Starting phenix.real_space_refine on Wed Jul 23 07:44:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jv2_22491/07_2025/7jv2_22491.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jv2_22491/07_2025/7jv2_22491.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7jv2_22491/07_2025/7jv2_22491.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jv2_22491/07_2025/7jv2_22491.map" model { file = "/net/cci-nas-00/data/ceres_data/7jv2_22491/07_2025/7jv2_22491.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jv2_22491/07_2025/7jv2_22491.cif" } resolution = 3.5 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= 0.023 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 8 5.16 5 C 1361 2.51 5 N 363 2.21 5 O 419 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 2151 Number of models: 1 Model: "" Number of chains: 3 Chain: "H" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 915 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "L" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 812 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "A" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 424 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 3, 'TRANS': 49} Chain breaks: 1 Time building chain proxies: 2.60, per 1000 atoms: 1.21 Number of scatterers: 2151 At special positions: 0 Unit cell: (68.25, 55.65, 66.15, 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 8 16.00 O 419 8.00 N 363 7.00 C 1361 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.01 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " 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: 0.52 Conformation dependent library (CDL) restraints added in 272.9 milliseconds 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 494 Finding SS restraints... Secondary structure from input PDB file: 3 helices and 8 sheets defined 5.0% alpha, 40.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'L' and resid 30 through 34 Processing helix chain 'L' and resid 81 through 85 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12 removed outlier: 5.839A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AA4, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AA5, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.513A pdb=" N TRP L 37 " --> pdb=" O LEU L 49 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 9 through 12 Processing sheet with id=AA7, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'A' and resid 473 through 474 90 hydrogen bonds defined for protein. 195 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: 0.55 Time building geometry restraints manager: 0.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 459 1.32 - 1.45: 593 1.45 - 1.57: 1134 1.57 - 1.69: 8 1.69 - 1.82: 10 Bond restraints: 2204 Sorted by residual: bond pdb=" CB ILE A 468 " pdb=" CG1 ILE A 468 " ideal model delta sigma weight residual 1.530 1.623 -0.093 2.00e-02 2.50e+03 2.17e+01 bond pdb=" CB LEU A 461 " pdb=" CG LEU A 461 " ideal model delta sigma weight residual 1.530 1.610 -0.080 2.00e-02 2.50e+03 1.59e+01 bond pdb=" CB LEU L 110 " pdb=" CG LEU L 110 " ideal model delta sigma weight residual 1.530 1.597 -0.067 2.00e-02 2.50e+03 1.13e+01 bond pdb=" CB ILE H 70 " pdb=" CG1 ILE H 70 " ideal model delta sigma weight residual 1.530 1.468 0.062 2.00e-02 2.50e+03 9.52e+00 bond pdb=" CG GLN L 1 " pdb=" CD GLN L 1 " ideal model delta sigma weight residual 1.516 1.587 -0.071 2.50e-02 1.60e+03 8.01e+00 ... (remaining 2199 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 2245 1.39 - 2.78: 582 2.78 - 4.18: 117 4.18 - 5.57: 37 5.57 - 6.96: 10 Bond angle restraints: 2991 Sorted by residual: angle pdb=" C GLN A 498 " pdb=" N PRO A 499 " pdb=" CA PRO A 499 " ideal model delta sigma weight residual 119.82 126.78 -6.96 9.80e-01 1.04e+00 5.04e+01 angle pdb=" C PHE A 490 " pdb=" N PRO A 491 " pdb=" CA PRO A 491 " ideal model delta sigma weight residual 119.56 125.42 -5.86 1.01e+00 9.80e-01 3.36e+01 angle pdb=" C GLU L 7 " pdb=" N PRO L 8 " pdb=" CA PRO L 8 " ideal model delta sigma weight residual 119.32 125.73 -6.41 1.14e+00 7.69e-01 3.16e+01 angle pdb=" C ALA L 45 " pdb=" N PRO L 46 " pdb=" CA PRO L 46 " ideal model delta sigma weight residual 119.76 125.21 -5.45 1.00e+00 1.00e+00 2.97e+01 angle pdb=" C ARG L 81 " pdb=" N PRO L 82 " pdb=" CA PRO L 82 " ideal model delta sigma weight residual 119.47 125.67 -6.20 1.16e+00 7.43e-01 2.86e+01 ... (remaining 2986 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.29: 1219 17.29 - 34.57: 35 34.57 - 51.85: 10 51.85 - 69.14: 3 69.14 - 86.42: 5 Dihedral angle restraints: 1272 sinusoidal: 479 harmonic: 793 Sorted by residual: dihedral pdb=" CB GLU H 46 " pdb=" CG GLU H 46 " pdb=" CD GLU H 46 " pdb=" OE1 GLU H 46 " ideal model delta sinusoidal sigma weight residual 0.00 -86.42 86.42 1 3.00e+01 1.11e-03 1.00e+01 dihedral pdb=" N TYR H 59 " pdb=" CA TYR H 59 " pdb=" CB TYR H 59 " pdb=" CG TYR H 59 " ideal model delta sinusoidal sigma weight residual -180.00 -123.33 -56.67 3 1.50e+01 4.44e-03 9.41e+00 dihedral pdb=" CB GLU H 6 " pdb=" CG GLU H 6 " pdb=" CD GLU H 6 " pdb=" OE1 GLU H 6 " ideal model delta sinusoidal sigma weight residual 0.00 -82.50 82.50 1 3.00e+01 1.11e-03 9.27e+00 ... (remaining 1269 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 216 0.069 - 0.139: 85 0.139 - 0.208: 11 0.208 - 0.277: 2 0.277 - 0.347: 2 Chirality restraints: 316 Sorted by residual: chirality pdb=" CG LEU L 110 " pdb=" CB LEU L 110 " pdb=" CD1 LEU L 110 " pdb=" CD2 LEU L 110 " both_signs ideal model delta sigma weight residual False -2.59 -2.94 0.35 2.00e-01 2.50e+01 3.00e+00 chirality pdb=" CG LEU A 461 " pdb=" CB LEU A 461 " pdb=" CD1 LEU A 461 " pdb=" CD2 LEU A 461 " both_signs ideal model delta sigma weight residual False -2.59 -2.93 0.34 2.00e-01 2.50e+01 2.96e+00 chirality pdb=" CB ILE A 468 " pdb=" CA ILE A 468 " pdb=" CG1 ILE A 468 " pdb=" CG2 ILE A 468 " both_signs ideal model delta sigma weight residual False 2.64 2.90 -0.26 2.00e-01 2.50e+01 1.64e+00 ... (remaining 313 not shown) Planarity restraints: 385 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR H 32 " -0.042 2.00e-02 2.50e+03 2.24e-02 1.00e+01 pdb=" CG TYR H 32 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR H 32 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR H 32 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR H 32 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR H 32 " 0.016 2.00e-02 2.50e+03 pdb=" CZ TYR H 32 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR H 32 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 105 " 0.036 2.00e-02 2.50e+03 1.86e-02 6.94e+00 pdb=" CG TYR H 105 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR H 105 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR H 105 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR H 105 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR H 105 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR H 105 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR H 105 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 33 " 0.030 2.00e-02 2.50e+03 1.50e-02 5.63e+00 pdb=" CG TRP H 33 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 TRP H 33 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 TRP H 33 " -0.019 2.00e-02 2.50e+03 pdb=" NE1 TRP H 33 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP H 33 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP H 33 " -0.015 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 33 " 0.016 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 33 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP H 33 " 0.015 2.00e-02 2.50e+03 ... (remaining 382 not shown) Histogram of nonbonded interaction distances: 2.59 - 3.05: 1312 3.05 - 3.51: 1905 3.51 - 3.97: 3466 3.97 - 4.44: 3915 4.44 - 4.90: 6436 Nonbonded interactions: 17034 Sorted by model distance: nonbonded pdb=" N HIS L 33 " pdb=" N TYR L 34 " model vdw 2.587 2.560 nonbonded pdb=" N LYS H 76 " pdb=" N ASN H 77 " model vdw 2.587 2.560 nonbonded pdb=" N SER H 71 " pdb=" O SER H 71 " model vdw 2.589 2.496 nonbonded pdb=" N ASP H 62 " pdb=" OD1 ASP H 62 " model vdw 2.594 3.120 nonbonded pdb=" O TYR L 34 " pdb=" CB TYR L 34 " model vdw 2.596 2.752 ... (remaining 17029 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: 2.640 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 11.420 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 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 : 0.015 0.093 2207 Z= 0.781 Angle : 1.392 6.959 2997 Z= 0.936 Chirality : 0.075 0.347 316 Planarity : 0.006 0.022 385 Dihedral : 11.432 86.421 769 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.32 % Allowed : 0.88 % Favored : 97.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.50), residues: 274 helix: None (None), residues: 0 sheet: 0.23 (0.50), residues: 102 loop : 0.93 (0.47), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.006 TRP H 33 HIS 0.002 0.001 HIS L 57 PHE 0.018 0.004 PHE L 101 TYR 0.042 0.007 TYR H 32 ARG 0.003 0.001 ARG H 72 Details of bonding type rmsd hydrogen bonds : bond 0.18284 ( 78) hydrogen bonds : angle 8.01654 ( 195) SS BOND : bond 0.01109 ( 3) SS BOND : angle 3.28913 ( 6) covalent geometry : bond 0.01471 ( 2204) covalent geometry : angle 1.38584 ( 2991) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 65 time to evaluate : 0.243 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 65 average time/residue: 0.1596 time to fit residues: 11.8847 Evaluate side-chains 45 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 22 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 6 optimal weight: 0.0870 chunk 13 optimal weight: 0.5980 chunk 10 optimal weight: 0.0980 chunk 21 optimal weight: 0.2980 chunk 8 optimal weight: 0.3980 chunk 12 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 24 optimal weight: 0.3980 overall best weight: 0.2558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.159461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.146762 restraints weight = 3124.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.149390 restraints weight = 1770.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.151122 restraints weight = 1166.091| |-----------------------------------------------------------------------------| r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 2207 Z= 0.173 Angle : 0.662 7.708 2997 Z= 0.354 Chirality : 0.044 0.139 316 Planarity : 0.004 0.023 385 Dihedral : 4.780 16.586 310 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.08 % Allowed : 9.25 % Favored : 87.67 % 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: 0.52 (0.48), residues: 274 helix: None (None), residues: 0 sheet: 0.26 (0.46), residues: 112 loop : 0.56 (0.48), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 33 HIS 0.002 0.001 HIS L 57 PHE 0.008 0.002 PHE L 101 TYR 0.014 0.002 TYR A 453 ARG 0.003 0.001 ARG L 63 Details of bonding type rmsd hydrogen bonds : bond 0.04309 ( 78) hydrogen bonds : angle 6.00005 ( 195) SS BOND : bond 0.00473 ( 3) SS BOND : angle 0.81646 ( 6) covalent geometry : bond 0.00396 ( 2204) covalent geometry : angle 0.66170 ( 2991) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.242 Fit side-chains revert: symmetry clash REVERT: L 31 SER cc_start: 0.7843 (m) cc_final: 0.7335 (t) REVERT: L 47 ARG cc_start: 0.8586 (ptm160) cc_final: 0.8330 (ptm160) REVERT: L 81 ARG cc_start: 0.6271 (mtp-110) cc_final: 0.6022 (mtt-85) REVERT: L 87 GLU cc_start: 0.8272 (mm-30) cc_final: 0.7887 (mm-30) outliers start: 7 outliers final: 6 residues processed: 54 average time/residue: 0.1367 time to fit residues: 8.7158 Evaluate side-chains 52 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain A residue 455 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 14 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 9 optimal weight: 0.2980 chunk 25 optimal weight: 0.9990 chunk 4 optimal weight: 0.0470 chunk 7 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 24 optimal weight: 0.4980 chunk 0 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 108 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.150877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.138134 restraints weight = 3131.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.140834 restraints weight = 1825.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.142684 restraints weight = 1216.297| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.3778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 2207 Z= 0.285 Angle : 0.726 7.070 2997 Z= 0.388 Chirality : 0.045 0.144 316 Planarity : 0.004 0.025 385 Dihedral : 5.410 17.579 310 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 3.96 % Allowed : 10.57 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.48), residues: 274 helix: None (None), residues: 0 sheet: 0.01 (0.46), residues: 115 loop : -0.16 (0.47), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP H 33 HIS 0.004 0.002 HIS L 57 PHE 0.010 0.002 PHE L 101 TYR 0.023 0.002 TYR H 60 ARG 0.002 0.001 ARG L 63 Details of bonding type rmsd hydrogen bonds : bond 0.04703 ( 78) hydrogen bonds : angle 6.50746 ( 195) SS BOND : bond 0.00715 ( 3) SS BOND : angle 0.95792 ( 6) covalent geometry : bond 0.00647 ( 2204) covalent geometry : angle 0.72517 ( 2991) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.234 Fit side-chains revert: symmetry clash REVERT: L 31 SER cc_start: 0.7965 (m) cc_final: 0.7440 (t) REVERT: L 81 ARG cc_start: 0.6553 (mtp-110) cc_final: 0.6244 (mtt-85) REVERT: L 87 GLU cc_start: 0.8426 (mm-30) cc_final: 0.7821 (mm-30) outliers start: 9 outliers final: 7 residues processed: 57 average time/residue: 0.1318 time to fit residues: 8.9483 Evaluate side-chains 55 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 95 SER Chi-restraints excluded: chain L residue 110 LEU Chi-restraints excluded: chain A residue 455 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 15 optimal weight: 0.0070 chunk 4 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 8 optimal weight: 0.8980 chunk 3 optimal weight: 0.4980 chunk 7 optimal weight: 0.3980 chunk 20 optimal weight: 0.0870 chunk 13 optimal weight: 0.9990 chunk 17 optimal weight: 0.4980 chunk 16 optimal weight: 0.7980 chunk 6 optimal weight: 0.0970 overall best weight: 0.2174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 460 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.156126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.143550 restraints weight = 3064.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.146273 restraints weight = 1771.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.148070 restraints weight = 1178.981| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.4046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 2207 Z= 0.152 Angle : 0.605 6.271 2997 Z= 0.321 Chirality : 0.041 0.126 316 Planarity : 0.003 0.023 385 Dihedral : 4.876 19.131 310 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 4.41 % Allowed : 13.66 % Favored : 81.94 % 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: -0.19 (0.49), residues: 274 helix: None (None), residues: 0 sheet: 0.02 (0.47), residues: 112 loop : -0.14 (0.47), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 33 HIS 0.002 0.001 HIS L 57 PHE 0.017 0.002 PHE L 101 TYR 0.015 0.001 TYR H 32 ARG 0.002 0.000 ARG L 63 Details of bonding type rmsd hydrogen bonds : bond 0.03877 ( 78) hydrogen bonds : angle 5.99346 ( 195) SS BOND : bond 0.00456 ( 3) SS BOND : angle 0.65729 ( 6) covalent geometry : bond 0.00352 ( 2204) covalent geometry : angle 0.60458 ( 2991) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.224 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 8 residues processed: 53 average time/residue: 0.1022 time to fit residues: 6.7855 Evaluate side-chains 54 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 110 LEU Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 495 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 3 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 4 optimal weight: 0.2980 chunk 14 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 17 optimal weight: 0.4980 chunk 21 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 7 optimal weight: 0.4980 chunk 25 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3591 r_free = 0.3591 target = 0.137260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.123681 restraints weight = 3290.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.126384 restraints weight = 1965.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.128208 restraints weight = 1332.930| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.4421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 2207 Z= 0.295 Angle : 0.746 6.312 2997 Z= 0.395 Chirality : 0.046 0.137 316 Planarity : 0.004 0.029 385 Dihedral : 5.453 20.214 310 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 7.05 % Allowed : 11.01 % Favored : 81.94 % 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: -0.67 (0.47), residues: 274 helix: None (None), residues: 0 sheet: -0.32 (0.47), residues: 107 loop : -0.47 (0.45), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP H 33 HIS 0.004 0.002 HIS L 57 PHE 0.018 0.002 PHE L 101 TYR 0.022 0.002 TYR H 60 ARG 0.002 0.000 ARG A 457 Details of bonding type rmsd hydrogen bonds : bond 0.04570 ( 78) hydrogen bonds : angle 6.64292 ( 195) SS BOND : bond 0.00751 ( 3) SS BOND : angle 0.99639 ( 6) covalent geometry : bond 0.00671 ( 2204) covalent geometry : angle 0.74580 ( 2991) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 50 time to evaluate : 0.253 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 12 residues processed: 57 average time/residue: 0.0976 time to fit residues: 6.9934 Evaluate side-chains 59 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 47 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 95 SER Chi-restraints excluded: chain L residue 110 LEU Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 500 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 17 optimal weight: 0.9980 chunk 18 optimal weight: 0.4980 chunk 6 optimal weight: 0.1980 chunk 5 optimal weight: 0.6980 chunk 9 optimal weight: 0.1980 chunk 7 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 14 optimal weight: 0.0970 chunk 13 optimal weight: 0.6980 chunk 4 optimal weight: 0.2980 chunk 2 optimal weight: 0.5980 overall best weight: 0.2578 ------------------------------------------------------------------------------- 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 = 0.152082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.139643 restraints weight = 3086.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.142003 restraints weight = 1828.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.143741 restraints weight = 1255.635| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.4558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 2207 Z= 0.169 Angle : 0.647 7.350 2997 Z= 0.336 Chirality : 0.042 0.125 316 Planarity : 0.004 0.031 385 Dihedral : 4.939 19.986 310 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 6.17 % Allowed : 14.98 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.47), residues: 274 helix: None (None), residues: 0 sheet: -0.44 (0.46), residues: 112 loop : -0.57 (0.45), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 33 HIS 0.001 0.001 HIS L 57 PHE 0.017 0.002 PHE L 101 TYR 0.013 0.002 TYR H 60 ARG 0.001 0.000 ARG H 72 Details of bonding type rmsd hydrogen bonds : bond 0.03735 ( 78) hydrogen bonds : angle 6.25559 ( 195) SS BOND : bond 0.00472 ( 3) SS BOND : angle 0.71052 ( 6) covalent geometry : bond 0.00394 ( 2204) covalent geometry : angle 0.64672 ( 2991) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 47 time to evaluate : 0.267 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 12 residues processed: 53 average time/residue: 0.1070 time to fit residues: 7.1662 Evaluate side-chains 58 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 110 LEU Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 500 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 17 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 20 optimal weight: 0.0970 chunk 19 optimal weight: 0.2980 chunk 3 optimal weight: 0.2980 chunk 10 optimal weight: 0.2980 chunk 0 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 24 optimal weight: 0.3980 overall best weight: 0.2778 ------------------------------------------------------------------------------- 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 = 0.3823 r_free = 0.3823 target = 0.153178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.140747 restraints weight = 3160.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.143312 restraints weight = 1852.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.145016 restraints weight = 1248.139| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.4669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 2207 Z= 0.176 Angle : 0.638 7.186 2997 Z= 0.331 Chirality : 0.042 0.124 316 Planarity : 0.004 0.034 385 Dihedral : 4.861 20.661 310 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 6.17 % Allowed : 14.10 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.48), residues: 274 helix: None (None), residues: 0 sheet: -0.56 (0.47), residues: 112 loop : -0.61 (0.46), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 33 HIS 0.002 0.001 HIS L 57 PHE 0.023 0.002 PHE L 101 TYR 0.016 0.002 TYR H 32 ARG 0.001 0.000 ARG H 67 Details of bonding type rmsd hydrogen bonds : bond 0.03723 ( 78) hydrogen bonds : angle 6.16693 ( 195) SS BOND : bond 0.00466 ( 3) SS BOND : angle 0.68235 ( 6) covalent geometry : bond 0.00406 ( 2204) covalent geometry : angle 0.63773 ( 2991) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 46 time to evaluate : 0.246 Fit side-chains outliers start: 14 outliers final: 14 residues processed: 52 average time/residue: 0.0806 time to fit residues: 5.5205 Evaluate side-chains 59 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 45 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 110 LEU Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 500 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 21 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 16 optimal weight: 0.1980 chunk 4 optimal weight: 0.1980 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 = 0.3594 r_free = 0.3594 target = 0.137059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.123800 restraints weight = 3281.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.126403 restraints weight = 1977.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.128068 restraints weight = 1342.009| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.4837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 2207 Z= 0.248 Angle : 0.715 7.394 2997 Z= 0.369 Chirality : 0.044 0.148 316 Planarity : 0.004 0.034 385 Dihedral : 5.184 21.335 310 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 8.37 % Allowed : 12.78 % Favored : 78.85 % 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: -1.23 (0.48), residues: 274 helix: None (None), residues: 0 sheet: -0.85 (0.47), residues: 112 loop : -0.72 (0.47), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP H 33 HIS 0.003 0.001 HIS L 57 PHE 0.025 0.002 PHE L 101 TYR 0.018 0.002 TYR H 60 ARG 0.002 0.000 ARG A 457 Details of bonding type rmsd hydrogen bonds : bond 0.04066 ( 78) hydrogen bonds : angle 6.46052 ( 195) SS BOND : bond 0.00605 ( 3) SS BOND : angle 0.83207 ( 6) covalent geometry : bond 0.00570 ( 2204) covalent geometry : angle 0.71442 ( 2991) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 45 time to evaluate : 0.251 Fit side-chains outliers start: 19 outliers final: 16 residues processed: 55 average time/residue: 0.0736 time to fit residues: 5.4078 Evaluate side-chains 61 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 45 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 95 SER Chi-restraints excluded: chain L residue 110 LEU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 500 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 25 optimal weight: 0.5980 chunk 26 optimal weight: 0.3980 chunk 12 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 19 optimal weight: 0.4980 chunk 6 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 10 optimal weight: 0.2980 chunk 4 optimal weight: 0.4980 chunk 22 optimal weight: 0.0370 overall best weight: 0.3458 ------------------------------------------------------------------------------- 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 = 0.3803 r_free = 0.3803 target = 0.151421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.139112 restraints weight = 3136.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.141606 restraints weight = 1865.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.143227 restraints weight = 1262.150| |-----------------------------------------------------------------------------| r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.4855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 2207 Z= 0.205 Angle : 0.677 7.657 2997 Z= 0.350 Chirality : 0.044 0.171 316 Planarity : 0.004 0.035 385 Dihedral : 5.060 21.404 310 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 7.05 % Allowed : 13.22 % Favored : 79.74 % 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: -1.33 (0.49), residues: 274 helix: None (None), residues: 0 sheet: -0.97 (0.47), residues: 112 loop : -0.75 (0.47), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP H 33 HIS 0.002 0.001 HIS L 57 PHE 0.023 0.002 PHE L 101 TYR 0.014 0.002 TYR H 60 ARG 0.001 0.000 ARG H 72 Details of bonding type rmsd hydrogen bonds : bond 0.03791 ( 78) hydrogen bonds : angle 6.39164 ( 195) SS BOND : bond 0.00504 ( 3) SS BOND : angle 0.71084 ( 6) covalent geometry : bond 0.00475 ( 2204) covalent geometry : angle 0.67722 ( 2991) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 45 time to evaluate : 0.250 Fit side-chains outliers start: 16 outliers final: 14 residues processed: 53 average time/residue: 0.0772 time to fit residues: 5.4876 Evaluate side-chains 59 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 45 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 95 SER Chi-restraints excluded: chain L residue 110 LEU Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 500 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 12 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 23 optimal weight: 0.0870 chunk 21 optimal weight: 0.5980 chunk 8 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 6 optimal weight: 0.4980 chunk 5 optimal weight: 0.0980 overall best weight: 0.4158 ------------------------------------------------------------------------------- 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 = 0.3787 r_free = 0.3787 target = 0.149940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.137635 restraints weight = 3134.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.140080 restraints weight = 1863.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.141728 restraints weight = 1268.209| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.4950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 2207 Z= 0.237 Angle : 0.715 7.752 2997 Z= 0.367 Chirality : 0.045 0.170 316 Planarity : 0.004 0.035 385 Dihedral : 5.204 21.618 310 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer: Outliers : 7.49 % Allowed : 12.78 % Favored : 79.74 % 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: -1.48 (0.49), residues: 274 helix: None (None), residues: 0 sheet: -1.12 (0.47), residues: 112 loop : -0.80 (0.47), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP H 33 HIS 0.002 0.001 HIS L 57 PHE 0.023 0.002 PHE L 101 TYR 0.016 0.002 TYR H 60 ARG 0.002 0.000 ARG H 72 Details of bonding type rmsd hydrogen bonds : bond 0.03954 ( 78) hydrogen bonds : angle 6.50345 ( 195) SS BOND : bond 0.00577 ( 3) SS BOND : angle 0.77343 ( 6) covalent geometry : bond 0.00547 ( 2204) covalent geometry : angle 0.71517 ( 2991) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 44 time to evaluate : 0.246 Fit side-chains outliers start: 17 outliers final: 15 residues processed: 53 average time/residue: 0.0772 time to fit residues: 5.4322 Evaluate side-chains 59 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 44 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 95 SER Chi-restraints excluded: chain L residue 110 LEU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 500 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 10 optimal weight: 0.9990 chunk 14 optimal weight: 0.2980 chunk 15 optimal weight: 0.1980 chunk 0 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 26 optimal weight: 0.0980 chunk 8 optimal weight: 0.9990 chunk 12 optimal weight: 0.4980 chunk 4 optimal weight: 0.2980 chunk 13 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 overall best weight: 0.2780 ------------------------------------------------------------------------------- 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 = 0.3809 r_free = 0.3809 target = 0.151558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.139505 restraints weight = 3122.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.141880 restraints weight = 1876.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.143321 restraints weight = 1277.028| |-----------------------------------------------------------------------------| r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.4975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 2207 Z= 0.176 Angle : 0.651 7.813 2997 Z= 0.334 Chirality : 0.043 0.156 316 Planarity : 0.004 0.036 385 Dihedral : 4.941 21.623 310 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 7.05 % Allowed : 13.66 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.49), residues: 274 helix: None (None), residues: 0 sheet: -1.02 (0.48), residues: 110 loop : -0.69 (0.47), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP H 47 HIS 0.002 0.001 HIS L 57 PHE 0.019 0.002 PHE L 101 TYR 0.012 0.002 TYR H 60 ARG 0.001 0.000 ARG H 72 Details of bonding type rmsd hydrogen bonds : bond 0.03564 ( 78) hydrogen bonds : angle 6.28845 ( 195) SS BOND : bond 0.00435 ( 3) SS BOND : angle 0.64811 ( 6) covalent geometry : bond 0.00409 ( 2204) covalent geometry : angle 0.65088 ( 2991) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1442.97 seconds wall clock time: 25 minutes 38.28 seconds (1538.28 seconds total)