80) cc_final: 0.5661 (t80) outliers start: 9 outliers final: 7 residues processed: 50 average time/residue: 0.1211 time to fit residues: 7.8648 Evaluate side-chains 51 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 436 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 0.6980 chunk 0 optimal weight: 9.9990 chunk 29 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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: 0.8086 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 3213 Z= 0.196 Angle : 0.473 6.629 4360 Z= 0.253 Chirality : 0.037 0.137 553 Planarity : 0.004 0.057 531 Dihedral : 3.703 15.733 436 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.17 % Allowed : 17.00 % Favored : 79.83 % 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: 2.47 (0.41), residues: 410 helix: 2.34 (0.28), residues: 327 sheet: 1.13 (1.36), residues: 16 loop : -1.96 (0.63), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 19 HIS 0.001 0.000 HIS A 41 PHE 0.011 0.001 PHE A 240 TYR 0.009 0.001 TYR A 305 ARG 0.001 0.000 ARG A 447 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 0.381 Fit side-chains revert: symmetry clash REVERT: A 21 LEU cc_start: 0.6028 (OUTLIER) cc_final: 0.5540 (tp) REVERT: A 255 MET cc_start: 0.8457 (mmt) cc_final: 0.8133 (mmt) REVERT: A 373 TYR cc_start: 0.6444 (t80) cc_final: 0.5669 (t80) outliers start: 11 outliers final: 6 residues processed: 56 average time/residue: 0.1185 time to fit residues: 8.7263 Evaluate side-chains 51 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 436 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 32 optimal weight: 0.0050 chunk 18 optimal weight: 0.7980 chunk 3 optimal weight: 0.0980 chunk 13 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 overall best weight: 0.4794 ------------------------------------------------------------------------------- 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: 0.8026 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 3213 Z= 0.160 Angle : 0.444 5.565 4360 Z= 0.236 Chirality : 0.036 0.132 553 Planarity : 0.004 0.074 531 Dihedral : 3.578 15.030 436 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.59 % Allowed : 17.87 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.74 (0.42), residues: 410 helix: 2.59 (0.29), residues: 326 sheet: 0.05 (1.38), residues: 18 loop : -1.89 (0.62), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 19 HIS 0.001 0.000 HIS A 41 PHE 0.006 0.001 PHE A 240 TYR 0.007 0.001 TYR A 305 ARG 0.001 0.000 ARG A 61 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.367 Fit side-chains revert: symmetry clash REVERT: A 21 LEU cc_start: 0.5898 (OUTLIER) cc_final: 0.5317 (tp) REVERT: A 255 MET cc_start: 0.8421 (mmt) cc_final: 0.8068 (mmt) REVERT: A 262 ILE cc_start: 0.7654 (OUTLIER) cc_final: 0.7438 (mt) REVERT: A 373 TYR cc_start: 0.6399 (t80) cc_final: 0.5675 (t80) outliers start: 9 outliers final: 5 residues processed: 52 average time/residue: 0.1230 time to fit residues: 8.3631 Evaluate side-chains 49 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 475 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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: 0.8105 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 3213 Z= 0.232 Angle : 0.498 6.047 4360 Z= 0.265 Chirality : 0.038 0.138 553 Planarity : 0.004 0.063 531 Dihedral : 3.674 16.229 436 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.59 % Allowed : 18.16 % Favored : 79.25 % 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: 2.43 (0.42), residues: 410 helix: 2.33 (0.29), residues: 327 sheet: 0.79 (1.30), residues: 16 loop : -1.99 (0.61), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 256 HIS 0.001 0.001 HIS A 41 PHE 0.014 0.001 PHE A 240 TYR 0.007 0.001 TYR A 305 ARG 0.001 0.000 ARG A 447 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.360 Fit side-chains revert: symmetry clash REVERT: A 255 MET cc_start: 0.8497 (mmt) cc_final: 0.8216 (mmt) REVERT: A 373 TYR cc_start: 0.6453 (t80) cc_final: 0.5649 (t80) outliers start: 9 outliers final: 7 residues processed: 52 average time/residue: 0.1287 time to fit residues: 8.9109 Evaluate side-chains 53 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 475 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 0.9990 chunk 19 optimal weight: 0.0870 chunk 3 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 35 optimal weight: 10.0000 chunk 37 optimal weight: 9.9990 chunk 34 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 overall best weight: 0.7762 ------------------------------------------------------------------------------- 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: 0.8068 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3213 Z= 0.189 Angle : 0.468 5.675 4360 Z= 0.249 Chirality : 0.037 0.136 553 Planarity : 0.004 0.058 531 Dihedral : 3.631 15.441 436 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.02 % Allowed : 17.87 % Favored : 80.12 % 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: 2.54 (0.42), residues: 410 helix: 2.44 (0.28), residues: 326 sheet: 0.79 (1.31), residues: 16 loop : -2.08 (0.60), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 19 HIS 0.001 0.000 HIS A 41 PHE 0.010 0.001 PHE A 240 TYR 0.006 0.001 TYR A 305 ARG 0.001 0.000 ARG A 147 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.358 Fit side-chains revert: symmetry clash REVERT: A 255 MET cc_start: 0.8463 (mmt) cc_final: 0.8065 (mmt) REVERT: A 373 TYR cc_start: 0.6394 (t80) cc_final: 0.5628 (t80) outliers start: 7 outliers final: 6 residues processed: 50 average time/residue: 0.1214 time to fit residues: 7.9086 Evaluate side-chains 51 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 475 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 36 optimal weight: 9.9990 chunk 24 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 37 optimal weight: 0.0870 overall best weight: 0.6758 ------------------------------------------------------------------------------- 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: 0.8054 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3213 Z= 0.177 Angle : 0.477 8.609 4360 Z= 0.247 Chirality : 0.037 0.134 553 Planarity : 0.004 0.056 531 Dihedral : 3.622 15.296 436 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.31 % Allowed : 17.58 % Favored : 80.12 % 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: 2.56 (0.42), residues: 410 helix: 2.46 (0.28), residues: 326 sheet: 0.75 (1.31), residues: 16 loop : -2.09 (0.60), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 276 HIS 0.001 0.000 HIS A 41 PHE 0.009 0.001 PHE A 240 TYR 0.006 0.001 TYR A 305 ARG 0.001 0.000 ARG A 61 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.366 Fit side-chains revert: symmetry clash REVERT: A 21 LEU cc_start: 0.5878 (OUTLIER) cc_final: 0.5519 (tp) REVERT: A 41 HIS cc_start: 0.6935 (m90) cc_final: 0.6645 (m170) REVERT: A 255 MET cc_start: 0.8432 (mmt) cc_final: 0.8049 (mmt) REVERT: A 373 TYR cc_start: 0.6383 (t80) cc_final: 0.5635 (t80) outliers start: 8 outliers final: 6 residues processed: 53 average time/residue: 0.1264 time to fit residues: 8.6962 Evaluate side-chains 53 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 475 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 0.1980 chunk 3 optimal weight: 0.3980 chunk 25 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 34 optimal weight: 4.9990 chunk 9 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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: 0.8036 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3213 Z= 0.174 Angle : 0.480 8.259 4360 Z= 0.248 Chirality : 0.037 0.134 553 Planarity : 0.004 0.055 531 Dihedral : 3.576 15.173 436 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.02 % Allowed : 17.87 % Favored : 80.12 % 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: 2.61 (0.41), residues: 410 helix: 2.50 (0.28), residues: 326 sheet: 0.79 (1.32), residues: 16 loop : -2.11 (0.60), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 276 HIS 0.001 0.000 HIS A 41 PHE 0.008 0.001 PHE A 240 TYR 0.005 0.001 TYR A 305 ARG 0.001 0.000 ARG A 147 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: A 21 LEU cc_start: 0.5891 (OUTLIER) cc_final: 0.5506 (tp) REVERT: A 41 HIS cc_start: 0.6900 (m90) cc_final: 0.6649 (m170) REVERT: A 255 MET cc_start: 0.8428 (mmt) cc_final: 0.8062 (mmt) REVERT: A 373 TYR cc_start: 0.6349 (t80) cc_final: 0.5622 (t80) outliers start: 7 outliers final: 6 residues processed: 49 average time/residue: 0.1121 time to fit residues: 7.3292 Evaluate side-chains 50 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 475 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 6.9990 chunk 1 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 21 optimal weight: 0.0570 chunk 27 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.150370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.115302 restraints weight = 3747.405| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 1.68 r_work: 0.3133 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3213 Z= 0.184 Angle : 0.491 8.976 4360 Z= 0.252 Chirality : 0.037 0.134 553 Planarity : 0.004 0.054 531 Dihedral : 3.569 15.307 436 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.02 % Allowed : 17.87 % Favored : 80.12 % 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: 2.58 (0.41), residues: 410 helix: 2.47 (0.28), residues: 326 sheet: 0.75 (1.30), residues: 16 loop : -2.11 (0.60), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 256 HIS 0.001 0.000 HIS A 41 PHE 0.009 0.001 PHE A 240 TYR 0.005 0.001 TYR A 305 ARG 0.001 0.000 ARG A 147 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1062.73 seconds wall clock time: 20 minutes 6.07 seconds (1206.07 seconds total)