Starting phenix.real_space_refine on Wed Mar 5 19:17:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wee_32448/03_2025/7wee_32448.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wee_32448/03_2025/7wee_32448.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wee_32448/03_2025/7wee_32448.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wee_32448/03_2025/7wee_32448.map" model { file = "/net/cci-nas-00/data/ceres_data/7wee_32448/03_2025/7wee_32448.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wee_32448/03_2025/7wee_32448.cif" } resolution = 4.0 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= 0.003 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 14 5.16 5 C 2139 2.51 5 N 560 2.21 5 O 637 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 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: 3350 Number of models: 1 Model: "" Number of chains: 3 Chain: "E" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1612 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 12, 'TRANS': 188} Chain: "H" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 938 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 7, 'TRANS': 111} Chain: "L" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 800 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Time building chain proxies: 4.11, per 1000 atoms: 1.23 Number of scatterers: 3350 At special positions: 0 Unit cell: (87.74, 66.34, 100.58, 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 14 16.00 O 637 8.00 N 560 7.00 C 2139 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 97 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 91 " distance=2.04 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: 1.27 Conformation dependent library (CDL) restraints added in 1.0 seconds 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 792 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 8 sheets defined 8.2% alpha, 31.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 349 through 353 removed outlier: 3.842A pdb=" N TRP E 353 " --> pdb=" O VAL E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 387 Processing helix chain 'E' and resid 405 through 407 No H-bonds generated for 'chain 'E' and resid 405 through 407' Processing helix chain 'E' and resid 438 through 443 removed outlier: 3.911A pdb=" N SER E 443 " --> pdb=" O ASN E 439 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 92 removed outlier: 3.727A pdb=" N THR H 92 " --> pdb=" O PRO H 89 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 86 Processing sheet with id=AA1, first strand: chain 'E' and resid 354 through 358 removed outlier: 4.321A pdb=" N ASN E 354 " --> pdb=" O SER E 399 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N SER E 399 " --> pdb=" O ASN E 354 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N CYS E 361 " --> pdb=" O CYS E 525 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 354 through 358 removed outlier: 4.321A pdb=" N ASN E 354 " --> pdb=" O SER E 399 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N SER E 399 " --> pdb=" O ASN E 354 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N ASN E 394 " --> pdb=" O GLU E 516 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLU E 516 " --> pdb=" O ASN E 394 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N CYS E 432 " --> pdb=" O LEU E 513 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'E' and resid 473 through 474 Processing sheet with id=AA5, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA6, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.984A pdb=" N ALA H 51 " --> pdb=" O TRP H 38 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ARG H 40 " --> pdb=" O TRP H 49 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N TRP H 49 " --> pdb=" O ARG H 40 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG H 60 " --> pdb=" O LEU H 52 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 12 removed outlier: 7.354A pdb=" N VAL L 11 " --> pdb=" O LEU L 109 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLN L 40 " --> pdb=" O LEU L 49 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N LEU L 49 " --> pdb=" O GLN L 40 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 19 through 24 97 hydrogen bonds defined for protein. 228 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: 0.73 Time building geometry restraints manager: 1.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1057 1.34 - 1.46: 864 1.46 - 1.58: 1503 1.58 - 1.69: 1 1.69 - 1.81: 16 Bond restraints: 3441 Sorted by residual: bond pdb=" CG PRO H 9 " pdb=" CD PRO H 9 " ideal model delta sigma weight residual 1.503 1.344 0.159 3.40e-02 8.65e+02 2.18e+01 bond pdb=" CB PRO H 9 " pdb=" CG PRO H 9 " ideal model delta sigma weight residual 1.492 1.672 -0.180 5.00e-02 4.00e+02 1.30e+01 bond pdb=" N PRO H 9 " pdb=" CD PRO H 9 " ideal model delta sigma weight residual 1.473 1.509 -0.036 1.40e-02 5.10e+03 6.63e+00 bond pdb=" N PRO H 9 " pdb=" CA PRO H 9 " ideal model delta sigma weight residual 1.469 1.448 0.021 1.28e-02 6.10e+03 2.71e+00 bond pdb=" CA ASN H 86 " pdb=" CB ASN H 86 " ideal model delta sigma weight residual 1.527 1.542 -0.015 1.61e-02 3.86e+03 8.50e-01 ... (remaining 3436 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.22: 4664 3.22 - 6.45: 21 6.45 - 9.67: 2 9.67 - 12.90: 1 12.90 - 16.12: 2 Bond angle restraints: 4690 Sorted by residual: angle pdb=" CA PRO H 9 " pdb=" N PRO H 9 " pdb=" CD PRO H 9 " ideal model delta sigma weight residual 112.00 95.88 16.12 1.40e+00 5.10e-01 1.33e+02 angle pdb=" N PRO H 9 " pdb=" CD PRO H 9 " pdb=" CG PRO H 9 " ideal model delta sigma weight residual 103.20 91.07 12.13 1.50e+00 4.44e-01 6.54e+01 angle pdb=" N ILE E 418 " pdb=" CA ILE E 418 " pdb=" C ILE E 418 " ideal model delta sigma weight residual 113.53 108.95 4.58 9.80e-01 1.04e+00 2.19e+01 angle pdb=" CA PRO H 9 " pdb=" CB PRO H 9 " pdb=" CG PRO H 9 " ideal model delta sigma weight residual 104.50 96.01 8.49 1.90e+00 2.77e-01 2.00e+01 angle pdb=" N PRO H 9 " pdb=" CA PRO H 9 " pdb=" CB PRO H 9 " ideal model delta sigma weight residual 103.25 99.58 3.67 1.05e+00 9.07e-01 1.22e+01 ... (remaining 4685 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.10: 1760 14.10 - 28.20: 193 28.20 - 42.29: 61 42.29 - 56.39: 12 56.39 - 70.49: 1 Dihedral angle restraints: 2027 sinusoidal: 782 harmonic: 1245 Sorted by residual: dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 91 " pdb=" CB CYS L 91 " ideal model delta sinusoidal sigma weight residual 93.00 22.51 70.49 1 1.00e+01 1.00e-02 6.39e+01 dihedral pdb=" CB CYS E 480 " pdb=" SG CYS E 480 " pdb=" SG CYS E 488 " pdb=" CB CYS E 488 " ideal model delta sinusoidal sigma weight residual 93.00 130.56 -37.56 1 1.00e+01 1.00e-02 1.99e+01 dihedral pdb=" CA LEU E 517 " pdb=" C LEU E 517 " pdb=" N LEU E 518 " pdb=" CA LEU E 518 " ideal model delta harmonic sigma weight residual 180.00 158.07 21.93 0 5.00e+00 4.00e-02 1.92e+01 ... (remaining 2024 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 358 0.039 - 0.079: 114 0.079 - 0.118: 37 0.118 - 0.157: 6 0.157 - 0.197: 2 Chirality restraints: 517 Sorted by residual: chirality pdb=" CB THR E 333 " pdb=" CA THR E 333 " pdb=" OG1 THR E 333 " pdb=" CG2 THR E 333 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 9.68e-01 chirality pdb=" CA PRO H 9 " pdb=" N PRO H 9 " pdb=" C PRO H 9 " pdb=" CB PRO H 9 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 7.89e-01 chirality pdb=" CA ASN H 86 " pdb=" N ASN H 86 " pdb=" C ASN H 86 " pdb=" CB ASN H 86 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.93e-01 ... (remaining 514 not shown) Planarity restraints: 600 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY H 8 " 0.056 5.00e-02 4.00e+02 7.59e-02 9.21e+00 pdb=" N PRO H 9 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO H 9 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO H 9 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP H 88 " -0.034 5.00e-02 4.00e+02 5.09e-02 4.14e+00 pdb=" N PRO H 89 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO H 89 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO H 89 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE E 490 " 0.023 5.00e-02 4.00e+02 3.46e-02 1.91e+00 pdb=" N PRO E 491 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO E 491 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO E 491 " 0.019 5.00e-02 4.00e+02 ... (remaining 597 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 50 2.67 - 3.23: 3069 3.23 - 3.79: 4699 3.79 - 4.34: 6398 4.34 - 4.90: 10716 Nonbonded interactions: 24932 Sorted by model distance: nonbonded pdb=" OG1 THR L 95 " pdb=" O SER L 98 " model vdw 2.116 3.040 nonbonded pdb=" OG1 THR H 104 " pdb=" OD1 ASP H 107 " model vdw 2.212 3.040 nonbonded pdb=" OG SER E 349 " pdb=" O LEU E 452 " model vdw 2.266 3.040 nonbonded pdb=" OG SER L 70 " pdb=" OG1 THR L 73 " model vdw 2.276 3.040 nonbonded pdb=" OG SER H 7 " pdb=" OG1 THR H 21 " model vdw 2.285 3.040 ... (remaining 24927 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: 0.000 Normalize map: mean=0, sd=1: 7.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.850 Find NCS groups from input model: 0.040 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 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 : 0.005 0.180 3441 Z= 0.345 Angle : 0.720 16.124 4690 Z= 0.408 Chirality : 0.044 0.197 517 Planarity : 0.005 0.076 600 Dihedral : 12.682 54.785 1217 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.40), residues: 423 helix: -3.73 (0.83), residues: 21 sheet: -0.23 (0.42), residues: 141 loop : -1.33 (0.38), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 436 HIS 0.005 0.001 HIS L 41 PHE 0.011 0.001 PHE L 65 TYR 0.011 0.001 TYR E 501 ARG 0.005 0.000 ARG L 45 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 389 ASP cc_start: 0.7649 (p0) cc_final: 0.6915 (p0) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.1224 time to fit residues: 10.3879 Evaluate side-chains 52 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.370 ------------------------------------------------------------------------------- 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: 9.9990 chunk 31 optimal weight: 5.9990 chunk 17 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 23 optimal weight: 9.9990 chunk 37 optimal weight: 9.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 = 0.3760 r_free = 0.3760 target = 0.126300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.097509 restraints weight = 7062.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.095101 restraints weight = 10645.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.091584 restraints weight = 7247.312| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 3441 Z= 0.405 Angle : 0.702 8.707 4690 Z= 0.371 Chirality : 0.048 0.148 517 Planarity : 0.005 0.051 600 Dihedral : 5.511 26.959 470 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.98 % Favored : 91.02 % Rotamer: Outliers : 1.89 % Allowed : 11.59 % Favored : 86.52 % 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 (0.41), residues: 423 helix: -3.44 (0.86), residues: 26 sheet: -0.11 (0.40), residues: 149 loop : -1.39 (0.41), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 436 HIS 0.002 0.001 HIS L 100 PHE 0.016 0.002 PHE E 374 TYR 0.016 0.002 TYR L 52 ARG 0.002 0.000 ARG E 454 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.302 Fit side-chains REVERT: E 389 ASP cc_start: 0.7969 (p0) cc_final: 0.7397 (p0) REVERT: E 474 GLN cc_start: 0.7244 (pp30) cc_final: 0.6874 (pp30) REVERT: H 45 LYS cc_start: 0.8604 (ptmm) cc_final: 0.8298 (ptmm) REVERT: L 50 LEU cc_start: 0.8521 (mp) cc_final: 0.8305 (tp) REVERT: L 108 LYS cc_start: 0.7982 (tppt) cc_final: 0.7592 (tptt) outliers start: 7 outliers final: 5 residues processed: 56 average time/residue: 0.1302 time to fit residues: 9.4437 Evaluate side-chains 55 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 71 ILE Chi-restraints excluded: chain L residue 40 GLN Chi-restraints excluded: chain L residue 63 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 39 optimal weight: 8.9990 chunk 26 optimal weight: 0.0770 chunk 7 optimal weight: 1.9990 chunk 32 optimal weight: 8.9990 chunk 15 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 35 optimal weight: 0.3980 overall best weight: 0.6540 ------------------------------------------------------------------------------- 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 = 0.3813 r_free = 0.3813 target = 0.130268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.103924 restraints weight = 6827.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.103264 restraints weight = 11675.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.104470 restraints weight = 9756.959| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 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 : 0.003 0.050 3441 Z= 0.163 Angle : 0.579 6.968 4690 Z= 0.301 Chirality : 0.044 0.145 517 Planarity : 0.004 0.053 600 Dihedral : 4.935 25.793 470 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.35 % Allowed : 16.98 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.41), residues: 423 helix: -3.41 (0.84), residues: 26 sheet: -0.09 (0.40), residues: 153 loop : -1.21 (0.41), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 436 HIS 0.001 0.000 HIS E 519 PHE 0.013 0.001 PHE L 103 TYR 0.013 0.001 TYR E 380 ARG 0.001 0.000 ARG L 45 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.412 Fit side-chains revert: symmetry clash REVERT: E 389 ASP cc_start: 0.7812 (p0) cc_final: 0.7314 (p0) REVERT: E 474 GLN cc_start: 0.7040 (pp30) cc_final: 0.6676 (pp30) REVERT: H 45 LYS cc_start: 0.8096 (ptmm) cc_final: 0.7781 (ptmm) REVERT: L 108 LYS cc_start: 0.7995 (tppt) cc_final: 0.7793 (tptp) outliers start: 5 outliers final: 4 residues processed: 63 average time/residue: 0.1238 time to fit residues: 10.3324 Evaluate side-chains 57 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 40 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 13 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 22 optimal weight: 8.9990 chunk 30 optimal weight: 0.7980 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.126927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.094711 restraints weight = 7011.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 69)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.089328 restraints weight = 8774.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.090329 restraints weight = 6607.440| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3441 Z= 0.280 Angle : 0.627 5.883 4690 Z= 0.330 Chirality : 0.046 0.145 517 Planarity : 0.005 0.057 600 Dihedral : 5.270 26.194 470 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 3.50 % Allowed : 16.98 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.40), residues: 423 helix: -3.57 (0.81), residues: 27 sheet: -0.06 (0.40), residues: 150 loop : -1.34 (0.41), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 436 HIS 0.001 0.001 HIS E 505 PHE 0.011 0.002 PHE E 429 TYR 0.012 0.002 TYR L 52 ARG 0.002 0.000 ARG E 454 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 55 time to evaluate : 0.399 Fit side-chains revert: symmetry clash REVERT: E 389 ASP cc_start: 0.7975 (p0) cc_final: 0.7426 (p0) REVERT: E 474 GLN cc_start: 0.7233 (pp30) cc_final: 0.6816 (pp30) REVERT: H 45 LYS cc_start: 0.8620 (ptmm) cc_final: 0.8374 (ptmm) REVERT: L 103 PHE cc_start: 0.4159 (OUTLIER) cc_final: 0.3588 (m-10) REVERT: L 108 LYS cc_start: 0.8095 (tppt) cc_final: 0.7852 (tptp) outliers start: 13 outliers final: 9 residues processed: 64 average time/residue: 0.1173 time to fit residues: 9.9276 Evaluate side-chains 68 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain H residue 3 THR Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 71 ILE Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 40 GLN Chi-restraints excluded: chain L residue 63 ASN Chi-restraints excluded: chain L residue 103 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 21 optimal weight: 0.9990 chunk 17 optimal weight: 0.3980 chunk 36 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 29 optimal weight: 10.0000 chunk 28 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 9 optimal weight: 0.4980 overall best weight: 0.7786 ------------------------------------------------------------------------------- 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 = 0.3805 r_free = 0.3805 target = 0.130025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 98)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.099386 restraints weight = 6953.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.093480 restraints weight = 8882.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.093970 restraints weight = 8246.841| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3441 Z= 0.167 Angle : 0.571 7.829 4690 Z= 0.297 Chirality : 0.044 0.156 517 Planarity : 0.004 0.060 600 Dihedral : 4.931 24.740 470 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.70 % Allowed : 21.02 % Favored : 76.28 % 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: -1.38 (0.40), residues: 423 helix: -3.47 (0.80), residues: 26 sheet: -0.04 (0.40), residues: 153 loop : -1.20 (0.41), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 109 HIS 0.002 0.000 HIS L 42 PHE 0.011 0.001 PHE H 24 TYR 0.008 0.001 TYR L 52 ARG 0.001 0.000 ARG H 60 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.348 Fit side-chains revert: symmetry clash REVERT: E 389 ASP cc_start: 0.7800 (p0) cc_final: 0.7326 (p0) REVERT: E 474 GLN cc_start: 0.7202 (pp30) cc_final: 0.6741 (pp30) REVERT: H 16 GLN cc_start: 0.6463 (mt0) cc_final: 0.6219 (mp10) REVERT: H 45 LYS cc_start: 0.8559 (ptmm) cc_final: 0.8302 (ptmm) REVERT: L 103 PHE cc_start: 0.4062 (OUTLIER) cc_final: 0.3515 (m-10) outliers start: 10 outliers final: 7 residues processed: 70 average time/residue: 0.1027 time to fit residues: 9.6404 Evaluate side-chains 65 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 40 GLN Chi-restraints excluded: chain L residue 63 ASN Chi-restraints excluded: chain L residue 103 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 33 optimal weight: 6.9990 chunk 19 optimal weight: 0.0980 chunk 1 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 0 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 17 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.8188 ------------------------------------------------------------------------------- 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 = 0.3765 r_free = 0.3765 target = 0.127081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.096789 restraints weight = 7093.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.095024 restraints weight = 10566.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 67)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.092061 restraints weight = 7329.379| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3441 Z= 0.277 Angle : 0.622 8.730 4690 Z= 0.324 Chirality : 0.045 0.168 517 Planarity : 0.005 0.055 600 Dihedral : 5.250 22.816 470 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 3.23 % Allowed : 22.64 % Favored : 74.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.40), residues: 423 helix: -3.53 (0.81), residues: 26 sheet: 0.01 (0.40), residues: 150 loop : -1.30 (0.40), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 436 HIS 0.002 0.001 HIS E 519 PHE 0.012 0.001 PHE E 515 TYR 0.013 0.002 TYR L 52 ARG 0.002 0.000 ARG E 454 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.390 Fit side-chains revert: symmetry clash REVERT: E 389 ASP cc_start: 0.8000 (p0) cc_final: 0.7509 (p0) REVERT: E 474 GLN cc_start: 0.7148 (pp30) cc_final: 0.6831 (pp30) REVERT: L 103 PHE cc_start: 0.3950 (OUTLIER) cc_final: 0.3322 (m-10) outliers start: 12 outliers final: 9 residues processed: 68 average time/residue: 0.1177 time to fit residues: 10.7302 Evaluate side-chains 63 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 71 ILE Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 40 GLN Chi-restraints excluded: chain L residue 63 ASN Chi-restraints excluded: chain L residue 103 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 6 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 7 optimal weight: 0.3980 chunk 36 optimal weight: 4.9990 chunk 5 optimal weight: 0.4980 chunk 32 optimal weight: 7.9990 chunk 25 optimal weight: 4.9990 chunk 9 optimal weight: 0.6980 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 = 0.3799 r_free = 0.3799 target = 0.129694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 111)---------------| | r_work = 0.3365 r_free = 0.3365 target = 0.099126 restraints weight = 6883.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 81)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.092819 restraints weight = 9380.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.092868 restraints weight = 9010.116| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3441 Z= 0.162 Angle : 0.591 8.377 4690 Z= 0.305 Chirality : 0.044 0.158 517 Planarity : 0.004 0.054 600 Dihedral : 4.944 22.825 470 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.70 % Allowed : 24.26 % Favored : 73.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.40), residues: 423 helix: -3.43 (0.81), residues: 26 sheet: 0.09 (0.42), residues: 143 loop : -1.31 (0.40), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 109 HIS 0.001 0.000 HIS L 42 PHE 0.011 0.001 PHE H 24 TYR 0.018 0.001 TYR E 501 ARG 0.001 0.000 ARG E 498 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.445 Fit side-chains revert: symmetry clash REVERT: E 389 ASP cc_start: 0.7831 (p0) cc_final: 0.7361 (p0) REVERT: E 474 GLN cc_start: 0.7137 (pp30) cc_final: 0.6675 (pp30) REVERT: L 103 PHE cc_start: 0.3867 (OUTLIER) cc_final: 0.3216 (m-10) outliers start: 10 outliers final: 8 residues processed: 64 average time/residue: 0.1104 time to fit residues: 9.4716 Evaluate side-chains 63 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 71 ILE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 40 GLN Chi-restraints excluded: chain L residue 63 ASN Chi-restraints excluded: chain L residue 103 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 9 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 34 optimal weight: 9.9990 chunk 16 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 111 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.126939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.095535 restraints weight = 7012.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.093006 restraints weight = 10089.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.090990 restraints weight = 6614.311| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3441 Z= 0.262 Angle : 0.622 6.819 4690 Z= 0.326 Chirality : 0.045 0.172 517 Planarity : 0.005 0.054 600 Dihedral : 5.211 21.978 470 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 2.96 % Allowed : 24.26 % Favored : 72.78 % 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: -1.44 (0.41), residues: 423 helix: -3.50 (0.81), residues: 26 sheet: 0.27 (0.43), residues: 140 loop : -1.43 (0.39), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 436 HIS 0.001 0.001 HIS H 100 PHE 0.010 0.001 PHE E 515 TYR 0.020 0.002 TYR E 501 ARG 0.002 0.000 ARG E 454 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.360 Fit side-chains revert: symmetry clash REVERT: E 389 ASP cc_start: 0.7960 (p0) cc_final: 0.7482 (p0) REVERT: E 474 GLN cc_start: 0.7173 (pp30) cc_final: 0.6819 (pp30) REVERT: L 103 PHE cc_start: 0.3966 (OUTLIER) cc_final: 0.3244 (m-10) outliers start: 11 outliers final: 9 residues processed: 65 average time/residue: 0.1012 time to fit residues: 8.8814 Evaluate side-chains 66 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 71 ILE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 40 GLN Chi-restraints excluded: chain L residue 63 ASN Chi-restraints excluded: chain L residue 103 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 12 optimal weight: 6.9990 chunk 30 optimal weight: 0.0670 chunk 8 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 31 optimal weight: 7.9990 chunk 34 optimal weight: 9.9990 chunk 2 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 14 optimal weight: 0.8980 overall best weight: 0.6720 ------------------------------------------------------------------------------- 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 = 0.3800 r_free = 0.3800 target = 0.129883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.098490 restraints weight = 6866.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 74)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.092499 restraints weight = 9116.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.093542 restraints weight = 6674.301| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 3441 Z= 0.162 Angle : 0.585 8.069 4690 Z= 0.301 Chirality : 0.044 0.161 517 Planarity : 0.004 0.053 600 Dihedral : 4.854 22.484 470 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.70 % Allowed : 24.26 % Favored : 73.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.40), residues: 423 helix: -3.80 (0.67), residues: 32 sheet: 0.23 (0.42), residues: 143 loop : -1.25 (0.40), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 436 HIS 0.001 0.000 HIS H 100 PHE 0.011 0.001 PHE H 24 TYR 0.017 0.001 TYR E 501 ARG 0.001 0.000 ARG L 45 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.351 Fit side-chains revert: symmetry clash REVERT: E 389 ASP cc_start: 0.7803 (p0) cc_final: 0.7340 (p0) REVERT: E 474 GLN cc_start: 0.7078 (pp30) cc_final: 0.6606 (pp30) REVERT: H 117 VAL cc_start: 0.6147 (t) cc_final: 0.5920 (m) REVERT: L 103 PHE cc_start: 0.3742 (OUTLIER) cc_final: 0.2915 (m-10) outliers start: 10 outliers final: 9 residues processed: 65 average time/residue: 0.0992 time to fit residues: 8.9438 Evaluate side-chains 66 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 71 ILE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 40 GLN Chi-restraints excluded: chain L residue 63 ASN Chi-restraints excluded: chain L residue 103 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 12 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 34 optimal weight: 10.0000 chunk 32 optimal weight: 9.9990 chunk 40 optimal weight: 0.9980 chunk 21 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 14 optimal weight: 0.3980 chunk 0 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3796 r_free = 0.3796 target = 0.129676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.097817 restraints weight = 6893.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.097817 restraints weight = 9582.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.097817 restraints weight = 9582.651| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3441 Z= 0.173 Angle : 0.579 6.440 4690 Z= 0.300 Chirality : 0.043 0.151 517 Planarity : 0.004 0.054 600 Dihedral : 4.768 20.401 470 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 2.96 % Allowed : 24.53 % Favored : 72.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.41), residues: 423 helix: -3.43 (0.81), residues: 26 sheet: 0.37 (0.42), residues: 142 loop : -1.36 (0.39), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 109 HIS 0.002 0.000 HIS E 519 PHE 0.010 0.001 PHE H 24 TYR 0.017 0.001 TYR E 501 ARG 0.001 0.000 ARG H 60 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.354 Fit side-chains revert: symmetry clash REVERT: E 389 ASP cc_start: 0.7791 (p0) cc_final: 0.7263 (p0) REVERT: E 474 GLN cc_start: 0.6888 (pp30) cc_final: 0.6487 (pp30) REVERT: H 117 VAL cc_start: 0.5576 (t) cc_final: 0.5359 (m) REVERT: L 103 PHE cc_start: 0.3533 (OUTLIER) cc_final: 0.2565 (m-10) outliers start: 11 outliers final: 8 residues processed: 65 average time/residue: 0.1033 time to fit residues: 9.0205 Evaluate side-chains 65 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 71 ILE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 40 GLN Chi-restraints excluded: chain L residue 63 ASN Chi-restraints excluded: chain L residue 103 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 14 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 27 optimal weight: 10.0000 chunk 31 optimal weight: 0.2980 chunk 8 optimal weight: 0.1980 chunk 23 optimal weight: 3.9990 chunk 33 optimal weight: 20.0000 chunk 13 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3807 r_free = 0.3807 target = 0.130528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.099064 restraints weight = 6899.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.093758 restraints weight = 8238.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.094550 restraints weight = 6292.180| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 3441 Z= 0.164 Angle : 0.580 7.469 4690 Z= 0.300 Chirality : 0.044 0.194 517 Planarity : 0.004 0.054 600 Dihedral : 4.702 21.437 470 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 2.43 % Allowed : 25.34 % Favored : 72.24 % 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: -1.29 (0.41), residues: 423 helix: -3.82 (0.66), residues: 32 sheet: 0.35 (0.43), residues: 142 loop : -1.20 (0.40), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 109 HIS 0.001 0.000 HIS E 519 PHE 0.013 0.001 PHE H 24 TYR 0.016 0.001 TYR E 501 ARG 0.001 0.000 ARG H 60 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1558.11 seconds wall clock time: 27 minutes 52.10 seconds (1672.10 seconds total)