Starting phenix.real_space_refine on Wed Mar 5 15:08:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pjp_17718/03_2025/8pjp_17718.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pjp_17718/03_2025/8pjp_17718.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8pjp_17718/03_2025/8pjp_17718.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pjp_17718/03_2025/8pjp_17718.map" model { file = "/net/cci-nas-00/data/ceres_data/8pjp_17718/03_2025/8pjp_17718.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pjp_17718/03_2025/8pjp_17718.cif" } resolution = 2.92 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= 0.002 sd= 0.048 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 9 5.16 5 C 1342 2.51 5 N 371 2.21 5 O 434 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 2157 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1197 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 156} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "C" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 931 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 29 Unusual residues: {'G3P': 1, 'WKE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.70, per 1000 atoms: 1.25 Number of scatterers: 2157 At special positions: 0 Unit cell: (61.06, 71.38, 111.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 9 16.00 P 1 15.00 O 434 8.00 N 371 7.00 C 1342 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 120 " - pdb=" SG CYS A 154 " distance=2.03 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 98 " 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.85 Conformation dependent library (CDL) restraints added in 247.2 milliseconds 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 516 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 5 sheets defined 26.2% alpha, 30.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 2 through 18 removed outlier: 3.523A pdb=" N LEU A 6 " --> pdb=" O THR A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 42 removed outlier: 4.376A pdb=" N TYR A 27 " --> pdb=" O ALA A 23 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLU A 35 " --> pdb=" O ALA A 31 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA A 36 " --> pdb=" O GLN A 32 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY A 42 " --> pdb=" O LEU A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 55 removed outlier: 3.569A pdb=" N VAL A 47 " --> pdb=" O GLN A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 65 Processing helix chain 'A' and resid 68 through 72 Processing helix chain 'A' and resid 146 through 150 Processing helix chain 'C' and resid 89 through 93 removed outlier: 3.517A pdb=" N THR C 93 " --> pdb=" O PRO C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 113 Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 83 removed outlier: 3.797A pdb=" N SER A 79 " --> pdb=" O GLN A 90 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 124 through 125 removed outlier: 3.511A pdb=" N ALA A 135 " --> pdb=" O THR A 125 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 6 through 9 removed outlier: 4.091A pdb=" N THR C 80 " --> pdb=" O ASP C 75 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.986A pdb=" N ILE C 36 " --> pdb=" O CYS C 52 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N CYS C 52 " --> pdb=" O ILE C 36 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N TRP C 38 " --> pdb=" O VAL C 50 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 13 through 14 removed outlier: 7.034A pdb=" N ALA C 100 " --> pdb=" O ASP C 116 " (cutoff:3.500A) 95 hydrogen bonds defined for protein. 249 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: 0.58 Time building geometry restraints manager: 0.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 709 1.34 - 1.46: 348 1.46 - 1.57: 1121 1.57 - 1.69: 1 1.69 - 1.81: 13 Bond restraints: 2192 Sorted by residual: bond pdb=" O1P G3P A 201 " pdb=" P G3P A 201 " ideal model delta sigma weight residual 1.726 1.609 0.117 2.00e-02 2.50e+03 3.44e+01 bond pdb=" C6 WKE A 202 " pdb=" O6 WKE A 202 " ideal model delta sigma weight residual 1.401 1.433 -0.032 2.00e-02 2.50e+03 2.48e+00 bond pdb=" C8 WKE A 202 " pdb=" C9 WKE A 202 " ideal model delta sigma weight residual 1.531 1.500 0.031 2.00e-02 2.50e+03 2.43e+00 bond pdb=" C10 WKE A 202 " pdb=" O5 WKE A 202 " ideal model delta sigma weight residual 1.405 1.432 -0.027 2.00e-02 2.50e+03 1.79e+00 bond pdb=" C9 WKE A 202 " pdb=" O4 WKE A 202 " ideal model delta sigma weight residual 1.404 1.431 -0.027 2.00e-02 2.50e+03 1.79e+00 ... (remaining 2187 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 2941 1.82 - 3.64: 25 3.64 - 5.46: 6 5.46 - 7.28: 4 7.28 - 9.10: 1 Bond angle restraints: 2977 Sorted by residual: angle pdb=" O1P G3P A 201 " pdb=" P G3P A 201 " pdb=" O4P G3P A 201 " ideal model delta sigma weight residual 100.65 109.75 -9.10 3.00e+00 1.11e-01 9.20e+00 angle pdb=" O2P G3P A 201 " pdb=" P G3P A 201 " pdb=" O4P G3P A 201 " ideal model delta sigma weight residual 115.71 109.69 6.02 3.00e+00 1.11e-01 4.02e+00 angle pdb=" C SER A 62 " pdb=" N SER A 63 " pdb=" CA SER A 63 " ideal model delta sigma weight residual 122.60 119.64 2.96 1.56e+00 4.11e-01 3.59e+00 angle pdb=" O3P G3P A 201 " pdb=" P G3P A 201 " pdb=" O4P G3P A 201 " ideal model delta sigma weight residual 115.20 109.66 5.54 3.00e+00 1.11e-01 3.42e+00 angle pdb=" O1P G3P A 201 " pdb=" P G3P A 201 " pdb=" O3P G3P A 201 " ideal model delta sigma weight residual 104.20 109.74 -5.54 3.00e+00 1.11e-01 3.41e+00 ... (remaining 2972 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.87: 1147 16.87 - 33.73: 119 33.73 - 50.60: 43 50.60 - 67.46: 7 67.46 - 84.33: 3 Dihedral angle restraints: 1319 sinusoidal: 507 harmonic: 812 Sorted by residual: dihedral pdb=" CB CYS C 24 " pdb=" SG CYS C 24 " pdb=" SG CYS C 98 " pdb=" CB CYS C 98 " ideal model delta sinusoidal sigma weight residual 93.00 55.87 37.13 1 1.00e+01 1.00e-02 1.95e+01 dihedral pdb=" CB GLU A 35 " pdb=" CG GLU A 35 " pdb=" CD GLU A 35 " pdb=" OE1 GLU A 35 " ideal model delta sinusoidal sigma weight residual 0.00 -84.33 84.33 1 3.00e+01 1.11e-03 9.61e+00 dihedral pdb=" N LYS A 101 " pdb=" CA LYS A 101 " pdb=" CB LYS A 101 " pdb=" CG LYS A 101 " ideal model delta sinusoidal sigma weight residual -60.00 -113.55 53.55 3 1.50e+01 4.44e-03 9.21e+00 ... (remaining 1316 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 212 0.025 - 0.050: 69 0.050 - 0.074: 35 0.074 - 0.099: 13 0.099 - 0.124: 16 Chirality restraints: 345 Sorted by residual: chirality pdb=" CA ILE C 105 " pdb=" N ILE C 105 " pdb=" C ILE C 105 " pdb=" CB ILE C 105 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.82e-01 chirality pdb=" CA VAL C 95 " pdb=" N VAL C 95 " pdb=" C VAL C 95 " pdb=" CB VAL C 95 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.46e-01 chirality pdb=" CA VAL A 80 " pdb=" N VAL A 80 " pdb=" C VAL A 80 " pdb=" CB VAL A 80 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.42e-01 ... (remaining 342 not shown) Planarity restraints: 380 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C7 WKE A 202 " 0.053 2.00e-02 2.50e+03 4.32e-02 2.34e+01 pdb=" C8 WKE A 202 " -0.015 2.00e-02 2.50e+03 pdb=" C9 WKE A 202 " 0.040 2.00e-02 2.50e+03 pdb=" N1 WKE A 202 " -0.068 2.00e-02 2.50e+03 pdb=" O3 WKE A 202 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N WKE A 202 " -0.019 2.00e-02 2.50e+03 1.21e-02 1.83e+00 pdb=" C3 WKE A 202 " 0.014 2.00e-02 2.50e+03 pdb=" C4 WKE A 202 " -0.004 2.00e-02 2.50e+03 pdb=" C5 WKE A 202 " -0.004 2.00e-02 2.50e+03 pdb=" O1 WKE A 202 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 21 " -0.015 5.00e-02 4.00e+02 2.29e-02 8.42e-01 pdb=" N PRO A 22 " 0.040 5.00e-02 4.00e+02 pdb=" CA PRO A 22 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 22 " -0.013 5.00e-02 4.00e+02 ... (remaining 377 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.87: 794 2.87 - 3.38: 1665 3.38 - 3.89: 3277 3.89 - 4.39: 3602 4.39 - 4.90: 6594 Nonbonded interactions: 15932 Sorted by model distance: nonbonded pdb=" O ASP C 32 " pdb=" OG SER C 55 " model vdw 2.365 3.040 nonbonded pdb=" NH2 ARG C 69 " pdb=" OD2 ASP C 92 " model vdw 2.456 3.120 nonbonded pdb=" N ASP C 116 " pdb=" OD1 ASP C 116 " model vdw 2.482 3.120 nonbonded pdb=" C3 G3P A 201 " pdb=" O1 G3P A 201 " model vdw 2.541 2.752 nonbonded pdb=" OE2 GLU A 49 " pdb=" ND2 ASN A 53 " model vdw 2.542 3.120 ... (remaining 15927 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.590 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 11.910 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:15.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.117 2192 Z= 0.203 Angle : 0.529 9.098 2977 Z= 0.245 Chirality : 0.040 0.124 345 Planarity : 0.003 0.043 380 Dihedral : 15.916 84.330 797 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.34 % Allowed : 18.75 % Favored : 79.91 % 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: 0.81 (0.52), residues: 282 helix: 1.00 (0.70), residues: 59 sheet: 0.81 (0.60), residues: 71 loop : 0.35 (0.55), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 108 HIS 0.001 0.000 HIS A 149 PHE 0.002 0.000 PHE A 1 TYR 0.005 0.000 TYR C 97 ARG 0.001 0.000 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 75 time to evaluate : 0.284 Fit side-chains REVERT: A 132 THR cc_start: 0.9216 (p) cc_final: 0.9013 (t) outliers start: 3 outliers final: 1 residues processed: 77 average time/residue: 0.8943 time to fit residues: 70.6174 Evaluate side-chains 64 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 63 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 23 optimal weight: 8.9990 chunk 21 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 13 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 17 optimal weight: 20.0000 chunk 27 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 79 ASN ** 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 = 0.3084 r_free = 0.3084 target = 0.076149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2528 r_free = 0.2528 target = 0.048296 restraints weight = 4711.655| |-----------------------------------------------------------------------------| r_work (start): 0.2492 rms_B_bonded: 2.78 r_work: 0.2374 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2261 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8999 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 2192 Z= 0.419 Angle : 0.649 6.692 2977 Z= 0.331 Chirality : 0.045 0.145 345 Planarity : 0.003 0.020 380 Dihedral : 4.863 31.730 340 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 6.25 % Allowed : 23.21 % Favored : 70.54 % 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: 0.63 (0.52), residues: 282 helix: 0.95 (0.71), residues: 59 sheet: 0.68 (0.61), residues: 72 loop : 0.19 (0.55), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 108 HIS 0.002 0.001 HIS A 149 PHE 0.012 0.001 PHE C 29 TYR 0.010 0.001 TYR C 97 ARG 0.003 0.000 ARG C 21 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.237 Fit side-chains revert: symmetry clash REVERT: A 142 ASP cc_start: 0.9130 (p0) cc_final: 0.8734 (p0) REVERT: C 75 ASP cc_start: 0.8578 (t0) cc_final: 0.8166 (t0) REVERT: C 78 LYS cc_start: 0.8395 (OUTLIER) cc_final: 0.8121 (ptpp) REVERT: C 79 ASN cc_start: 0.9094 (m110) cc_final: 0.8860 (m110) outliers start: 14 outliers final: 7 residues processed: 77 average time/residue: 0.9293 time to fit residues: 73.3729 Evaluate side-chains 71 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain C residue 78 LYS Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 122 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 6 optimal weight: 2.9990 chunk 18 optimal weight: 8.9990 chunk 20 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 19 optimal weight: 8.9990 chunk 23 optimal weight: 6.9990 chunk 21 optimal weight: 8.9990 chunk 4 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 79 ASN ** 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 = 0.3127 r_free = 0.3127 target = 0.078526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2583 r_free = 0.2583 target = 0.050522 restraints weight = 4664.287| |-----------------------------------------------------------------------------| r_work (start): 0.2542 rms_B_bonded: 2.82 r_work: 0.2426 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2314 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8959 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2192 Z= 0.202 Angle : 0.568 8.141 2977 Z= 0.284 Chirality : 0.042 0.134 345 Planarity : 0.003 0.020 380 Dihedral : 4.289 31.991 339 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 4.91 % Allowed : 24.11 % Favored : 70.98 % 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: 0.70 (0.52), residues: 282 helix: 1.14 (0.72), residues: 59 sheet: 0.89 (0.61), residues: 72 loop : 0.07 (0.54), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 108 HIS 0.001 0.001 HIS C 64 PHE 0.003 0.001 PHE C 70 TYR 0.006 0.001 TYR C 117 ARG 0.002 0.000 ARG C 21 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.259 Fit side-chains revert: symmetry clash REVERT: A 142 ASP cc_start: 0.9108 (p0) cc_final: 0.8732 (p0) REVERT: C 15 GLN cc_start: 0.8884 (pm20) cc_final: 0.8448 (pm20) REVERT: C 46 GLU cc_start: 0.8542 (mm-30) cc_final: 0.8321 (tp30) REVERT: C 75 ASP cc_start: 0.8578 (t0) cc_final: 0.8111 (t0) REVERT: C 78 LYS cc_start: 0.8554 (OUTLIER) cc_final: 0.8249 (ptpp) REVERT: C 79 ASN cc_start: 0.9034 (m110) cc_final: 0.8820 (m110) REVERT: C 88 LEU cc_start: 0.9302 (mm) cc_final: 0.9000 (mm) outliers start: 11 outliers final: 5 residues processed: 73 average time/residue: 0.9273 time to fit residues: 69.4041 Evaluate side-chains 69 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain C residue 78 LYS Chi-restraints excluded: chain C residue 87 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 22 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 1 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 chunk 2 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 12 optimal weight: 0.9980 chunk 14 optimal weight: 6.9990 chunk 7 optimal weight: 0.9980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 79 ASN ** 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 = 0.3141 r_free = 0.3141 target = 0.078877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2609 r_free = 0.2609 target = 0.051529 restraints weight = 4645.130| |-----------------------------------------------------------------------------| r_work (start): 0.2560 rms_B_bonded: 2.74 r_work: 0.2444 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2331 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8986 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2192 Z= 0.175 Angle : 0.553 8.935 2977 Z= 0.272 Chirality : 0.041 0.132 345 Planarity : 0.003 0.021 380 Dihedral : 4.197 33.938 339 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 4.46 % Allowed : 24.55 % Favored : 70.98 % 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: 0.79 (0.52), residues: 282 helix: 1.26 (0.72), residues: 59 sheet: 0.99 (0.62), residues: 71 loop : 0.09 (0.54), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 108 HIS 0.001 0.001 HIS A 149 PHE 0.012 0.001 PHE C 29 TYR 0.006 0.001 TYR C 117 ARG 0.004 0.000 ARG C 21 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.226 Fit side-chains revert: symmetry clash REVERT: A 142 ASP cc_start: 0.9094 (p0) cc_final: 0.8734 (p0) REVERT: C 15 GLN cc_start: 0.8875 (pm20) cc_final: 0.8393 (pm20) REVERT: C 46 GLU cc_start: 0.8514 (mm-30) cc_final: 0.8264 (tp30) REVERT: C 75 ASP cc_start: 0.8624 (t0) cc_final: 0.8135 (t0) REVERT: C 78 LYS cc_start: 0.8582 (OUTLIER) cc_final: 0.8268 (ptpp) REVERT: C 88 LEU cc_start: 0.9258 (mm) cc_final: 0.8916 (mm) outliers start: 10 outliers final: 8 residues processed: 69 average time/residue: 0.9483 time to fit residues: 67.0046 Evaluate side-chains 69 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 120 CYS Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain C residue 78 LYS Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 116 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 16 optimal weight: 20.0000 chunk 8 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 19 optimal weight: 10.0000 chunk 26 optimal weight: 7.9990 chunk 21 optimal weight: 1.9990 chunk 17 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 11 optimal weight: 4.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 79 ASN ** 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 = 0.3097 r_free = 0.3097 target = 0.076806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2539 r_free = 0.2539 target = 0.048723 restraints weight = 4733.888| |-----------------------------------------------------------------------------| r_work (start): 0.2500 rms_B_bonded: 2.84 r_work: 0.2385 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2275 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8970 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 2192 Z= 0.300 Angle : 0.610 8.689 2977 Z= 0.304 Chirality : 0.043 0.138 345 Planarity : 0.003 0.019 380 Dihedral : 4.596 40.603 339 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.57 % Allowed : 25.89 % Favored : 70.54 % 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: 0.61 (0.52), residues: 282 helix: 1.04 (0.71), residues: 59 sheet: 1.08 (0.60), residues: 77 loop : -0.17 (0.54), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 108 HIS 0.002 0.001 HIS A 149 PHE 0.010 0.001 PHE C 29 TYR 0.008 0.001 TYR C 97 ARG 0.004 0.000 ARG C 21 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.228 Fit side-chains revert: symmetry clash REVERT: A 142 ASP cc_start: 0.9138 (p0) cc_final: 0.8798 (p0) REVERT: C 15 GLN cc_start: 0.8953 (pm20) cc_final: 0.8516 (pm20) REVERT: C 46 GLU cc_start: 0.8554 (mm-30) cc_final: 0.8296 (tp30) REVERT: C 75 ASP cc_start: 0.8623 (t0) cc_final: 0.8140 (t0) REVERT: C 78 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.8199 (ptpp) REVERT: C 88 LEU cc_start: 0.9248 (mm) cc_final: 0.8915 (mm) outliers start: 8 outliers final: 6 residues processed: 67 average time/residue: 1.0799 time to fit residues: 73.9686 Evaluate side-chains 69 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain C residue 78 LYS Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 87 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 6 optimal weight: 0.0770 chunk 26 optimal weight: 0.1980 chunk 11 optimal weight: 4.9990 chunk 16 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 23 optimal weight: 0.4980 chunk 20 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 ASN ** 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 = 0.3150 r_free = 0.3150 target = 0.079672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2612 r_free = 0.2612 target = 0.051849 restraints weight = 4730.034| |-----------------------------------------------------------------------------| r_work (start): 0.2573 rms_B_bonded: 2.87 r_work: 0.2457 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2347 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8903 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 2192 Z= 0.163 Angle : 0.568 9.362 2977 Z= 0.280 Chirality : 0.041 0.127 345 Planarity : 0.003 0.023 380 Dihedral : 4.225 36.810 339 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.12 % Allowed : 26.34 % Favored : 70.54 % 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: 1.05 (0.53), residues: 282 helix: 1.83 (0.74), residues: 53 sheet: 1.12 (0.56), residues: 87 loop : 0.05 (0.57), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 108 HIS 0.001 0.000 HIS A 149 PHE 0.002 0.001 PHE C 70 TYR 0.004 0.001 TYR C 117 ARG 0.004 0.000 ARG C 21 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.252 Fit side-chains revert: symmetry clash REVERT: A 35 GLU cc_start: 0.9275 (tm-30) cc_final: 0.8950 (tm-30) REVERT: A 142 ASP cc_start: 0.9148 (p0) cc_final: 0.8749 (p0) REVERT: C 15 GLN cc_start: 0.8906 (pm20) cc_final: 0.8460 (pm20) REVERT: C 46 GLU cc_start: 0.8529 (mm-30) cc_final: 0.8278 (tp30) REVERT: C 75 ASP cc_start: 0.8596 (t0) cc_final: 0.8085 (t0) REVERT: C 78 LYS cc_start: 0.8545 (mtmm) cc_final: 0.8200 (ptpp) REVERT: C 88 LEU cc_start: 0.9270 (mm) cc_final: 0.8910 (mm) outliers start: 7 outliers final: 6 residues processed: 72 average time/residue: 0.9428 time to fit residues: 69.6168 Evaluate side-chains 67 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 120 CYS Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 116 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 21 optimal weight: 6.9990 chunk 23 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 27 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 14 optimal weight: 0.0010 chunk 16 optimal weight: 6.9990 chunk 4 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 ASN ** 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 = 0.3152 r_free = 0.3152 target = 0.079904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2620 r_free = 0.2620 target = 0.052151 restraints weight = 4709.061| |-----------------------------------------------------------------------------| r_work (start): 0.2580 rms_B_bonded: 2.83 r_work: 0.2463 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2353 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8891 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 2192 Z= 0.169 Angle : 0.578 10.640 2977 Z= 0.287 Chirality : 0.042 0.128 345 Planarity : 0.003 0.022 380 Dihedral : 4.168 36.921 339 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.68 % Allowed : 29.02 % Favored : 68.30 % 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: 0.94 (0.53), residues: 282 helix: 1.13 (0.72), residues: 59 sheet: 1.24 (0.56), residues: 87 loop : 0.07 (0.59), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 108 HIS 0.001 0.000 HIS A 149 PHE 0.009 0.001 PHE C 29 TYR 0.004 0.001 TYR C 97 ARG 0.004 0.000 ARG C 21 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.240 Fit side-chains revert: symmetry clash REVERT: A 35 GLU cc_start: 0.9284 (tm-30) cc_final: 0.8923 (tm-30) REVERT: A 142 ASP cc_start: 0.9155 (p0) cc_final: 0.8769 (p0) REVERT: C 15 GLN cc_start: 0.8871 (pm20) cc_final: 0.8410 (pm20) REVERT: C 46 GLU cc_start: 0.8512 (mm-30) cc_final: 0.8245 (tp30) REVERT: C 75 ASP cc_start: 0.8612 (t0) cc_final: 0.8080 (t0) REVERT: C 78 LYS cc_start: 0.8558 (mtmm) cc_final: 0.8184 (ptpp) REVERT: C 88 LEU cc_start: 0.9265 (mm) cc_final: 0.8897 (mm) outliers start: 6 outliers final: 4 residues processed: 67 average time/residue: 1.0613 time to fit residues: 72.7042 Evaluate side-chains 65 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 61 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 CYS Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain C residue 87 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 17 optimal weight: 7.9990 chunk 12 optimal weight: 9.9990 chunk 25 optimal weight: 20.0000 chunk 1 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 7 optimal weight: 4.9990 chunk 9 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 79 ASN ** 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 = 0.3108 r_free = 0.3108 target = 0.077359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2557 r_free = 0.2557 target = 0.049450 restraints weight = 4845.726| |-----------------------------------------------------------------------------| r_work (start): 0.2529 rms_B_bonded: 2.85 r_work: 0.2412 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2300 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8958 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 2192 Z= 0.259 Angle : 0.628 9.785 2977 Z= 0.313 Chirality : 0.043 0.134 345 Planarity : 0.003 0.020 380 Dihedral : 4.540 43.298 339 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.23 % Allowed : 30.80 % Favored : 66.96 % 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: 0.79 (0.53), residues: 282 helix: 1.04 (0.72), residues: 59 sheet: 1.11 (0.57), residues: 87 loop : -0.02 (0.58), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 108 HIS 0.002 0.000 HIS A 149 PHE 0.003 0.001 PHE C 39 TYR 0.007 0.001 TYR C 97 ARG 0.005 0.000 ARG C 21 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.231 Fit side-chains revert: symmetry clash REVERT: A 142 ASP cc_start: 0.9165 (p0) cc_final: 0.8820 (p0) REVERT: C 15 GLN cc_start: 0.8921 (pm20) cc_final: 0.8458 (pm20) REVERT: C 46 GLU cc_start: 0.8530 (mm-30) cc_final: 0.8261 (tp30) REVERT: C 75 ASP cc_start: 0.8621 (t0) cc_final: 0.8080 (t0) REVERT: C 78 LYS cc_start: 0.8531 (mtmm) cc_final: 0.8149 (ptpp) REVERT: C 88 LEU cc_start: 0.9247 (mm) cc_final: 0.8920 (mm) outliers start: 5 outliers final: 4 residues processed: 67 average time/residue: 1.0659 time to fit residues: 73.0470 Evaluate side-chains 65 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 61 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 CYS Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain C residue 87 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 17 optimal weight: 0.9990 chunk 25 optimal weight: 20.0000 chunk 26 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 15 optimal weight: 7.9990 chunk 3 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 11 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 79 ASN ** 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 = 0.3127 r_free = 0.3127 target = 0.078402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2583 r_free = 0.2583 target = 0.050623 restraints weight = 4750.693| |-----------------------------------------------------------------------------| r_work (start): 0.2546 rms_B_bonded: 2.83 r_work: 0.2429 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2318 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8938 moved from start: 0.3412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 2192 Z= 0.211 Angle : 0.625 10.295 2977 Z= 0.310 Chirality : 0.042 0.134 345 Planarity : 0.003 0.021 380 Dihedral : 4.384 42.415 339 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.12 % Allowed : 30.36 % Favored : 66.52 % 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: 0.87 (0.53), residues: 282 helix: 1.10 (0.73), residues: 59 sheet: 1.15 (0.57), residues: 87 loop : 0.03 (0.58), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 108 HIS 0.001 0.000 HIS A 149 PHE 0.009 0.001 PHE C 29 TYR 0.005 0.001 TYR C 97 ARG 0.004 0.000 ARG C 21 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.232 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.9313 (tm-30) cc_final: 0.8965 (tm-30) REVERT: A 142 ASP cc_start: 0.9154 (p0) cc_final: 0.8781 (p0) REVERT: C 46 GLU cc_start: 0.8531 (mm-30) cc_final: 0.8254 (tp30) REVERT: C 75 ASP cc_start: 0.8634 (t0) cc_final: 0.8104 (t0) REVERT: C 78 LYS cc_start: 0.8542 (mtmm) cc_final: 0.8167 (ptpp) REVERT: C 88 LEU cc_start: 0.9282 (mm) cc_final: 0.8951 (mm) outliers start: 7 outliers final: 7 residues processed: 67 average time/residue: 0.9858 time to fit residues: 67.6460 Evaluate side-chains 67 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 120 CYS Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 87 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 17 optimal weight: 0.4980 chunk 26 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 18 optimal weight: 8.9990 chunk 27 optimal weight: 5.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 79 ASN ** 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 = 0.3122 r_free = 0.3122 target = 0.078034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2577 r_free = 0.2577 target = 0.050302 restraints weight = 4662.495| |-----------------------------------------------------------------------------| r_work (start): 0.2539 rms_B_bonded: 2.82 r_work: 0.2423 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2311 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8944 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 2192 Z= 0.225 Angle : 0.625 10.142 2977 Z= 0.312 Chirality : 0.043 0.135 345 Planarity : 0.003 0.020 380 Dihedral : 4.455 43.874 339 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.12 % Allowed : 29.91 % Favored : 66.96 % 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: 0.81 (0.53), residues: 282 helix: 1.05 (0.73), residues: 59 sheet: 1.06 (0.57), residues: 87 loop : 0.05 (0.58), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 108 HIS 0.001 0.000 HIS A 149 PHE 0.002 0.001 PHE C 39 TYR 0.005 0.001 TYR C 97 ARG 0.005 0.000 ARG C 21 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.253 Fit side-chains revert: symmetry clash REVERT: A 35 GLU cc_start: 0.9325 (tm-30) cc_final: 0.8967 (tm-30) REVERT: A 142 ASP cc_start: 0.9160 (p0) cc_final: 0.8822 (p0) REVERT: C 15 GLN cc_start: 0.8896 (pm20) cc_final: 0.8411 (pm20) REVERT: C 46 GLU cc_start: 0.8516 (mm-30) cc_final: 0.8250 (tp30) REVERT: C 75 ASP cc_start: 0.8650 (t0) cc_final: 0.8121 (t0) REVERT: C 78 LYS cc_start: 0.8531 (mtmm) cc_final: 0.8157 (ptpp) REVERT: C 88 LEU cc_start: 0.9280 (mm) cc_final: 0.8924 (mm) outliers start: 7 outliers final: 7 residues processed: 67 average time/residue: 0.9730 time to fit residues: 66.7993 Evaluate side-chains 67 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 120 CYS Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 87 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 7 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 chunk 13 optimal weight: 9.9990 chunk 8 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 79 ASN ** 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 = 0.3119 r_free = 0.3119 target = 0.077914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2574 r_free = 0.2574 target = 0.050132 restraints weight = 4766.026| |-----------------------------------------------------------------------------| r_work (start): 0.2535 rms_B_bonded: 2.83 r_work: 0.2419 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2308 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8946 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 2192 Z= 0.235 Angle : 0.637 10.201 2977 Z= 0.317 Chirality : 0.042 0.135 345 Planarity : 0.003 0.020 380 Dihedral : 4.494 44.688 339 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.12 % Allowed : 29.91 % Favored : 66.96 % 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: 0.77 (0.53), residues: 282 helix: 1.04 (0.72), residues: 59 sheet: 1.00 (0.57), residues: 87 loop : 0.04 (0.59), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 108 HIS 0.001 0.000 HIS A 149 PHE 0.009 0.001 PHE C 29 TYR 0.006 0.001 TYR C 97 ARG 0.005 0.000 ARG C 21 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2685.28 seconds wall clock time: 46 minutes 28.09 seconds (2788.09 seconds total)