Starting phenix.real_space_refine on Sat Aug 3 04:32:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b9r_44389/08_2024/9b9r_44389.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b9r_44389/08_2024/9b9r_44389.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b9r_44389/08_2024/9b9r_44389.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b9r_44389/08_2024/9b9r_44389.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b9r_44389/08_2024/9b9r_44389.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b9r_44389/08_2024/9b9r_44389.cif" } resolution = 3.7 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= 0.001 sd= 0.017 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 S 36 5.16 5 C 2220 2.51 5 N 612 2.21 5 O 624 1.98 5 H 3436 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 6928 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 1732 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 1, 'TRANS': 109} Chain breaks: 1 Chain: "B" Number of atoms: 1732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 1732 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 1, 'TRANS': 109} Chain breaks: 1 Chain: "C" Number of atoms: 1732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 1732 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 1, 'TRANS': 109} Chain breaks: 1 Chain: "D" Number of atoms: 1732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 1732 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 1, 'TRANS': 109} Chain breaks: 1 Time building chain proxies: 3.60, per 1000 atoms: 0.52 Number of scatterers: 6928 At special positions: 0 Unit cell: (95.85, 71.55, 87.75, 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 36 16.00 O 624 8.00 N 612 7.00 C 2220 6.00 H 3436 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 5.31 Conformation dependent library (CDL) restraints added in 695.6 milliseconds 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 856 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 4 sheets defined 66.9% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 5 through 21 Processing helix chain 'A' and resid 38 through 46 Processing helix chain 'A' and resid 46 through 53 Processing helix chain 'A' and resid 73 through 87 removed outlier: 3.550A pdb=" N TYR A 85 " --> pdb=" O ILE A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 106 Processing helix chain 'A' and resid 108 through 119 Processing helix chain 'B' and resid 5 through 21 Processing helix chain 'B' and resid 38 through 46 Processing helix chain 'B' and resid 46 through 54 Processing helix chain 'B' and resid 73 through 87 Processing helix chain 'B' and resid 95 through 106 Processing helix chain 'B' and resid 108 through 120 Processing helix chain 'C' and resid 5 through 21 Processing helix chain 'C' and resid 38 through 46 Processing helix chain 'C' and resid 46 through 54 Processing helix chain 'C' and resid 73 through 87 Processing helix chain 'C' and resid 95 through 106 Processing helix chain 'C' and resid 108 through 120 Processing helix chain 'D' and resid 5 through 21 Processing helix chain 'D' and resid 38 through 46 Processing helix chain 'D' and resid 46 through 53 Processing helix chain 'D' and resid 73 through 87 Processing helix chain 'D' and resid 95 through 106 Processing helix chain 'D' and resid 108 through 120 Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 37 Processing sheet with id=AA2, first strand: chain 'B' and resid 33 through 37 Processing sheet with id=AA3, first strand: chain 'C' and resid 33 through 37 Processing sheet with id=AA4, first strand: chain 'D' and resid 33 through 37 233 hydrogen bonds defined for protein. 675 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: 2.18 Time building geometry restraints manager: 5.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 3420 1.03 - 1.23: 16 1.23 - 1.42: 1532 1.42 - 1.62: 1972 1.62 - 1.81: 56 Bond restraints: 6996 Sorted by residual: bond pdb=" CA VAL A 111 " pdb=" C VAL A 111 " ideal model delta sigma weight residual 1.524 1.512 0.012 1.39e-02 5.18e+03 7.43e-01 bond pdb=" N VAL A 99 " pdb=" CA VAL A 99 " ideal model delta sigma weight residual 1.459 1.448 0.011 1.30e-02 5.92e+03 7.19e-01 bond pdb=" CA VAL C 41 " pdb=" C VAL C 41 " ideal model delta sigma weight residual 1.524 1.513 0.011 1.33e-02 5.65e+03 6.66e-01 bond pdb=" CA VAL B 111 " pdb=" C VAL B 111 " ideal model delta sigma weight residual 1.524 1.513 0.011 1.39e-02 5.18e+03 6.37e-01 bond pdb=" CA ASP A 98 " pdb=" C ASP A 98 " ideal model delta sigma weight residual 1.524 1.513 0.010 1.32e-02 5.74e+03 6.31e-01 ... (remaining 6991 not shown) Histogram of bond angle deviations from ideal: 100.81 - 106.93: 92 106.93 - 113.04: 8043 113.04 - 119.16: 1394 119.16 - 125.28: 2660 125.28 - 131.40: 371 Bond angle restraints: 12560 Sorted by residual: angle pdb=" N VAL A 99 " pdb=" CA VAL A 99 " pdb=" C VAL A 99 " ideal model delta sigma weight residual 111.09 106.37 4.72 1.25e+00 6.40e-01 1.43e+01 angle pdb=" N GLY C 92 " pdb=" CA GLY C 92 " pdb=" C GLY C 92 " ideal model delta sigma weight residual 113.18 105.36 7.82 2.37e+00 1.78e-01 1.09e+01 angle pdb=" C ASP D 25 " pdb=" N CYS D 26 " pdb=" CA CYS D 26 " ideal model delta sigma weight residual 121.75 116.88 4.87 1.73e+00 3.34e-01 7.92e+00 angle pdb=" N GLY D 31 " pdb=" CA GLY D 31 " pdb=" C GLY D 31 " ideal model delta sigma weight residual 111.02 105.82 5.20 1.86e+00 2.89e-01 7.81e+00 angle pdb=" N GLY B 31 " pdb=" CA GLY B 31 " pdb=" C GLY B 31 " ideal model delta sigma weight residual 111.02 105.89 5.13 1.86e+00 2.89e-01 7.60e+00 ... (remaining 12555 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.01: 3072 13.01 - 26.01: 171 26.01 - 39.02: 24 39.02 - 52.02: 29 52.02 - 65.03: 8 Dihedral angle restraints: 3304 sinusoidal: 1716 harmonic: 1588 Sorted by residual: dihedral pdb=" CA ASP C 68 " pdb=" CB ASP C 68 " pdb=" CG ASP C 68 " pdb=" OD1 ASP C 68 " ideal model delta sinusoidal sigma weight residual -30.00 -83.44 53.44 1 2.00e+01 2.50e-03 9.70e+00 dihedral pdb=" CA ASP A 68 " pdb=" CB ASP A 68 " pdb=" CG ASP A 68 " pdb=" OD1 ASP A 68 " ideal model delta sinusoidal sigma weight residual -30.00 -80.96 50.96 1 2.00e+01 2.50e-03 8.88e+00 dihedral pdb=" CB MET B 97 " pdb=" CG MET B 97 " pdb=" SD MET B 97 " pdb=" CE MET B 97 " ideal model delta sinusoidal sigma weight residual -60.00 -109.23 49.23 3 1.50e+01 4.44e-03 8.75e+00 ... (remaining 3301 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 402 0.033 - 0.066: 91 0.066 - 0.099: 53 0.099 - 0.132: 7 0.132 - 0.165: 7 Chirality restraints: 560 Sorted by residual: chirality pdb=" CA ILE D 28 " pdb=" N ILE D 28 " pdb=" C ILE D 28 " pdb=" CB ILE D 28 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.83e-01 chirality pdb=" CA ILE B 28 " pdb=" N ILE B 28 " pdb=" C ILE B 28 " pdb=" CB ILE B 28 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.89e-01 chirality pdb=" CA ILE A 28 " pdb=" N ILE A 28 " pdb=" C ILE A 28 " pdb=" CB ILE A 28 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.85e-01 ... (remaining 557 not shown) Planarity restraints: 1040 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER C 40 " -0.018 2.00e-02 2.50e+03 3.67e-02 1.35e+01 pdb=" C SER C 40 " 0.064 2.00e-02 2.50e+03 pdb=" O SER C 40 " -0.024 2.00e-02 2.50e+03 pdb=" N VAL C 41 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 97 " -0.013 2.00e-02 2.50e+03 2.64e-02 6.95e+00 pdb=" C MET A 97 " 0.046 2.00e-02 2.50e+03 pdb=" O MET A 97 " -0.017 2.00e-02 2.50e+03 pdb=" N ASP A 98 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 110 " 0.011 2.00e-02 2.50e+03 2.28e-02 5.18e+00 pdb=" C SER B 110 " -0.039 2.00e-02 2.50e+03 pdb=" O SER B 110 " 0.015 2.00e-02 2.50e+03 pdb=" N VAL B 111 " 0.013 2.00e-02 2.50e+03 ... (remaining 1037 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.12: 113 2.12 - 2.74: 12115 2.74 - 3.36: 19705 3.36 - 3.98: 24861 3.98 - 4.60: 39064 Nonbonded interactions: 95858 Sorted by model distance: nonbonded pdb=" HG SER B 46 " pdb=" O LEU B 106 " model vdw 1.498 2.450 nonbonded pdb=" HG SER A 46 " pdb=" O LEU A 106 " model vdw 1.573 2.450 nonbonded pdb=" O ASP D 82 " pdb=" HG1 THR D 86 " model vdw 1.587 2.450 nonbonded pdb=" O ASP B 82 " pdb=" HG1 THR B 86 " model vdw 1.606 2.450 nonbonded pdb=" O ASP A 82 " pdb=" HG1 THR A 86 " model vdw 1.667 2.450 ... (remaining 95853 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 1.870 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: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 25.090 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 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: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 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 : 0.002 0.020 3560 Z= 0.148 Angle : 0.680 7.817 4808 Z= 0.458 Chirality : 0.039 0.165 560 Planarity : 0.005 0.037 608 Dihedral : 11.042 65.027 1244 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.33), residues: 428 helix: 0.35 (0.25), residues: 284 sheet: None (None), residues: 0 loop : 0.72 (0.43), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS B 6 PHE 0.014 0.002 PHE D 11 TYR 0.017 0.003 TYR A 85 ARG 0.007 0.001 ARG B 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 214 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 ASP cc_start: 0.9283 (t70) cc_final: 0.8848 (t0) REVERT: A 112 VAL cc_start: 0.9567 (t) cc_final: 0.9362 (m) REVERT: B 35 PHE cc_start: 0.8604 (m-80) cc_final: 0.7837 (m-80) REVERT: B 82 ASP cc_start: 0.8346 (m-30) cc_final: 0.7854 (t0) REVERT: C 41 VAL cc_start: 0.9239 (t) cc_final: 0.8863 (m) REVERT: C 45 CYS cc_start: 0.7349 (m) cc_final: 0.7067 (m) REVERT: C 111 VAL cc_start: 0.9186 (t) cc_final: 0.8956 (t) REVERT: D 15 ASN cc_start: 0.9305 (t0) cc_final: 0.9025 (t0) REVERT: D 16 TYR cc_start: 0.8588 (t80) cc_final: 0.8329 (t80) REVERT: D 20 HIS cc_start: 0.8943 (m-70) cc_final: 0.8520 (m-70) REVERT: D 30 VAL cc_start: 0.8675 (t) cc_final: 0.8400 (p) REVERT: D 68 ASP cc_start: 0.9508 (t0) cc_final: 0.9217 (t0) REVERT: D 82 ASP cc_start: 0.9171 (m-30) cc_final: 0.8967 (m-30) outliers start: 0 outliers final: 0 residues processed: 214 average time/residue: 0.2737 time to fit residues: 72.9545 Evaluate side-chains 141 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 37 optimal weight: 3.9990 chunk 33 optimal weight: 0.4980 chunk 18 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 13 optimal weight: 0.3980 chunk 20 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS B 15 ASN B 20 HIS ** B 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.5221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3560 Z= 0.200 Angle : 0.588 4.929 4808 Z= 0.330 Chirality : 0.039 0.170 560 Planarity : 0.003 0.026 608 Dihedral : 3.815 15.227 464 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Rotamer: Outliers : 2.34 % Allowed : 16.67 % Favored : 80.99 % 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: 2.07 (0.37), residues: 428 helix: 1.75 (0.28), residues: 288 sheet: None (None), residues: 0 loop : 0.75 (0.45), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 20 PHE 0.017 0.002 PHE D 77 TYR 0.007 0.001 TYR C 16 ARG 0.002 0.000 ARG D 50 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 146 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 GLU cc_start: 0.9216 (mp0) cc_final: 0.8843 (mp0) REVERT: A 68 ASP cc_start: 0.9565 (t70) cc_final: 0.9301 (t0) REVERT: A 90 MET cc_start: 0.5477 (mmm) cc_final: 0.4965 (mmm) REVERT: B 8 GLU cc_start: 0.9183 (mp0) cc_final: 0.8854 (mp0) REVERT: B 36 LYS cc_start: 0.9456 (mttt) cc_final: 0.9160 (mmmm) REVERT: B 82 ASP cc_start: 0.8286 (m-30) cc_final: 0.7815 (t0) REVERT: B 83 MET cc_start: 0.8322 (tmt) cc_final: 0.7607 (tmm) REVERT: B 86 THR cc_start: 0.7918 (p) cc_final: 0.7634 (p) REVERT: D 9 GLN cc_start: 0.9254 (pt0) cc_final: 0.8901 (mp10) REVERT: D 15 ASN cc_start: 0.9421 (t0) cc_final: 0.9207 (t0) REVERT: D 16 TYR cc_start: 0.8834 (t80) cc_final: 0.8611 (t80) REVERT: D 20 HIS cc_start: 0.8884 (m-70) cc_final: 0.8528 (m-70) REVERT: D 64 MET cc_start: 0.8832 (ppp) cc_final: 0.8014 (ppp) REVERT: D 68 ASP cc_start: 0.9571 (t0) cc_final: 0.9239 (t0) REVERT: D 82 ASP cc_start: 0.9241 (m-30) cc_final: 0.9030 (m-30) outliers start: 9 outliers final: 5 residues processed: 154 average time/residue: 0.2566 time to fit residues: 49.8861 Evaluate side-chains 136 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 131 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 HIS Chi-restraints excluded: chain B residue 15 ASN Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 87 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 22 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 35 optimal weight: 9.9990 chunk 39 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS C 34 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.6200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3560 Z= 0.197 Angle : 0.560 4.430 4808 Z= 0.311 Chirality : 0.037 0.189 560 Planarity : 0.003 0.020 608 Dihedral : 3.806 13.985 464 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 2.34 % Allowed : 19.79 % Favored : 77.86 % 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: 2.02 (0.37), residues: 428 helix: 1.82 (0.29), residues: 288 sheet: None (None), residues: 0 loop : 0.48 (0.44), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 48 PHE 0.016 0.001 PHE D 77 TYR 0.004 0.001 TYR C 16 ARG 0.002 0.000 ARG D 50 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 132 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 CYS cc_start: 0.9461 (t) cc_final: 0.9145 (t) REVERT: A 68 ASP cc_start: 0.9589 (t70) cc_final: 0.9331 (t0) REVERT: A 90 MET cc_start: 0.5508 (mmm) cc_final: 0.5107 (mmm) REVERT: B 8 GLU cc_start: 0.9267 (mp0) cc_final: 0.8926 (mp0) REVERT: B 15 ASN cc_start: 0.9024 (OUTLIER) cc_final: 0.8646 (m110) REVERT: B 22 GLN cc_start: 0.9458 (tp40) cc_final: 0.9015 (mt0) REVERT: B 36 LYS cc_start: 0.9514 (mttt) cc_final: 0.9303 (mmmm) REVERT: B 45 CYS cc_start: 0.7671 (m) cc_final: 0.5515 (m) REVERT: B 82 ASP cc_start: 0.8344 (m-30) cc_final: 0.7874 (t0) REVERT: B 83 MET cc_start: 0.8363 (tmt) cc_final: 0.7689 (tmm) REVERT: B 86 THR cc_start: 0.8237 (p) cc_final: 0.7892 (p) REVERT: C 84 MET cc_start: 0.9485 (ttp) cc_final: 0.9255 (tpp) REVERT: D 9 GLN cc_start: 0.9242 (pt0) cc_final: 0.8875 (mp10) REVERT: D 15 ASN cc_start: 0.9450 (t0) cc_final: 0.9236 (t0) REVERT: D 64 MET cc_start: 0.8967 (ppp) cc_final: 0.8166 (ppp) REVERT: D 68 ASP cc_start: 0.9557 (t0) cc_final: 0.9257 (t0) outliers start: 9 outliers final: 5 residues processed: 138 average time/residue: 0.2323 time to fit residues: 41.2073 Evaluate side-chains 127 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 121 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain B residue 15 ASN Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 94 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 39 optimal weight: 4.9990 chunk 30 optimal weight: 0.1980 chunk 20 optimal weight: 5.9990 chunk 4 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.6905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3560 Z= 0.174 Angle : 0.555 6.765 4808 Z= 0.300 Chirality : 0.038 0.168 560 Planarity : 0.002 0.016 608 Dihedral : 3.813 13.262 464 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 1.82 % Allowed : 19.53 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.37), residues: 428 helix: 1.81 (0.29), residues: 288 sheet: None (None), residues: 0 loop : 0.39 (0.44), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 48 PHE 0.011 0.001 PHE D 77 TYR 0.009 0.001 TYR D 16 ARG 0.003 0.000 ARG B 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 128 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 GLU cc_start: 0.9154 (mp0) cc_final: 0.8928 (mp0) REVERT: A 68 ASP cc_start: 0.9574 (t70) cc_final: 0.9354 (t0) REVERT: A 90 MET cc_start: 0.6180 (mmm) cc_final: 0.5753 (mmm) REVERT: B 8 GLU cc_start: 0.9315 (mp0) cc_final: 0.9009 (mp0) REVERT: B 36 LYS cc_start: 0.9563 (mttt) cc_final: 0.9326 (mmmm) REVERT: B 82 ASP cc_start: 0.8213 (m-30) cc_final: 0.7671 (t70) REVERT: B 83 MET cc_start: 0.8236 (tmt) cc_final: 0.7388 (tmm) REVERT: B 86 THR cc_start: 0.7952 (p) cc_final: 0.7621 (p) REVERT: C 75 GLU cc_start: 0.9435 (mp0) cc_final: 0.9162 (mp0) REVERT: C 84 MET cc_start: 0.9495 (ttp) cc_final: 0.9232 (tpp) REVERT: C 90 MET cc_start: 0.6839 (mmp) cc_final: 0.6544 (mmm) REVERT: D 9 GLN cc_start: 0.9264 (pt0) cc_final: 0.9002 (mp10) REVERT: D 15 ASN cc_start: 0.9473 (t0) cc_final: 0.9247 (t0) REVERT: D 64 MET cc_start: 0.8992 (ppp) cc_final: 0.8123 (ppp) REVERT: D 68 ASP cc_start: 0.9544 (t0) cc_final: 0.8960 (t0) outliers start: 7 outliers final: 5 residues processed: 131 average time/residue: 0.2569 time to fit residues: 42.8498 Evaluate side-chains 122 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 117 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 87 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 HIS B 107 HIS ** C 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.8906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 3560 Z= 0.434 Angle : 0.752 6.676 4808 Z= 0.432 Chirality : 0.039 0.151 560 Planarity : 0.004 0.022 608 Dihedral : 4.293 18.966 464 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.91 % Allowed : 21.61 % Favored : 74.48 % 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: 0.54 (0.36), residues: 428 helix: 0.71 (0.28), residues: 288 sheet: None (None), residues: 0 loop : -0.17 (0.45), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.003 HIS C 20 PHE 0.026 0.003 PHE B 3 TYR 0.015 0.002 TYR C 16 ARG 0.003 0.001 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 109 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 GLU cc_start: 0.9327 (mp0) cc_final: 0.9126 (mp0) REVERT: B 22 GLN cc_start: 0.9513 (tp40) cc_final: 0.9158 (mt0) REVERT: B 36 LYS cc_start: 0.9654 (mttt) cc_final: 0.9445 (mmmm) REVERT: B 64 MET cc_start: 0.8480 (pmm) cc_final: 0.8279 (pmm) REVERT: B 70 GLU cc_start: 0.9512 (mp0) cc_final: 0.9309 (pm20) REVERT: B 82 ASP cc_start: 0.8987 (m-30) cc_final: 0.8409 (t0) REVERT: B 83 MET cc_start: 0.9184 (tmt) cc_final: 0.8884 (tmm) REVERT: D 64 MET cc_start: 0.9109 (ppp) cc_final: 0.8217 (ppp) REVERT: D 68 ASP cc_start: 0.9469 (t0) cc_final: 0.9152 (t0) REVERT: D 91 LEU cc_start: 0.8968 (mt) cc_final: 0.8509 (mm) outliers start: 15 outliers final: 14 residues processed: 116 average time/residue: 0.2520 time to fit residues: 37.1319 Evaluate side-chains 120 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 106 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 100 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 14 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.9162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3560 Z= 0.247 Angle : 0.605 6.506 4808 Z= 0.338 Chirality : 0.037 0.142 560 Planarity : 0.003 0.021 608 Dihedral : 4.129 16.939 464 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.86 % Allowed : 25.26 % Favored : 71.88 % 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: 0.80 (0.37), residues: 428 helix: 0.94 (0.28), residues: 288 sheet: None (None), residues: 0 loop : -0.13 (0.45), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 107 PHE 0.013 0.002 PHE A 77 TYR 0.009 0.001 TYR D 16 ARG 0.002 0.000 ARG A 50 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 120 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 GLU cc_start: 0.9219 (mp0) cc_final: 0.8936 (mp0) REVERT: B 22 GLN cc_start: 0.9465 (tp40) cc_final: 0.9143 (mp10) REVERT: B 70 GLU cc_start: 0.9502 (mp0) cc_final: 0.9257 (pm20) REVERT: B 82 ASP cc_start: 0.8943 (m-30) cc_final: 0.8485 (t70) REVERT: B 83 MET cc_start: 0.9186 (tmt) cc_final: 0.8934 (tmm) REVERT: D 64 MET cc_start: 0.9188 (ppp) cc_final: 0.8394 (ppp) REVERT: D 68 ASP cc_start: 0.9436 (t0) cc_final: 0.9121 (t0) REVERT: D 91 LEU cc_start: 0.9099 (mt) cc_final: 0.8533 (mm) outliers start: 11 outliers final: 11 residues processed: 123 average time/residue: 0.2608 time to fit residues: 41.0790 Evaluate side-chains 121 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 110 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 100 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 4.9990 chunk 35 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.9622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 3560 Z= 0.300 Angle : 0.659 6.278 4808 Z= 0.369 Chirality : 0.038 0.140 560 Planarity : 0.003 0.017 608 Dihedral : 4.142 17.427 464 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 3.91 % Allowed : 26.30 % Favored : 69.79 % 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: 0.49 (0.36), residues: 428 helix: 0.72 (0.28), residues: 288 sheet: None (None), residues: 0 loop : -0.30 (0.45), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS C 20 PHE 0.014 0.002 PHE A 77 TYR 0.010 0.001 TYR D 16 ARG 0.003 0.000 ARG D 18 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 108 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 GLU cc_start: 0.9240 (mp0) cc_final: 0.8964 (mp0) REVERT: B 70 GLU cc_start: 0.9504 (mp0) cc_final: 0.9179 (pm20) REVERT: B 82 ASP cc_start: 0.8997 (m-30) cc_final: 0.8524 (t0) REVERT: D 9 GLN cc_start: 0.9285 (pt0) cc_final: 0.8991 (pt0) REVERT: D 64 MET cc_start: 0.9071 (ppp) cc_final: 0.8213 (ppp) REVERT: D 68 ASP cc_start: 0.9447 (t0) cc_final: 0.9165 (t0) outliers start: 15 outliers final: 14 residues processed: 116 average time/residue: 0.2793 time to fit residues: 41.3747 Evaluate side-chains 122 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 108 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain B residue 45 CYS Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 100 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 20 optimal weight: 0.6980 chunk 3 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 39 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 15 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.9681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3560 Z= 0.195 Angle : 0.612 6.956 4808 Z= 0.329 Chirality : 0.037 0.139 560 Planarity : 0.002 0.017 608 Dihedral : 4.075 15.749 464 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 2.08 % Allowed : 26.56 % Favored : 71.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.37), residues: 428 helix: 1.18 (0.29), residues: 288 sheet: None (None), residues: 0 loop : -0.24 (0.45), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 6 PHE 0.008 0.001 PHE A 77 TYR 0.005 0.001 TYR D 16 ARG 0.001 0.000 ARG B 50 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 114 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 GLU cc_start: 0.9240 (mp0) cc_final: 0.8922 (mp0) REVERT: A 83 MET cc_start: 0.9509 (tmm) cc_final: 0.9231 (tmm) REVERT: B 22 GLN cc_start: 0.9397 (tp40) cc_final: 0.9147 (mp10) REVERT: B 70 GLU cc_start: 0.9492 (mp0) cc_final: 0.9203 (pm20) REVERT: B 82 ASP cc_start: 0.8959 (m-30) cc_final: 0.8468 (t0) REVERT: D 64 MET cc_start: 0.9090 (ppp) cc_final: 0.8308 (ppp) REVERT: D 91 LEU cc_start: 0.9004 (mt) cc_final: 0.8409 (mm) outliers start: 8 outliers final: 7 residues processed: 118 average time/residue: 0.2542 time to fit residues: 38.4204 Evaluate side-chains 119 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 112 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain B residue 15 ASN Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 94 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 35 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 25 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.9808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3560 Z= 0.200 Angle : 0.609 6.985 4808 Z= 0.331 Chirality : 0.037 0.138 560 Planarity : 0.003 0.030 608 Dihedral : 3.993 14.024 464 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.82 % Allowed : 27.60 % Favored : 70.57 % 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: 1.20 (0.38), residues: 428 helix: 1.32 (0.29), residues: 288 sheet: None (None), residues: 0 loop : -0.16 (0.45), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 6 PHE 0.010 0.001 PHE D 35 TYR 0.014 0.001 TYR D 16 ARG 0.002 0.000 ARG A 50 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 109 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 GLU cc_start: 0.9251 (mp0) cc_final: 0.8949 (mp0) REVERT: A 97 MET cc_start: 0.9066 (ptp) cc_final: 0.8819 (pmm) REVERT: B 17 GLN cc_start: 0.9537 (mt0) cc_final: 0.8915 (mt0) REVERT: B 22 GLN cc_start: 0.9405 (tp40) cc_final: 0.9156 (mp10) REVERT: B 70 GLU cc_start: 0.9446 (mp0) cc_final: 0.9158 (pm20) REVERT: B 82 ASP cc_start: 0.8965 (m-30) cc_final: 0.8531 (t0) REVERT: B 97 MET cc_start: 0.9366 (tpp) cc_final: 0.8980 (mmt) REVERT: C 90 MET cc_start: 0.7862 (mmp) cc_final: 0.7549 (mmm) REVERT: D 64 MET cc_start: 0.9083 (ppp) cc_final: 0.8301 (ppp) outliers start: 7 outliers final: 6 residues processed: 113 average time/residue: 0.2629 time to fit residues: 38.0142 Evaluate side-chains 114 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 108 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 94 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 26 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.9983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3560 Z= 0.226 Angle : 0.628 6.822 4808 Z= 0.343 Chirality : 0.037 0.135 560 Planarity : 0.003 0.018 608 Dihedral : 3.990 16.133 464 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.08 % Allowed : 27.34 % Favored : 70.57 % 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: 1.14 (0.38), residues: 428 helix: 1.26 (0.29), residues: 288 sheet: None (None), residues: 0 loop : -0.18 (0.46), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 20 PHE 0.010 0.001 PHE A 77 TYR 0.007 0.001 TYR D 16 ARG 0.001 0.000 ARG A 50 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 108 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 GLU cc_start: 0.9270 (mp0) cc_final: 0.8940 (mp0) REVERT: B 70 GLU cc_start: 0.9422 (mp0) cc_final: 0.9027 (pm20) REVERT: B 82 ASP cc_start: 0.8991 (m-30) cc_final: 0.8536 (t0) REVERT: B 97 MET cc_start: 0.9368 (tpp) cc_final: 0.8968 (mmt) REVERT: C 90 MET cc_start: 0.7868 (mmp) cc_final: 0.7554 (mmm) REVERT: D 64 MET cc_start: 0.9107 (ppp) cc_final: 0.8306 (ppp) outliers start: 8 outliers final: 7 residues processed: 111 average time/residue: 0.2497 time to fit residues: 35.3209 Evaluate side-chains 115 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 108 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 100 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 4 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 chunk 26 optimal weight: 0.7980 chunk 17 optimal weight: 5.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 15 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 = 0.3259 r_free = 0.3259 target = 0.058097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.050760 restraints weight = 51210.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.053163 restraints weight = 20856.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.054750 restraints weight = 10741.839| |-----------------------------------------------------------------------------| r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.9995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3560 Z= 0.195 Angle : 0.621 6.771 4808 Z= 0.334 Chirality : 0.037 0.141 560 Planarity : 0.002 0.016 608 Dihedral : 3.941 14.102 464 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.56 % Allowed : 27.60 % Favored : 70.83 % 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: 1.37 (0.38), residues: 428 helix: 1.45 (0.30), residues: 288 sheet: None (None), residues: 0 loop : -0.12 (0.46), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 6 PHE 0.008 0.001 PHE A 77 TYR 0.014 0.001 TYR D 16 ARG 0.002 0.000 ARG D 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2411.65 seconds wall clock time: 42 minutes 27.90 seconds (2547.90 seconds total)