Starting phenix.real_space_refine on Fri Dec 27 06:18:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ctd_26986/12_2024/8ctd_26986.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ctd_26986/12_2024/8ctd_26986.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ctd_26986/12_2024/8ctd_26986.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ctd_26986/12_2024/8ctd_26986.map" model { file = "/net/cci-nas-00/data/ceres_data/8ctd_26986/12_2024/8ctd_26986.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ctd_26986/12_2024/8ctd_26986.cif" } resolution = 3.42 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= 0.006 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: 6 Type Number sf(0) Gaussians Hg 1 10.96 5 S 20 5.16 5 Na 3 4.78 5 C 2051 2.51 5 N 498 2.21 5 O 557 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 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: 3130 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3126 Classifications: {'peptide': 411} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 399} Chain breaks: 3 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' HG': 1, ' NA': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1608 SG CYS A 269 46.477 24.191 27.992 1.00 77.16 S ATOM 2889 SG CYS A 441 42.130 25.493 25.757 1.00158.28 S Time building chain proxies: 2.64, per 1000 atoms: 0.84 Number of scatterers: 3130 At special positions: 0 Unit cell: (71.478, 66.063, 76.893, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Hg 1 79.96 S 20 16.00 Na 3 11.00 O 557 8.00 N 498 7.00 C 2051 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: 0.94 Conformation dependent library (CDL) restraints added in 442.1 milliseconds 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 760 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 1 sheets defined 83.7% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 18 through 39 removed outlier: 3.836A pdb=" N ARG A 39 " --> pdb=" O GLY A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.655A pdb=" N ALA A 53 " --> pdb=" O LYS A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 66 removed outlier: 3.678A pdb=" N ILE A 66 " --> pdb=" O MET A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 82 removed outlier: 3.831A pdb=" N ILE A 72 " --> pdb=" O LEU A 68 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER A 73 " --> pdb=" O PRO A 69 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU A 82 " --> pdb=" O GLY A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 117 removed outlier: 3.840A pdb=" N LYS A 89 " --> pdb=" O ASN A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 121 removed outlier: 4.408A pdb=" N THR A 121 " --> pdb=" O PRO A 118 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 118 through 121' Processing helix chain 'A' and resid 138 through 143 removed outlier: 3.639A pdb=" N LEU A 143 " --> pdb=" O VAL A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 150 removed outlier: 3.586A pdb=" N PHE A 150 " --> pdb=" O ILE A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 158 Processing helix chain 'A' and resid 212 through 230 Processing helix chain 'A' and resid 233 through 272 removed outlier: 3.598A pdb=" N PHE A 240 " --> pdb=" O LEU A 236 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N TRP A 256 " --> pdb=" O GLN A 252 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N TYR A 257 " --> pdb=" O ILE A 253 " (cutoff:3.500A) Proline residue: A 259 - end of helix Processing helix chain 'A' and resid 276 through 282 removed outlier: 3.897A pdb=" N ARG A 280 " --> pdb=" O TRP A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 299 Processing helix chain 'A' and resid 300 through 309 Processing helix chain 'A' and resid 312 through 320 removed outlier: 4.365A pdb=" N PHE A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N MET A 320 " --> pdb=" O PHE A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 331 removed outlier: 3.785A pdb=" N LEU A 324 " --> pdb=" O MET A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 348 removed outlier: 4.165A pdb=" N GLU A 346 " --> pdb=" O ARG A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 363 Proline residue: A 360 - end of helix Processing helix chain 'A' and resid 367 through 385 Processing helix chain 'A' and resid 390 through 408 Processing helix chain 'A' and resid 418 through 426 removed outlier: 3.911A pdb=" N VAL A 422 " --> pdb=" O THR A 418 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL A 426 " --> pdb=" O VAL A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 435 removed outlier: 3.612A pdb=" N ASP A 432 " --> pdb=" O PRO A 429 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL A 433 " --> pdb=" O ALA A 430 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR A 434 " --> pdb=" O GLU A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 445 removed outlier: 3.719A pdb=" N CYS A 441 " --> pdb=" O ILE A 437 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N LEU A 442 " --> pdb=" O ALA A 438 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG A 445 " --> pdb=" O CYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 466 removed outlier: 4.134A pdb=" N ASN A 451 " --> pdb=" O ARG A 447 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY A 460 " --> pdb=" O ALA A 456 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 167 224 hydrogen bonds defined for protein. 666 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: 0.75 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 581 1.33 - 1.45: 675 1.45 - 1.57: 1878 1.57 - 1.69: 0 1.69 - 1.81: 37 Bond restraints: 3171 Sorted by residual: bond pdb=" N ILE A 436 " pdb=" CA ILE A 436 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.29e-02 6.01e+03 7.59e+00 bond pdb=" N ILE A 437 " pdb=" CA ILE A 437 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.19e-02 7.06e+03 7.43e+00 bond pdb=" N VAL A 439 " pdb=" CA VAL A 439 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.37e-02 5.33e+03 6.92e+00 bond pdb=" N ASP A 351 " pdb=" CA ASP A 351 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.23e-02 6.61e+03 6.67e+00 bond pdb=" N ASP A 440 " pdb=" CA ASP A 440 " ideal model delta sigma weight residual 1.459 1.490 -0.030 1.21e-02 6.83e+03 6.33e+00 ... (remaining 3166 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.30: 4089 1.30 - 2.60: 174 2.60 - 3.90: 25 3.90 - 5.20: 14 5.20 - 6.50: 2 Bond angle restraints: 4304 Sorted by residual: angle pdb=" N VAL A 439 " pdb=" CA VAL A 439 " pdb=" C VAL A 439 " ideal model delta sigma weight residual 112.83 109.40 3.43 9.90e-01 1.02e+00 1.20e+01 angle pdb=" C LYS A 16 " pdb=" N ASN A 17 " pdb=" CA ASN A 17 " ideal model delta sigma weight residual 121.54 128.00 -6.46 1.91e+00 2.74e-01 1.14e+01 angle pdb=" C VAL A 411 " pdb=" N PRO A 412 " pdb=" CA PRO A 412 " ideal model delta sigma weight residual 119.56 122.82 -3.26 1.01e+00 9.80e-01 1.04e+01 angle pdb=" CA MET A 449 " pdb=" C MET A 449 " pdb=" O MET A 449 " ideal model delta sigma weight residual 120.82 117.67 3.15 1.05e+00 9.07e-01 8.98e+00 angle pdb=" CA MET A 367 " pdb=" C MET A 367 " pdb=" O MET A 367 " ideal model delta sigma weight residual 121.86 117.92 3.94 1.39e+00 5.18e-01 8.03e+00 ... (remaining 4299 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.86: 1585 13.86 - 27.72: 203 27.72 - 41.57: 82 41.57 - 55.43: 20 55.43 - 69.29: 5 Dihedral angle restraints: 1895 sinusoidal: 718 harmonic: 1177 Sorted by residual: dihedral pdb=" CA ARG A 61 " pdb=" CB ARG A 61 " pdb=" CG ARG A 61 " pdb=" CD ARG A 61 " ideal model delta sinusoidal sigma weight residual -60.00 -119.48 59.48 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CB MET A 229 " pdb=" CG MET A 229 " pdb=" SD MET A 229 " pdb=" CE MET A 229 " ideal model delta sinusoidal sigma weight residual 60.00 1.97 58.03 3 1.50e+01 4.44e-03 9.46e+00 dihedral pdb=" N LEU A 325 " pdb=" CA LEU A 325 " pdb=" CB LEU A 325 " pdb=" CG LEU A 325 " ideal model delta sinusoidal sigma weight residual -60.00 -115.89 55.89 3 1.50e+01 4.44e-03 9.37e+00 ... (remaining 1892 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 388 0.040 - 0.081: 122 0.081 - 0.121: 27 0.121 - 0.161: 11 0.161 - 0.202: 1 Chirality restraints: 549 Sorted by residual: 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 2.71 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA LYS A 117 " pdb=" N LYS A 117 " pdb=" C LYS A 117 " pdb=" CB LYS A 117 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.42e-01 chirality pdb=" CA ILE A 436 " pdb=" N ILE A 436 " pdb=" C ILE A 436 " pdb=" CB ILE A 436 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.39e-01 ... (remaining 546 not shown) Planarity restraints: 523 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A 258 " 0.037 5.00e-02 4.00e+02 5.59e-02 4.99e+00 pdb=" N PRO A 259 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 259 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 259 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A 434 " 0.010 2.00e-02 2.50e+03 2.04e-02 4.17e+00 pdb=" C THR A 434 " -0.035 2.00e-02 2.50e+03 pdb=" O THR A 434 " 0.013 2.00e-02 2.50e+03 pdb=" N LEU A 435 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 373 " -0.004 2.00e-02 2.50e+03 9.03e-03 1.63e+00 pdb=" CG TYR A 373 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR A 373 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR A 373 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR A 373 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR A 373 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 373 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 373 " 0.002 2.00e-02 2.50e+03 ... (remaining 520 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 660 2.78 - 3.31: 3212 3.31 - 3.84: 5069 3.84 - 4.37: 5614 4.37 - 4.90: 9944 Nonbonded interactions: 24499 Sorted by model distance: nonbonded pdb=" OG1 THR A 101 " pdb="NA NA A 603 " model vdw 2.248 2.470 nonbonded pdb=" O ASP A 444 " pdb=" OD1 ASP A 444 " model vdw 2.266 3.040 nonbonded pdb=" SG CYS A 441 " pdb="HG HG A 604 " model vdw 2.291 2.880 nonbonded pdb=" O ALA A 456 " pdb=" OG1 THR A 459 " model vdw 2.291 3.040 nonbonded pdb=" OH TYR A 373 " pdb=" OD1 ASP A 440 " model vdw 2.311 3.040 ... (remaining 24494 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: 0.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.500 Find NCS groups from input model: 0.020 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 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 0.036 3171 Z= 0.225 Angle : 0.630 6.501 4304 Z= 0.398 Chirality : 0.044 0.202 549 Planarity : 0.004 0.056 523 Dihedral : 15.424 69.290 1135 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.00 % Allowed : 22.22 % Favored : 77.78 % 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: 0.84 (0.44), residues: 404 helix: 1.12 (0.31), residues: 317 sheet: 0.22 (1.19), residues: 18 loop : -1.82 (0.69), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 276 HIS 0.000 0.000 HIS A 41 PHE 0.009 0.001 PHE A 341 TYR 0.021 0.001 TYR A 373 ARG 0.002 0.000 ARG A 447 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.381 Fit side-chains REVERT: A 117 LYS cc_start: 0.7208 (pttt) cc_final: 0.6915 (pttp) REVERT: A 286 MET cc_start: 0.7264 (mtp) cc_final: 0.7001 (mtt) REVERT: A 315 ARG cc_start: 0.7733 (mtt180) cc_final: 0.7310 (mtt180) REVERT: A 373 TYR cc_start: 0.6514 (t80) cc_final: 0.5804 (t80) REVERT: A 385 ASN cc_start: 0.6365 (m-40) cc_final: 0.5958 (m-40) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.1659 time to fit residues: 15.0527 Evaluate side-chains 63 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.365 ------------------------------------------------------------------------------- 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: 3.9990 chunk 31 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 10 optimal weight: 7.9990 chunk 20 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 12 optimal weight: 0.0370 chunk 19 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.7258 ------------------------------------------------------------------------------- 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: 0.7655 moved from start: 0.1036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3171 Z= 0.184 Angle : 0.541 6.955 4304 Z= 0.278 Chirality : 0.039 0.136 549 Planarity : 0.004 0.054 523 Dihedral : 3.510 15.380 431 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 2.92 % Allowed : 21.64 % Favored : 75.44 % 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: 1.30 (0.44), residues: 404 helix: 1.45 (0.31), residues: 320 sheet: -0.02 (1.15), residues: 18 loop : -1.70 (0.70), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 276 HIS 0.000 0.000 HIS A 41 PHE 0.015 0.001 PHE A 457 TYR 0.022 0.002 TYR A 97 ARG 0.003 0.000 ARG A 93 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.369 Fit side-chains REVERT: A 117 LYS cc_start: 0.7598 (pttt) cc_final: 0.7104 (pttp) REVERT: A 286 MET cc_start: 0.7126 (mtp) cc_final: 0.6760 (mtt) REVERT: A 373 TYR cc_start: 0.6984 (t80) cc_final: 0.6177 (t80) REVERT: A 385 ASN cc_start: 0.6406 (m-40) cc_final: 0.6172 (m-40) outliers start: 10 outliers final: 7 residues processed: 67 average time/residue: 0.1380 time to fit residues: 11.5892 Evaluate side-chains 68 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 426 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 10 optimal weight: 0.0270 chunk 37 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 36 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- 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: 0.7649 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3171 Z= 0.161 Angle : 0.493 5.369 4304 Z= 0.256 Chirality : 0.038 0.135 549 Planarity : 0.004 0.054 523 Dihedral : 3.501 17.862 431 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 4.09 % Allowed : 21.64 % Favored : 74.27 % 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: 1.53 (0.44), residues: 404 helix: 1.64 (0.31), residues: 316 sheet: -0.13 (1.18), residues: 18 loop : -1.48 (0.66), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 276 HIS 0.001 0.000 HIS A 296 PHE 0.013 0.001 PHE A 457 TYR 0.010 0.001 TYR A 97 ARG 0.002 0.000 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 0.355 Fit side-chains REVERT: A 117 LYS cc_start: 0.7495 (pttt) cc_final: 0.7130 (pttp) REVERT: A 286 MET cc_start: 0.7158 (mtp) cc_final: 0.6765 (mtt) REVERT: A 328 LEU cc_start: 0.7021 (OUTLIER) cc_final: 0.6713 (tt) outliers start: 14 outliers final: 8 residues processed: 74 average time/residue: 0.1500 time to fit residues: 13.7005 Evaluate side-chains 70 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 426 VAL 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: 7.9990 chunk 19 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 17 optimal weight: 0.0970 chunk 25 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 39 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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: 0.7688 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3171 Z= 0.212 Angle : 0.536 8.149 4304 Z= 0.275 Chirality : 0.039 0.144 549 Planarity : 0.004 0.055 523 Dihedral : 3.593 18.487 431 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 4.68 % Allowed : 22.81 % Favored : 72.51 % 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: 1.39 (0.44), residues: 404 helix: 1.56 (0.31), residues: 321 sheet: -0.54 (1.17), residues: 18 loop : -1.80 (0.68), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 276 HIS 0.001 0.001 HIS A 296 PHE 0.011 0.001 PHE A 457 TYR 0.015 0.001 TYR A 97 ARG 0.002 0.000 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.353 Fit side-chains REVERT: A 117 LYS cc_start: 0.7429 (pttt) cc_final: 0.7129 (pttp) REVERT: A 286 MET cc_start: 0.7220 (mtp) cc_final: 0.6777 (mtt) REVERT: A 315 ARG cc_start: 0.7690 (mtt180) cc_final: 0.7309 (mtt180) REVERT: A 328 LEU cc_start: 0.6934 (OUTLIER) cc_final: 0.6629 (tt) REVERT: A 373 TYR cc_start: 0.7061 (t80) cc_final: 0.6798 (t80) outliers start: 16 outliers final: 13 residues processed: 77 average time/residue: 0.1554 time to fit residues: 14.5180 Evaluate side-chains 77 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 453 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 29 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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: 0.7683 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3171 Z= 0.192 Angle : 0.521 7.600 4304 Z= 0.268 Chirality : 0.038 0.141 549 Planarity : 0.004 0.055 523 Dihedral : 3.596 17.966 431 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 5.56 % Allowed : 21.93 % Favored : 72.51 % 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: 1.41 (0.44), residues: 404 helix: 1.59 (0.31), residues: 316 sheet: -0.69 (1.16), residues: 18 loop : -1.55 (0.64), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 276 HIS 0.001 0.000 HIS A 296 PHE 0.015 0.001 PHE A 341 TYR 0.016 0.001 TYR A 97 ARG 0.002 0.000 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 63 time to evaluate : 0.354 Fit side-chains REVERT: A 117 LYS cc_start: 0.7508 (pttt) cc_final: 0.7180 (pttp) REVERT: A 208 ASP cc_start: 0.7495 (OUTLIER) cc_final: 0.7178 (t70) REVERT: A 315 ARG cc_start: 0.7689 (mtt180) cc_final: 0.7341 (mtt180) REVERT: A 328 LEU cc_start: 0.6928 (OUTLIER) cc_final: 0.6714 (tt) REVERT: A 373 TYR cc_start: 0.7102 (t80) cc_final: 0.6850 (t80) outliers start: 19 outliers final: 14 residues processed: 74 average time/residue: 0.1529 time to fit residues: 13.8538 Evaluate side-chains 76 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 60 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 453 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3171 Z= 0.179 Angle : 0.525 8.718 4304 Z= 0.267 Chirality : 0.038 0.143 549 Planarity : 0.004 0.054 523 Dihedral : 3.591 18.772 431 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 4.97 % Allowed : 23.10 % Favored : 71.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.44), residues: 404 helix: 1.66 (0.31), residues: 316 sheet: -0.75 (1.16), residues: 18 loop : -1.51 (0.65), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 276 HIS 0.001 0.000 HIS A 296 PHE 0.011 0.001 PHE A 457 TYR 0.015 0.001 TYR A 97 ARG 0.002 0.000 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 64 time to evaluate : 0.358 Fit side-chains REVERT: A 208 ASP cc_start: 0.7495 (OUTLIER) cc_final: 0.7178 (t70) REVERT: A 286 MET cc_start: 0.7161 (mtp) cc_final: 0.6909 (mtp) REVERT: A 315 ARG cc_start: 0.7682 (mtt180) cc_final: 0.7339 (mtt180) REVERT: A 373 TYR cc_start: 0.7009 (t80) cc_final: 0.6738 (t80) outliers start: 17 outliers final: 13 residues processed: 73 average time/residue: 0.1380 time to fit residues: 12.4815 Evaluate side-chains 74 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 453 LEU 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: 0.8980 chunk 33 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 24 optimal weight: 0.0980 chunk 18 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 23 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3171 Z= 0.174 Angle : 0.519 8.073 4304 Z= 0.264 Chirality : 0.037 0.142 549 Planarity : 0.004 0.054 523 Dihedral : 3.562 19.088 431 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 4.68 % Allowed : 24.27 % Favored : 71.05 % 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: 1.57 (0.44), residues: 404 helix: 1.70 (0.31), residues: 316 sheet: -0.78 (1.15), residues: 18 loop : -1.45 (0.65), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 276 HIS 0.001 0.000 HIS A 41 PHE 0.011 0.001 PHE A 457 TYR 0.009 0.001 TYR A 373 ARG 0.001 0.000 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.404 Fit side-chains REVERT: A 208 ASP cc_start: 0.7458 (OUTLIER) cc_final: 0.7131 (t70) REVERT: A 286 MET cc_start: 0.7169 (mtp) cc_final: 0.6896 (mtp) REVERT: A 315 ARG cc_start: 0.7685 (mtt180) cc_final: 0.7346 (mtt180) REVERT: A 328 LEU cc_start: 0.7046 (OUTLIER) cc_final: 0.6777 (tt) REVERT: A 373 TYR cc_start: 0.7002 (t80) cc_final: 0.6740 (t80) outliers start: 16 outliers final: 12 residues processed: 74 average time/residue: 0.1441 time to fit residues: 13.0802 Evaluate side-chains 78 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 453 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 36 optimal weight: 0.0970 chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3171 Z= 0.175 Angle : 0.523 7.961 4304 Z= 0.268 Chirality : 0.038 0.150 549 Planarity : 0.004 0.053 523 Dihedral : 3.600 19.949 431 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 4.39 % Allowed : 25.15 % Favored : 70.47 % 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: 1.50 (0.44), residues: 404 helix: 1.67 (0.31), residues: 317 sheet: -0.79 (1.14), residues: 18 loop : -1.63 (0.64), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 276 HIS 0.001 0.000 HIS A 41 PHE 0.020 0.001 PHE A 341 TYR 0.035 0.002 TYR A 97 ARG 0.001 0.000 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.374 Fit side-chains revert: symmetry clash REVERT: A 286 MET cc_start: 0.7229 (mtp) cc_final: 0.6948 (mtp) REVERT: A 315 ARG cc_start: 0.7679 (mtt180) cc_final: 0.7337 (mtt180) REVERT: A 328 LEU cc_start: 0.7067 (OUTLIER) cc_final: 0.6543 (tt) REVERT: A 373 TYR cc_start: 0.6962 (t80) cc_final: 0.6711 (t80) outliers start: 15 outliers final: 13 residues processed: 71 average time/residue: 0.1490 time to fit residues: 13.0202 Evaluate side-chains 77 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 453 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3171 Z= 0.195 Angle : 0.553 10.381 4304 Z= 0.280 Chirality : 0.038 0.156 549 Planarity : 0.004 0.054 523 Dihedral : 3.637 18.594 431 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 4.68 % Allowed : 25.44 % Favored : 69.88 % 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: 1.41 (0.44), residues: 404 helix: 1.57 (0.31), residues: 317 sheet: -0.78 (1.14), residues: 18 loop : -1.45 (0.67), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 276 HIS 0.001 0.000 HIS A 41 PHE 0.013 0.001 PHE A 457 TYR 0.032 0.002 TYR A 97 ARG 0.002 0.000 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.358 Fit side-chains REVERT: A 286 MET cc_start: 0.7122 (mtp) cc_final: 0.6833 (mtp) REVERT: A 315 ARG cc_start: 0.7784 (mtt180) cc_final: 0.7449 (mtt180) outliers start: 16 outliers final: 15 residues processed: 73 average time/residue: 0.1529 time to fit residues: 13.6944 Evaluate side-chains 78 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 453 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 6.9990 chunk 3 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 19 optimal weight: 0.3980 chunk 34 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3171 Z= 0.201 Angle : 0.585 10.363 4304 Z= 0.289 Chirality : 0.038 0.156 549 Planarity : 0.004 0.054 523 Dihedral : 3.658 18.794 431 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 4.39 % Allowed : 26.32 % Favored : 69.30 % 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: 1.47 (0.44), residues: 404 helix: 1.59 (0.31), residues: 317 sheet: -0.74 (1.15), residues: 18 loop : -1.35 (0.70), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 276 HIS 0.001 0.000 HIS A 41 PHE 0.019 0.001 PHE A 341 TYR 0.033 0.002 TYR A 97 ARG 0.002 0.000 ARG A 342 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.368 Fit side-chains REVERT: A 286 MET cc_start: 0.7200 (mtp) cc_final: 0.6896 (mtp) REVERT: A 315 ARG cc_start: 0.7791 (mtt180) cc_final: 0.7510 (mtt180) outliers start: 15 outliers final: 14 residues processed: 70 average time/residue: 0.1369 time to fit residues: 12.0128 Evaluate side-chains 76 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 453 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 27 optimal weight: 0.0770 chunk 26 optimal weight: 1.9990 chunk 24 optimal weight: 0.3980 chunk 16 optimal weight: 0.4980 chunk 15 optimal weight: 0.9980 chunk 40 optimal weight: 0.0270 overall best weight: 0.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.191759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.144574 restraints weight = 2211.892| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 1.25 r_work: 0.3448 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3171 Z= 0.152 Angle : 0.547 10.492 4304 Z= 0.271 Chirality : 0.037 0.145 549 Planarity : 0.004 0.053 523 Dihedral : 3.567 18.766 431 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 3.80 % Allowed : 26.32 % Favored : 69.88 % 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: 1.75 (0.44), residues: 404 helix: 1.81 (0.31), residues: 312 sheet: 0.04 (1.06), residues: 16 loop : -1.31 (0.65), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 276 HIS 0.000 0.000 HIS A 296 PHE 0.015 0.001 PHE A 341 TYR 0.027 0.002 TYR A 97 ARG 0.002 0.000 ARG A 342 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1123.93 seconds wall clock time: 21 minutes 9.26 seconds (1269.26 seconds total)