Starting phenix.real_space_refine on Wed Mar 5 17:44:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ctd_26986/03_2025/8ctd_26986.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ctd_26986/03_2025/8ctd_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_26986/03_2025/8ctd_26986.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ctd_26986/03_2025/8ctd_26986.map" model { file = "/net/cci-nas-00/data/ceres_data/8ctd_26986/03_2025/8ctd_26986.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ctd_26986/03_2025/8ctd_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-5624/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: 2.58, per 1000 atoms: 0.82 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: 0.74 Conformation dependent library (CDL) restraints added in 355.7 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: 0.30 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: 0.85 Time building geometry restraints manager: 0.90 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: 0.720 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.350 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.150 ------------------------------------------------------------------------------- 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 : 0.307 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: 0.1542 time to fit residues: 14.0056 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 : 0.335 ------------------------------------------------------------------------------- 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: 0.9980 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.190303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.138696 restraints weight = 2663.771| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.52 r_work: 0.3423 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 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 : 0.316 Fit side-chains REVERT: A 117 LYS cc_start: 0.7418 (pttt) cc_final: 0.6949 (pttp) REVERT: A 286 MET cc_start: 0.7359 (mtp) cc_final: 0.6978 (mtt) REVERT: A 373 TYR cc_start: 0.7028 (t80) cc_final: 0.6230 (t80) REVERT: A 385 ASN cc_start: 0.6524 (m-40) cc_final: 0.6264 (m-40) outliers start: 10 outliers final: 7 residues processed: 67 average time/residue: 0.1341 time to fit residues: 11.2929 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 : 0.326 ------------------------------------------------------------------------------- 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 38 optimal weight: 0.6980 chunk 2 optimal weight: 9.9990 chunk 37 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 35 optimal weight: 9.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.189838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.138107 restraints weight = 2637.710| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 1.49 r_work: 0.3423 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.1325 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= 0.176 Angle : 0.500 5.405 4304 Z= 0.260 Chirality : 0.038 0.139 549 Planarity : 0.004 0.054 523 Dihedral : 3.524 17.987 431 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 4.39 % Allowed : 21.35 % 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: 1.45 (0.45), residues: 404 helix: 1.58 (0.31), residues: 321 sheet: -0.15 (1.18), residues: 18 loop : -1.76 (0.69), residues: 65 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 0.012 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 81 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.330 Fit side-chains REVERT: A 117 LYS cc_start: 0.7335 (pttt) cc_final: 0.6990 (pttp) REVERT: A 286 MET cc_start: 0.7366 (mtp) cc_final: 0.6959 (mtt) REVERT: A 328 LEU cc_start: 0.6894 (OUTLIER) cc_final: 0.6586 (tt) REVERT: A 373 TYR cc_start: 0.7048 (t80) cc_final: 0.6769 (t80) outliers start: 15 outliers final: 9 residues processed: 75 average time/residue: 0.1315 time to fit residues: 12.3319 Evaluate side-chains 71 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.328 ------------------------------------------------------------------------------- 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 299 VAL 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 33 optimal weight: 0.0870 chunk 29 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 2 optimal weight: 0.2980 chunk 34 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 22 optimal weight: 0.8980 chunk 10 optimal weight: 9.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.191598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.139981 restraints weight = 2607.700| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 1.50 r_work: 0.3422 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.1539 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= 0.163 Angle : 0.514 8.252 4304 Z= 0.261 Chirality : 0.038 0.137 549 Planarity : 0.004 0.054 523 Dihedral : 3.546 20.146 431 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 4.09 % Allowed : 23.68 % Favored : 72.22 % 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: 1.54 (0.44), residues: 404 helix: 1.68 (0.31), residues: 321 sheet: -0.52 (1.17), residues: 18 loop : -1.83 (0.68), residues: 65 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 0.012 0.001 PHE A 457 TYR 0.016 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 83 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.328 Fit side-chains REVERT: A 328 LEU cc_start: 0.6942 (OUTLIER) cc_final: 0.6689 (tt) REVERT: A 373 TYR cc_start: 0.7033 (t80) cc_final: 0.6750 (t80) outliers start: 14 outliers final: 10 residues processed: 76 average time/residue: 0.1374 time to fit residues: 13.1963 Evaluate side-chains 73 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.361 ------------------------------------------------------------------------------- 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 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 15 optimal weight: 0.3980 chunk 7 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4097 r_free = 0.4097 target = 0.189891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.142038 restraints weight = 2216.287| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 1.28 r_work: 0.3426 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3171 Z= 0.182 Angle : 0.514 8.084 4304 Z= 0.262 Chirality : 0.038 0.140 549 Planarity : 0.004 0.054 523 Dihedral : 3.530 19.051 431 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 5.26 % Allowed : 21.05 % Favored : 73.68 % 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: 1.52 (0.44), residues: 404 helix: 1.67 (0.31), residues: 316 sheet: -0.67 (1.17), residues: 18 loop : -1.53 (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 0.016 0.001 PHE A 341 TYR 0.012 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 81 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 63 time to evaluate : 0.375 Fit side-chains REVERT: A 286 MET cc_start: 0.7372 (mtp) cc_final: 0.7131 (mtp) REVERT: A 315 ARG cc_start: 0.7689 (mtt180) cc_final: 0.7352 (mtt180) REVERT: A 373 TYR cc_start: 0.7156 (t80) cc_final: 0.6932 (t80) outliers start: 18 outliers final: 15 residues processed: 74 average time/residue: 0.1473 time to fit residues: 13.5564 Evaluate side-chains 75 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 60 time to evaluate : 0.336 ------------------------------------------------------------------------------- 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 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 33 optimal weight: 0.1980 chunk 4 optimal weight: 0.9980 chunk 38 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 40 optimal weight: 0.4980 chunk 24 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.190918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.143300 restraints weight = 2312.241| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 1.31 r_work: 0.3437 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3171 Z= 0.161 Angle : 0.512 8.842 4304 Z= 0.257 Chirality : 0.037 0.135 549 Planarity : 0.004 0.053 523 Dihedral : 3.520 20.128 431 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 4.39 % Allowed : 23.68 % 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: 1.61 (0.44), residues: 404 helix: 1.74 (0.31), residues: 316 sheet: -0.77 (1.16), residues: 18 loop : -1.53 (0.64), residues: 70 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 0.011 0.001 PHE A 457 TYR 0.009 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 79 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.312 Fit side-chains REVERT: A 286 MET cc_start: 0.7358 (mtp) cc_final: 0.7095 (mtp) REVERT: A 315 ARG cc_start: 0.7684 (mtt180) cc_final: 0.7350 (mtt180) REVERT: A 373 TYR cc_start: 0.7114 (t80) cc_final: 0.6875 (t80) outliers start: 15 outliers final: 12 residues processed: 72 average time/residue: 0.1409 time to fit residues: 12.5933 Evaluate side-chains 73 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.337 ------------------------------------------------------------------------------- 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 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 10 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 7 optimal weight: 5.9990 chunk 31 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 14 optimal weight: 4.9990 chunk 18 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4081 r_free = 0.4081 target = 0.188755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.139912 restraints weight = 2255.414| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 1.32 r_work: 0.3422 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.1851 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= 0.177 Angle : 0.525 8.081 4304 Z= 0.264 Chirality : 0.038 0.142 549 Planarity : 0.004 0.054 523 Dihedral : 3.528 19.073 431 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 4.39 % Allowed : 23.39 % Favored : 72.22 % 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: 1.52 (0.44), residues: 404 helix: 1.67 (0.31), residues: 321 sheet: -0.78 (1.15), residues: 18 loop : -1.73 (0.68), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 276 HIS 0.000 0.000 HIS A 41 PHE 0.010 0.001 PHE A 457 TYR 0.032 0.002 TYR A 97 ARG 0.002 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 79 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.308 Fit side-chains REVERT: A 286 MET cc_start: 0.7373 (mtp) cc_final: 0.7074 (mtp) REVERT: A 315 ARG cc_start: 0.7685 (mtt180) cc_final: 0.7376 (mtt180) REVERT: A 328 LEU cc_start: 0.6993 (OUTLIER) cc_final: 0.6675 (tt) REVERT: A 373 TYR cc_start: 0.7086 (t80) cc_final: 0.6847 (t80) outliers start: 15 outliers final: 10 residues processed: 71 average time/residue: 0.1399 time to fit residues: 12.2047 Evaluate side-chains 73 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.308 ------------------------------------------------------------------------------- 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 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 39 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 38 optimal weight: 6.9990 chunk 28 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 = 0.4084 r_free = 0.4084 target = 0.189232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.141522 restraints weight = 2242.184| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 1.27 r_work: 0.3411 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3171 Z= 0.200 Angle : 0.534 8.089 4304 Z= 0.271 Chirality : 0.038 0.146 549 Planarity : 0.004 0.054 523 Dihedral : 3.603 18.057 431 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 3.80 % Allowed : 24.85 % Favored : 71.35 % 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: 1.45 (0.44), residues: 404 helix: 1.60 (0.31), residues: 321 sheet: -0.80 (1.15), residues: 18 loop : -1.62 (0.68), residues: 65 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 0.017 0.001 PHE A 341 TYR 0.021 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 78 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.341 Fit side-chains REVERT: A 286 MET cc_start: 0.7309 (mtp) cc_final: 0.6998 (mtp) REVERT: A 315 ARG cc_start: 0.7692 (mtt180) cc_final: 0.7399 (mtt180) REVERT: A 328 LEU cc_start: 0.6968 (OUTLIER) cc_final: 0.6755 (tt) REVERT: A 373 TYR cc_start: 0.7128 (t80) cc_final: 0.6913 (t80) outliers start: 13 outliers final: 12 residues processed: 73 average time/residue: 0.1436 time to fit residues: 12.9144 Evaluate side-chains 75 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.340 ------------------------------------------------------------------------------- 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 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 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 13 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 24 optimal weight: 0.0970 chunk 4 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 3 optimal weight: 0.5980 chunk 30 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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 = 0.4058 r_free = 0.4058 target = 0.187106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.137114 restraints weight = 2262.431| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 1.32 r_work: 0.3416 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.2040 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= 0.172 Angle : 0.567 10.371 4304 Z= 0.278 Chirality : 0.038 0.141 549 Planarity : 0.004 0.053 523 Dihedral : 3.596 19.626 431 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 3.51 % Allowed : 25.73 % Favored : 70.76 % 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: 1.66 (0.31), residues: 321 sheet: -0.79 (1.14), residues: 18 loop : -1.45 (0.70), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 276 HIS 0.000 0.000 HIS A 41 PHE 0.011 0.001 PHE A 457 TYR 0.040 0.002 TYR A 97 ARG 0.003 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 75 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.295 Fit side-chains REVERT: A 286 MET cc_start: 0.7283 (mtp) cc_final: 0.6978 (mtp) REVERT: A 315 ARG cc_start: 0.7761 (mtt180) cc_final: 0.7506 (mtt180) outliers start: 12 outliers final: 11 residues processed: 70 average time/residue: 0.1328 time to fit residues: 11.6463 Evaluate side-chains 72 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 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 104 ILE Chi-restraints excluded: chain A residue 167 GLU 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 10 optimal weight: 6.9990 chunk 35 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 15 optimal weight: 0.0970 chunk 27 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 24 optimal weight: 0.0060 chunk 39 optimal weight: 0.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- 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 = 0.4097 r_free = 0.4097 target = 0.190540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.142870 restraints weight = 2172.560| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 1.28 r_work: 0.3427 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3171 Z= 0.175 Angle : 0.553 10.335 4304 Z= 0.276 Chirality : 0.037 0.140 549 Planarity : 0.004 0.053 523 Dihedral : 3.594 20.174 431 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 3.22 % Allowed : 26.02 % Favored : 70.76 % 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: 1.64 (0.44), residues: 404 helix: 1.74 (0.31), residues: 317 sheet: -0.82 (1.14), residues: 18 loop : -1.43 (0.68), residues: 69 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 0.016 0.001 PHE A 341 TYR 0.040 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 74 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.336 Fit side-chains REVERT: A 142 MET cc_start: 0.6864 (tmm) cc_final: 0.6654 (mmm) REVERT: A 286 MET cc_start: 0.7333 (mtp) cc_final: 0.7019 (mtp) REVERT: A 315 ARG cc_start: 0.7794 (mtt180) cc_final: 0.7584 (mtt180) REVERT: A 328 LEU cc_start: 0.7088 (OUTLIER) cc_final: 0.6750 (tt) outliers start: 11 outliers final: 10 residues processed: 69 average time/residue: 0.1541 time to fit residues: 13.1825 Evaluate side-chains 72 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.315 ------------------------------------------------------------------------------- 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 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 36 optimal weight: 0.0770 chunk 7 optimal weight: 1.9990 chunk 35 optimal weight: 0.4980 chunk 11 optimal weight: 0.0040 chunk 24 optimal weight: 0.0670 chunk 34 optimal weight: 1.9990 chunk 14 optimal weight: 0.1980 chunk 12 optimal weight: 0.2980 chunk 13 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 37 optimal weight: 20.0000 overall best weight: 0.1288 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 GLN A 348 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.194629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.148463 restraints weight = 2253.067| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 1.25 r_work: 0.3496 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3385 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.2262 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= 0.140 Angle : 0.554 12.318 4304 Z= 0.267 Chirality : 0.037 0.126 549 Planarity : 0.004 0.053 523 Dihedral : 3.529 18.608 431 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.05 % Allowed : 27.49 % 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: 1.86 (0.44), residues: 404 helix: 1.95 (0.31), residues: 308 sheet: 0.02 (1.10), residues: 16 loop : -1.40 (0.62), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP A 276 HIS 0.001 0.000 HIS A 296 PHE 0.014 0.001 PHE A 457 TYR 0.038 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: 2269.93 seconds wall clock time: 39 minutes 34.96 seconds (2374.96 seconds total)