Starting phenix.real_space_refine on Fri Dec 27 06:40:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wrl_32732/12_2024/7wrl_32732.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wrl_32732/12_2024/7wrl_32732.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wrl_32732/12_2024/7wrl_32732.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wrl_32732/12_2024/7wrl_32732.map" model { file = "/net/cci-nas-00/data/ceres_data/7wrl_32732/12_2024/7wrl_32732.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wrl_32732/12_2024/7wrl_32732.cif" } resolution = 3.51 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= 0.043 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: 4 Type Number sf(0) Gaussians S 15 5.16 5 C 2052 2.51 5 N 548 2.21 5 O 636 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 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: 3251 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 971 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "B" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 776 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "R" Number of atoms: 1504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1504 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 10, 'TRANS': 176} Chain breaks: 1 Time building chain proxies: 3.20, per 1000 atoms: 0.98 Number of scatterers: 3251 At special positions: 0 Unit cell: (63.72, 82.08, 76.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 15 16.00 O 636 8.00 N 548 7.00 C 2052 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS R 379 " - pdb=" SG CYS R 432 " distance=2.03 Simple disulfide: pdb=" SG CYS R 391 " - pdb=" SG CYS R 525 " distance=2.03 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: 0.70 Conformation dependent library (CDL) restraints added in 400.9 milliseconds 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 764 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 11 sheets defined 5.0% alpha, 19.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 62 through 65 removed outlier: 3.969A pdb=" N GLN A 65 " --> pdb=" O ASP A 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 62 through 65' Processing helix chain 'A' and resid 87 through 91 removed outlier: 3.608A pdb=" N THR A 91 " --> pdb=" O SER A 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 384 through 390 removed outlier: 3.578A pdb=" N LEU R 387 " --> pdb=" O PRO R 384 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ASN R 388 " --> pdb=" O THR R 385 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASP R 389 " --> pdb=" O LYS R 386 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU R 390 " --> pdb=" O LEU R 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 384 through 390' Processing helix chain 'R' and resid 498 through 502 removed outlier: 3.785A pdb=" N TYR R 501 " --> pdb=" O ARG R 498 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLY R 502 " --> pdb=" O PRO R 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 498 through 502' Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 6 Processing sheet with id=AA2, first strand: chain 'A' and resid 17 through 19 Processing sheet with id=AA3, first strand: chain 'A' and resid 34 through 39 removed outlier: 6.876A pdb=" N SER A 34 " --> pdb=" O ARG A 50 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N ARG A 50 " --> pdb=" O SER A 34 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N TRP A 36 " --> pdb=" O MET A 48 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 72 through 73 removed outlier: 3.508A pdb=" N ASP A 73 " --> pdb=" O THR A 78 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N THR A 78 " --> pdb=" O ASP A 73 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 92 through 93 Processing sheet with id=AA6, first strand: chain 'A' and resid 97 through 101 removed outlier: 4.703A pdb=" N VAL A 119 " --> pdb=" O ARG A 98 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N VAL A 100 " --> pdb=" O MET A 117 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N MET A 117 " --> pdb=" O VAL A 100 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 18 through 22 removed outlier: 3.831A pdb=" N SER B 65 " --> pdb=" O THR B 76 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 46 through 50 removed outlier: 6.537A pdb=" N TRP B 37 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 356 through 358 Processing sheet with id=AB1, first strand: chain 'R' and resid 361 through 362 removed outlier: 6.995A pdb=" N CYS R 361 " --> pdb=" O CYS R 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'R' and resid 452 through 454 51 hydrogen bonds defined for protein. 117 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: 0.79 Time building geometry restraints manager: 0.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1017 1.34 - 1.46: 739 1.46 - 1.57: 1558 1.57 - 1.69: 0 1.69 - 1.81: 18 Bond restraints: 3332 Sorted by residual: bond pdb=" C ASP A 109 " pdb=" N PHE A 110 " ideal model delta sigma weight residual 1.334 1.305 0.030 1.49e-02 4.50e+03 3.93e+00 bond pdb=" CB CYS B 90 " pdb=" SG CYS B 90 " ideal model delta sigma weight residual 1.808 1.757 0.051 3.30e-02 9.18e+02 2.39e+00 bond pdb=" C LYS A 13 " pdb=" N PRO A 14 " ideal model delta sigma weight residual 1.330 1.349 -0.019 1.25e-02 6.40e+03 2.35e+00 bond pdb=" N ALA R 411 " pdb=" CA ALA R 411 " ideal model delta sigma weight residual 1.457 1.436 0.021 1.41e-02 5.03e+03 2.13e+00 bond pdb=" C ALA R 372 " pdb=" N PRO R 373 " ideal model delta sigma weight residual 1.334 1.367 -0.033 2.34e-02 1.83e+03 2.04e+00 ... (remaining 3327 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 4176 1.79 - 3.58: 285 3.58 - 5.37: 55 5.37 - 7.16: 9 7.16 - 8.95: 4 Bond angle restraints: 4529 Sorted by residual: angle pdb=" N VAL R 483 " pdb=" CA VAL R 483 " pdb=" C VAL R 483 " ideal model delta sigma weight residual 106.21 110.82 -4.61 1.07e+00 8.73e-01 1.86e+01 angle pdb=" C GLY R 485 " pdb=" N PHE R 486 " pdb=" CA PHE R 486 " ideal model delta sigma weight residual 121.54 129.41 -7.87 1.91e+00 2.74e-01 1.70e+01 angle pdb=" N VAL R 367 " pdb=" CA VAL R 367 " pdb=" C VAL R 367 " ideal model delta sigma weight residual 112.29 108.61 3.68 9.40e-01 1.13e+00 1.53e+01 angle pdb=" OG1 THR B 94 " pdb=" CB THR B 94 " pdb=" CG2 THR B 94 " ideal model delta sigma weight residual 109.30 102.03 7.27 2.00e+00 2.50e-01 1.32e+01 angle pdb=" C TYR B 51 " pdb=" N ASP B 52 " pdb=" CA ASP B 52 " ideal model delta sigma weight residual 121.71 116.85 4.86 1.39e+00 5.18e-01 1.22e+01 ... (remaining 4524 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.40: 1709 17.40 - 34.79: 196 34.79 - 52.19: 33 52.19 - 69.59: 5 69.59 - 86.98: 1 Dihedral angle restraints: 1944 sinusoidal: 734 harmonic: 1210 Sorted by residual: dihedral pdb=" CA LYS A 13 " pdb=" C LYS A 13 " pdb=" N PRO A 14 " pdb=" CA PRO A 14 " ideal model delta harmonic sigma weight residual -180.00 -145.72 -34.28 0 5.00e+00 4.00e-02 4.70e+01 dihedral pdb=" CA TYR A 60 " pdb=" C TYR A 60 " pdb=" N ALA A 61 " pdb=" CA ALA A 61 " ideal model delta harmonic sigma weight residual 180.00 156.47 23.53 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA ARG R 466 " pdb=" C ARG R 466 " pdb=" N ASP R 467 " pdb=" CA ASP R 467 " ideal model delta harmonic sigma weight residual 180.00 158.19 21.81 0 5.00e+00 4.00e-02 1.90e+01 ... (remaining 1941 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 307 0.047 - 0.094: 120 0.094 - 0.141: 43 0.141 - 0.188: 11 0.188 - 0.235: 4 Chirality restraints: 485 Sorted by residual: chirality pdb=" CB ILE A 51 " pdb=" CA ILE A 51 " pdb=" CG1 ILE A 51 " pdb=" CG2 ILE A 51 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CA TYR B 51 " pdb=" N TYR B 51 " pdb=" C TYR B 51 " pdb=" CB TYR B 51 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CB VAL R 483 " pdb=" CA VAL R 483 " pdb=" CG1 VAL R 483 " pdb=" CG2 VAL R 483 " both_signs ideal model delta sigma weight residual False -2.63 -2.85 0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 482 not shown) Planarity restraints: 586 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS R 462 " 0.050 5.00e-02 4.00e+02 7.53e-02 9.08e+00 pdb=" N PRO R 463 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO R 463 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO R 463 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 338 " -0.014 2.00e-02 2.50e+03 1.75e-02 5.37e+00 pdb=" CG PHE R 338 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE R 338 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE R 338 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE R 338 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE R 338 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE R 338 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG B 56 " 0.037 5.00e-02 4.00e+02 5.59e-02 5.00e+00 pdb=" N PRO B 57 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO B 57 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 57 " 0.031 5.00e-02 4.00e+02 ... (remaining 583 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 986 2.81 - 3.33: 2686 3.33 - 3.86: 5412 3.86 - 4.38: 6037 4.38 - 4.90: 10870 Nonbonded interactions: 25991 Sorted by model distance: nonbonded pdb=" OG1 THR R 415 " pdb=" OD2 ASP R 420 " model vdw 2.289 3.040 nonbonded pdb=" OH TYR B 32 " pdb=" OD2 ASP R 405 " model vdw 2.312 3.040 nonbonded pdb=" ND2 ASN B 54 " pdb=" O GLY B 66 " model vdw 2.322 3.120 nonbonded pdb=" O SER A 25 " pdb=" OG SER A 25 " model vdw 2.327 3.040 nonbonded pdb=" OD2 ASP R 398 " pdb=" OH TYR R 423 " model vdw 2.327 3.040 ... (remaining 25986 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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 group one per residue 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: 0.010 Normalize map: mean=0, sd=1: 2.220 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.340 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:3.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 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 : 0.006 0.054 3332 Z= 0.401 Angle : 1.031 8.952 4529 Z= 0.594 Chirality : 0.060 0.235 485 Planarity : 0.008 0.075 586 Dihedral : 14.713 86.983 1171 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.38 % Favored : 86.62 % Rotamer: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.56 % 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: -4.19 (0.37), residues: 411 helix: -4.93 (0.34), residues: 27 sheet: -2.41 (0.46), residues: 118 loop : -2.86 (0.34), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP A 47 HIS 0.002 0.001 HIS B 41 PHE 0.040 0.003 PHE R 338 TYR 0.032 0.003 TYR B 51 ARG 0.023 0.001 ARG A 84 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.369 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.1812 time to fit residues: 14.8826 Evaluate side-chains 50 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 5.9990 chunk 30 optimal weight: 0.1980 chunk 16 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 31 optimal weight: 0.0270 chunk 12 optimal weight: 0.0980 chunk 19 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 36 optimal weight: 10.0000 chunk 11 optimal weight: 0.7980 overall best weight: 0.4038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 ASN B 54 ASN ** R 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 3332 Z= 0.202 Angle : 0.607 5.627 4529 Z= 0.332 Chirality : 0.044 0.158 485 Planarity : 0.006 0.063 586 Dihedral : 6.262 25.335 466 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.68 % Favored : 88.32 % Rotamer: Outliers : 1.13 % Allowed : 10.14 % Favored : 88.73 % 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: -3.78 (0.38), residues: 411 helix: -4.43 (0.58), residues: 27 sheet: -1.58 (0.47), residues: 116 loop : -2.91 (0.34), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 120 HIS 0.002 0.001 HIS B 41 PHE 0.019 0.001 PHE R 338 TYR 0.019 0.002 TYR B 51 ARG 0.002 0.000 ARG R 457 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 70 time to evaluate : 0.308 Fit side-chains REVERT: R 405 ASP cc_start: 0.8563 (p0) cc_final: 0.8296 (p0) outliers start: 4 outliers final: 3 residues processed: 71 average time/residue: 0.1552 time to fit residues: 13.3380 Evaluate side-chains 62 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 59 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain B residue 53 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 3.9990 chunk 24 optimal weight: 0.0980 chunk 10 optimal weight: 0.8980 chunk 36 optimal weight: 10.0000 chunk 39 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 chunk 12 optimal weight: 0.0670 chunk 29 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 18 optimal weight: 6.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 ASN R 487 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3332 Z= 0.190 Angle : 0.577 5.716 4529 Z= 0.313 Chirality : 0.044 0.154 485 Planarity : 0.005 0.057 586 Dihedral : 5.628 20.544 466 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.22 % Favored : 89.78 % Rotamer: Outliers : 3.10 % Allowed : 12.96 % Favored : 83.94 % 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: -3.48 (0.38), residues: 411 helix: -4.35 (0.61), residues: 27 sheet: -1.24 (0.50), residues: 112 loop : -2.73 (0.34), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 120 HIS 0.002 0.001 HIS B 41 PHE 0.010 0.001 PHE R 347 TYR 0.019 0.001 TYR B 51 ARG 0.001 0.000 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.373 Fit side-chains revert: symmetry clash REVERT: B 44 LYS cc_start: 0.7178 (mptt) cc_final: 0.6336 (ptmm) outliers start: 11 outliers final: 8 residues processed: 69 average time/residue: 0.1495 time to fit residues: 12.6868 Evaluate side-chains 61 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain R residue 341 VAL Chi-restraints excluded: chain R residue 374 PHE Chi-restraints excluded: chain R residue 393 THR Chi-restraints excluded: chain R residue 465 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 38 optimal weight: 3.9990 chunk 19 optimal weight: 10.0000 chunk 34 optimal weight: 4.9990 chunk 10 optimal weight: 0.0010 chunk 32 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 overall best weight: 1.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 ASN ** R 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 3332 Z= 0.424 Angle : 0.698 6.260 4529 Z= 0.384 Chirality : 0.047 0.192 485 Planarity : 0.005 0.056 586 Dihedral : 6.125 22.675 466 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.38 % Favored : 86.62 % Rotamer: Outliers : 2.25 % Allowed : 16.06 % Favored : 81.69 % 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: -3.83 (0.37), residues: 411 helix: -4.50 (0.57), residues: 27 sheet: -1.78 (0.47), residues: 121 loop : -2.85 (0.34), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP A 120 HIS 0.001 0.000 HIS R 505 PHE 0.020 0.002 PHE R 377 TYR 0.025 0.002 TYR B 51 ARG 0.002 0.000 ARG R 454 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.395 Fit side-chains revert: symmetry clash REVERT: B 44 LYS cc_start: 0.7257 (mptt) cc_final: 0.6256 (ptmm) outliers start: 8 outliers final: 8 residues processed: 55 average time/residue: 0.1704 time to fit residues: 11.5890 Evaluate side-chains 55 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain R residue 341 VAL Chi-restraints excluded: chain R residue 393 THR Chi-restraints excluded: chain R residue 465 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 19 optimal weight: 7.9990 chunk 34 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 22 optimal weight: 0.0570 overall best weight: 0.7102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 ASN ** R 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3332 Z= 0.228 Angle : 0.601 6.010 4529 Z= 0.327 Chirality : 0.045 0.155 485 Planarity : 0.005 0.057 586 Dihedral : 5.623 19.988 466 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.19 % Favored : 88.81 % Rotamer: Outliers : 3.66 % Allowed : 16.06 % Favored : 80.28 % 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: -3.66 (0.38), residues: 411 helix: -4.41 (0.61), residues: 27 sheet: -1.57 (0.45), residues: 129 loop : -2.79 (0.36), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 99 HIS 0.000 0.000 HIS B 41 PHE 0.022 0.002 PHE R 490 TYR 0.021 0.002 TYR B 51 ARG 0.002 0.000 ARG A 84 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 54 time to evaluate : 0.358 Fit side-chains REVERT: A 84 ARG cc_start: 0.7695 (mtm110) cc_final: 0.7399 (mtm110) REVERT: B 44 LYS cc_start: 0.7263 (mptt) cc_final: 0.6385 (ptmm) outliers start: 13 outliers final: 9 residues processed: 63 average time/residue: 0.1664 time to fit residues: 12.7256 Evaluate side-chains 58 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain R residue 341 VAL Chi-restraints excluded: chain R residue 374 PHE Chi-restraints excluded: chain R residue 393 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 3 optimal weight: 0.3980 chunk 12 optimal weight: 0.3980 chunk 20 optimal weight: 0.2980 chunk 37 optimal weight: 3.9990 chunk 4 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 ASN ** R 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3332 Z= 0.194 Angle : 0.584 6.971 4529 Z= 0.315 Chirality : 0.044 0.153 485 Planarity : 0.004 0.056 586 Dihedral : 5.368 21.311 466 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.95 % Favored : 89.05 % Rotamer: Outliers : 2.82 % Allowed : 19.15 % Favored : 78.03 % 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: -3.43 (0.39), residues: 411 helix: -4.33 (0.65), residues: 27 sheet: -1.22 (0.48), residues: 120 loop : -2.72 (0.36), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 99 HIS 0.000 0.000 HIS B 41 PHE 0.015 0.001 PHE R 490 TYR 0.021 0.001 TYR B 51 ARG 0.002 0.000 ARG B 56 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.363 Fit side-chains REVERT: B 44 LYS cc_start: 0.7242 (mptt) cc_final: 0.6389 (ptmm) outliers start: 10 outliers final: 9 residues processed: 59 average time/residue: 0.1696 time to fit residues: 12.3149 Evaluate side-chains 60 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain R residue 374 PHE Chi-restraints excluded: chain R residue 501 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 0.0040 chunk 32 optimal weight: 3.9990 chunk 38 optimal weight: 0.0020 chunk 24 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 15 optimal weight: 0.0980 chunk 11 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 overall best weight: 0.3000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 ASN ** R 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3332 Z= 0.170 Angle : 0.570 7.062 4529 Z= 0.306 Chirality : 0.043 0.152 485 Planarity : 0.004 0.055 586 Dihedral : 5.145 19.819 466 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.76 % Favored : 91.24 % Rotamer: Outliers : 3.10 % Allowed : 20.56 % Favored : 76.34 % 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: -3.27 (0.40), residues: 411 helix: -4.27 (0.67), residues: 27 sheet: -1.01 (0.49), residues: 120 loop : -2.66 (0.36), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 99 HIS 0.000 0.000 HIS B 41 PHE 0.013 0.001 PHE R 490 TYR 0.019 0.001 TYR B 51 ARG 0.002 0.000 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.359 Fit side-chains REVERT: B 44 LYS cc_start: 0.7296 (mptt) cc_final: 0.6491 (ptmm) REVERT: R 386 LYS cc_start: 0.8401 (ptpp) cc_final: 0.8144 (ptpp) REVERT: R 444 LYS cc_start: 0.6289 (tppt) cc_final: 0.5560 (pttt) outliers start: 11 outliers final: 8 residues processed: 70 average time/residue: 0.1356 time to fit residues: 11.9644 Evaluate side-chains 58 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain R residue 341 VAL Chi-restraints excluded: chain R residue 374 PHE Chi-restraints excluded: chain R residue 501 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 36 optimal weight: 0.0010 chunk 33 optimal weight: 0.4980 chunk 21 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 ASN ** R 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3332 Z= 0.211 Angle : 0.585 7.146 4529 Z= 0.313 Chirality : 0.044 0.153 485 Planarity : 0.004 0.054 586 Dihedral : 5.112 18.882 466 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.95 % Favored : 89.05 % Rotamer: Outliers : 2.25 % Allowed : 22.82 % Favored : 74.93 % 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: -3.24 (0.39), residues: 411 helix: -4.68 (0.61), residues: 21 sheet: -1.03 (0.49), residues: 120 loop : -2.64 (0.35), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 99 HIS 0.000 0.000 HIS R 505 PHE 0.012 0.001 PHE R 490 TYR 0.020 0.001 TYR B 51 ARG 0.002 0.000 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.386 Fit side-chains REVERT: B 44 LYS cc_start: 0.7125 (mptt) cc_final: 0.6273 (ptmm) REVERT: R 444 LYS cc_start: 0.6315 (tppt) cc_final: 0.5601 (pttt) outliers start: 8 outliers final: 8 residues processed: 60 average time/residue: 0.1513 time to fit residues: 11.3444 Evaluate side-chains 61 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain R residue 341 VAL Chi-restraints excluded: chain R residue 374 PHE Chi-restraints excluded: chain R residue 501 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 18 optimal weight: 7.9990 chunk 26 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 chunk 19 optimal weight: 0.0000 chunk 25 optimal weight: 0.4980 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 ASN ** R 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3332 Z= 0.221 Angle : 0.590 7.363 4529 Z= 0.317 Chirality : 0.044 0.154 485 Planarity : 0.004 0.054 586 Dihedral : 5.138 18.892 466 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.71 % Favored : 89.29 % Rotamer: Outliers : 2.25 % Allowed : 22.54 % Favored : 75.21 % 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: -3.27 (0.40), residues: 411 helix: -4.29 (0.68), residues: 27 sheet: -1.05 (0.49), residues: 120 loop : -2.64 (0.36), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 99 HIS 0.000 0.000 HIS B 41 PHE 0.013 0.001 PHE R 490 TYR 0.020 0.001 TYR B 51 ARG 0.002 0.000 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.353 Fit side-chains revert: symmetry clash REVERT: A 84 ARG cc_start: 0.7672 (mtm110) cc_final: 0.7215 (mtm110) REVERT: R 444 LYS cc_start: 0.6282 (tppt) cc_final: 0.5596 (pttt) outliers start: 8 outliers final: 8 residues processed: 60 average time/residue: 0.1424 time to fit residues: 10.8710 Evaluate side-chains 60 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain R residue 341 VAL Chi-restraints excluded: chain R residue 374 PHE Chi-restraints excluded: chain R residue 501 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 8 optimal weight: 0.3980 chunk 31 optimal weight: 0.9990 chunk 13 optimal weight: 0.4980 chunk 32 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 ASN ** R 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3332 Z= 0.229 Angle : 0.602 7.835 4529 Z= 0.323 Chirality : 0.045 0.154 485 Planarity : 0.004 0.054 586 Dihedral : 5.111 18.933 466 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.71 % Favored : 89.29 % Rotamer: Outliers : 2.54 % Allowed : 23.10 % Favored : 74.37 % 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: -3.27 (0.39), residues: 411 helix: -4.23 (0.72), residues: 27 sheet: -1.03 (0.49), residues: 115 loop : -2.63 (0.35), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 120 HIS 0.001 0.000 HIS B 41 PHE 0.013 0.001 PHE R 490 TYR 0.020 0.002 TYR B 51 ARG 0.002 0.000 ARG A 102 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.372 Fit side-chains revert: symmetry clash REVERT: A 84 ARG cc_start: 0.7703 (mtm110) cc_final: 0.7361 (mtm110) outliers start: 9 outliers final: 9 residues processed: 64 average time/residue: 0.1590 time to fit residues: 12.6342 Evaluate side-chains 66 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain R residue 341 VAL Chi-restraints excluded: chain R residue 374 PHE Chi-restraints excluded: chain R residue 501 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 0.0070 chunk 36 optimal weight: 7.9990 chunk 21 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 39 optimal weight: 0.2980 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 ASN ** R 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.143551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.115241 restraints weight = 5153.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.118704 restraints weight = 3147.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.121130 restraints weight = 2323.341| |-----------------------------------------------------------------------------| r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3332 Z= 0.192 Angle : 0.585 7.900 4529 Z= 0.312 Chirality : 0.043 0.153 485 Planarity : 0.004 0.054 586 Dihedral : 4.960 19.140 466 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.46 % Favored : 89.54 % Rotamer: Outliers : 2.54 % Allowed : 22.82 % Favored : 74.65 % 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: -3.24 (0.40), residues: 411 helix: -4.15 (0.74), residues: 27 sheet: -1.02 (0.49), residues: 122 loop : -2.64 (0.36), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 99 HIS 0.000 0.000 HIS R 505 PHE 0.012 0.001 PHE R 490 TYR 0.020 0.001 TYR B 51 ARG 0.002 0.000 ARG A 102 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1326.43 seconds wall clock time: 25 minutes 13.63 seconds (1513.63 seconds total)