Starting phenix.real_space_refine on Fri Apr 5 19:10:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8poc_17788/04_2024/8poc_17788.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8poc_17788/04_2024/8poc_17788.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8poc_17788/04_2024/8poc_17788.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8poc_17788/04_2024/8poc_17788.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8poc_17788/04_2024/8poc_17788.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8poc_17788/04_2024/8poc_17788.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 28 5.16 5 C 3108 2.51 5 N 880 2.21 5 O 908 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 38": "OE1" <-> "OE2" Residue "A GLU 40": "OE1" <-> "OE2" Residue "A TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 38": "OE1" <-> "OE2" Residue "B TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 146": "OE1" <-> "OE2" Residue "C TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 38": "OE1" <-> "OE2" Residue "C GLU 68": "OE1" <-> "OE2" Residue "C GLU 70": "OE1" <-> "OE2" Residue "C GLU 89": "OE1" <-> "OE2" Residue "D TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 38": "OE1" <-> "OE2" Residue "D GLU 70": "OE1" <-> "OE2" Residue "D GLU 89": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 4924 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1231 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 6, 'TRANS': 147} Chain: "B" Number of atoms: 1231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1231 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 6, 'TRANS': 147} Chain: "C" Number of atoms: 1231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1231 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 6, 'TRANS': 147} Chain: "D" Number of atoms: 1231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1231 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 6, 'TRANS': 147} Time building chain proxies: 3.09, per 1000 atoms: 0.63 Number of scatterers: 4924 At special positions: 0 Unit cell: (86.49, 76.26, 77.19, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 28 16.00 O 908 8.00 N 880 7.00 C 3108 6.00 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: 1.75 Conformation dependent library (CDL) restraints added in 929.3 milliseconds 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1136 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 4 sheets defined 60.1% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 2 through 15 Processing helix chain 'A' and resid 20 through 37 Processing helix chain 'A' and resid 38 through 56 removed outlier: 3.539A pdb=" N ARG A 55 " --> pdb=" O GLN A 51 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N TYR A 56 " --> pdb=" O LEU A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 79 removed outlier: 4.100A pdb=" N LEU A 77 " --> pdb=" O ARG A 73 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N PHE A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 131 removed outlier: 3.896A pdb=" N GLY A 131 " --> pdb=" O LEU A 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 15 Processing helix chain 'B' and resid 20 through 37 Processing helix chain 'B' and resid 38 through 56 removed outlier: 3.574A pdb=" N ARG B 55 " --> pdb=" O GLN B 51 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N TYR B 56 " --> pdb=" O LEU B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 79 removed outlier: 4.039A pdb=" N LEU B 77 " --> pdb=" O ARG B 73 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N PHE B 78 " --> pdb=" O VAL B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 130 Processing helix chain 'C' and resid 2 through 15 Processing helix chain 'C' and resid 20 through 37 Processing helix chain 'C' and resid 38 through 56 removed outlier: 3.596A pdb=" N ARG C 55 " --> pdb=" O GLN C 51 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N TYR C 56 " --> pdb=" O LEU C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 79 removed outlier: 4.027A pdb=" N LEU C 77 " --> pdb=" O ARG C 73 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N PHE C 78 " --> pdb=" O VAL C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 130 Processing helix chain 'D' and resid 2 through 15 Processing helix chain 'D' and resid 20 through 37 Processing helix chain 'D' and resid 38 through 56 removed outlier: 3.548A pdb=" N ARG D 55 " --> pdb=" O GLN D 51 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N TYR D 56 " --> pdb=" O LEU D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 79 removed outlier: 4.039A pdb=" N LEU D 77 " --> pdb=" O ARG D 73 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N PHE D 78 " --> pdb=" O VAL D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 131 removed outlier: 3.905A pdb=" N GLY D 131 " --> pdb=" O LEU D 127 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 82 through 87 Processing sheet with id=AA2, first strand: chain 'B' and resid 82 through 87 Processing sheet with id=AA3, first strand: chain 'C' and resid 82 through 87 Processing sheet with id=AA4, first strand: chain 'D' and resid 82 through 87 336 hydrogen bonds defined for protein. 966 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: 1.34 Time building geometry restraints manager: 1.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1680 1.34 - 1.46: 1134 1.46 - 1.58: 2174 1.58 - 1.70: 0 1.70 - 1.81: 48 Bond restraints: 5036 Sorted by residual: bond pdb=" CG1 ILE A 94 " pdb=" CD1 ILE A 94 " ideal model delta sigma weight residual 1.513 1.470 0.043 3.90e-02 6.57e+02 1.20e+00 bond pdb=" CB GLN B 14 " pdb=" CG GLN B 14 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.15e+00 bond pdb=" CG1 ILE D 94 " pdb=" CD1 ILE D 94 " ideal model delta sigma weight residual 1.513 1.472 0.041 3.90e-02 6.57e+02 1.13e+00 bond pdb=" CB GLN C 14 " pdb=" CG GLN C 14 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.11e+00 bond pdb=" CG LEU A 85 " pdb=" CD2 LEU A 85 " ideal model delta sigma weight residual 1.521 1.491 0.030 3.30e-02 9.18e+02 8.51e-01 ... (remaining 5031 not shown) Histogram of bond angle deviations from ideal: 100.32 - 107.05: 139 107.05 - 113.79: 2690 113.79 - 120.52: 2106 120.52 - 127.26: 1837 127.26 - 133.99: 60 Bond angle restraints: 6832 Sorted by residual: angle pdb=" C GLN D 16 " pdb=" N LEU D 17 " pdb=" CA LEU D 17 " ideal model delta sigma weight residual 122.31 113.78 8.53 2.34e+00 1.83e-01 1.33e+01 angle pdb=" C GLN C 16 " pdb=" N LEU C 17 " pdb=" CA LEU C 17 " ideal model delta sigma weight residual 122.31 114.00 8.31 2.34e+00 1.83e-01 1.26e+01 angle pdb=" C GLN B 16 " pdb=" N LEU B 17 " pdb=" CA LEU B 17 " ideal model delta sigma weight residual 122.31 114.55 7.76 2.34e+00 1.83e-01 1.10e+01 angle pdb=" CA GLN C 14 " pdb=" CB GLN C 14 " pdb=" CG GLN C 14 " ideal model delta sigma weight residual 114.10 119.51 -5.41 2.00e+00 2.50e-01 7.32e+00 angle pdb=" CA GLN B 14 " pdb=" CB GLN B 14 " pdb=" CG GLN B 14 " ideal model delta sigma weight residual 114.10 119.51 -5.41 2.00e+00 2.50e-01 7.30e+00 ... (remaining 6827 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.13: 2649 17.13 - 34.26: 276 34.26 - 51.39: 35 51.39 - 68.52: 6 68.52 - 85.65: 18 Dihedral angle restraints: 2984 sinusoidal: 1208 harmonic: 1776 Sorted by residual: dihedral pdb=" CA ASN B 35 " pdb=" C ASN B 35 " pdb=" N ALA B 36 " pdb=" CA ALA B 36 " ideal model delta harmonic sigma weight residual 180.00 -164.77 -15.23 0 5.00e+00 4.00e-02 9.27e+00 dihedral pdb=" CA ARG A 13 " pdb=" CB ARG A 13 " pdb=" CG ARG A 13 " pdb=" CD ARG A 13 " ideal model delta sinusoidal sigma weight residual -60.00 -113.88 53.88 3 1.50e+01 4.44e-03 9.24e+00 dihedral pdb=" CA ARG B 13 " pdb=" CB ARG B 13 " pdb=" CG ARG B 13 " pdb=" CD ARG B 13 " ideal model delta sinusoidal sigma weight residual -60.00 -113.61 53.61 3 1.50e+01 4.44e-03 9.22e+00 ... (remaining 2981 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 569 0.038 - 0.075: 151 0.075 - 0.113: 4 0.113 - 0.150: 0 0.150 - 0.188: 4 Chirality restraints: 728 Sorted by residual: chirality pdb=" CA ILE A 94 " pdb=" N ILE A 94 " pdb=" C ILE A 94 " pdb=" CB ILE A 94 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.82e-01 chirality pdb=" CA ILE D 94 " pdb=" N ILE D 94 " pdb=" C ILE D 94 " pdb=" CB ILE D 94 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.40e-01 chirality pdb=" CA ILE C 94 " pdb=" N ILE C 94 " pdb=" C ILE C 94 " pdb=" CB ILE C 94 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.65e-01 ... (remaining 725 not shown) Planarity restraints: 896 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 99 " -0.024 5.00e-02 4.00e+02 3.64e-02 2.12e+00 pdb=" N PRO C 100 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO C 100 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 100 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 11 " 0.008 2.00e-02 2.50e+03 1.03e-02 2.11e+00 pdb=" CG TYR B 11 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR B 11 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR B 11 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR B 11 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR B 11 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR B 11 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 11 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 99 " 0.024 5.00e-02 4.00e+02 3.62e-02 2.09e+00 pdb=" N PRO B 100 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO B 100 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 100 " 0.020 5.00e-02 4.00e+02 ... (remaining 893 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 1472 2.84 - 3.35: 4800 3.35 - 3.87: 7565 3.87 - 4.38: 7525 4.38 - 4.90: 14384 Nonbonded interactions: 35746 Sorted by model distance: nonbonded pdb=" O GLU D 68 " pdb=" ND2 ASN D 72 " model vdw 2.324 2.520 nonbonded pdb=" N GLU A 89 " pdb=" OE1 GLU A 89 " model vdw 2.340 2.520 nonbonded pdb=" N GLU C 89 " pdb=" OE1 GLU C 89 " model vdw 2.343 2.520 nonbonded pdb=" O GLU B 68 " pdb=" ND2 ASN B 72 " model vdw 2.346 2.520 nonbonded pdb=" NH2 ARG C 112 " pdb=" OE1 GLU C 142 " model vdw 2.382 2.520 ... (remaining 35741 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 0.710 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: 3.840 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 17.530 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 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 0.043 5036 Z= 0.221 Angle : 0.667 8.532 6832 Z= 0.349 Chirality : 0.034 0.188 728 Planarity : 0.004 0.037 896 Dihedral : 14.858 85.653 1848 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % 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: 2.14 (0.33), residues: 608 helix: 2.97 (0.27), residues: 344 sheet: 0.47 (0.44), residues: 96 loop : -1.49 (0.42), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 126 HIS 0.006 0.002 HIS A 96 PHE 0.007 0.001 PHE D 44 TYR 0.025 0.001 TYR B 11 ARG 0.009 0.001 ARG D 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 0.593 Fit side-chains REVERT: C 93 GLU cc_start: 0.8285 (mt-10) cc_final: 0.8035 (mt-10) REVERT: D 1 MET cc_start: 0.7142 (mpp) cc_final: 0.6579 (mpp) REVERT: D 89 GLU cc_start: 0.8233 (pm20) cc_final: 0.7990 (pm20) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.1671 time to fit residues: 28.7193 Evaluate side-chains 108 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 25 optimal weight: 6.9990 chunk 15 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 28 optimal weight: 0.0770 chunk 35 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 overall best weight: 0.9140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 GLN B 79 HIS B 104 ASN C 79 HIS D 14 GLN D 96 HIS ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5036 Z= 0.234 Angle : 0.560 5.016 6832 Z= 0.281 Chirality : 0.035 0.177 728 Planarity : 0.004 0.035 896 Dihedral : 3.424 15.153 692 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.88 % Allowed : 11.92 % Favored : 85.19 % 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: 2.29 (0.34), residues: 608 helix: 2.95 (0.27), residues: 356 sheet: 0.72 (0.47), residues: 96 loop : -1.55 (0.45), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 126 HIS 0.004 0.001 HIS B 96 PHE 0.008 0.002 PHE D 25 TYR 0.007 0.001 TYR A 153 ARG 0.004 0.000 ARG D 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 131 time to evaluate : 0.610 Fit side-chains REVERT: B 93 GLU cc_start: 0.8470 (tt0) cc_final: 0.8090 (mt-10) REVERT: C 93 GLU cc_start: 0.8308 (mt-10) cc_final: 0.8044 (mt-10) REVERT: D 1 MET cc_start: 0.7852 (mpp) cc_final: 0.7597 (mpp) outliers start: 15 outliers final: 10 residues processed: 134 average time/residue: 0.1666 time to fit residues: 28.4051 Evaluate side-chains 137 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 127 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 140 CYS Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 140 CYS Chi-restraints excluded: chain D residue 148 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 58 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 18 optimal weight: 0.7980 chunk 43 optimal weight: 10.0000 chunk 53 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN B 79 HIS C 96 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5036 Z= 0.223 Angle : 0.534 4.685 6832 Z= 0.269 Chirality : 0.034 0.176 728 Planarity : 0.004 0.034 896 Dihedral : 3.330 14.646 692 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.27 % Allowed : 15.77 % Favored : 80.96 % 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: 2.43 (0.34), residues: 608 helix: 3.03 (0.27), residues: 356 sheet: 0.76 (0.47), residues: 96 loop : -1.40 (0.46), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 21 HIS 0.005 0.001 HIS B 79 PHE 0.006 0.001 PHE A 25 TYR 0.011 0.001 TYR B 11 ARG 0.003 0.000 ARG D 152 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 126 time to evaluate : 0.544 Fit side-chains REVERT: B 93 GLU cc_start: 0.8531 (tt0) cc_final: 0.8099 (mt-10) REVERT: C 93 GLU cc_start: 0.8445 (mt-10) cc_final: 0.8099 (mt-10) REVERT: C 152 ARG cc_start: 0.8724 (tpp80) cc_final: 0.8130 (mtt90) REVERT: D 1 MET cc_start: 0.7926 (mpp) cc_final: 0.7628 (mpp) outliers start: 17 outliers final: 10 residues processed: 133 average time/residue: 0.1647 time to fit residues: 27.8229 Evaluate side-chains 128 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 118 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain B residue 3 ASP Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 140 CYS Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 140 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 0.6980 chunk 28 optimal weight: 20.0000 chunk 6 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 5036 Z= 0.358 Angle : 0.611 6.043 6832 Z= 0.306 Chirality : 0.036 0.166 728 Planarity : 0.004 0.034 896 Dihedral : 3.556 15.602 692 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 5.19 % Allowed : 17.69 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.34), residues: 608 helix: 2.90 (0.27), residues: 356 sheet: 0.79 (0.47), residues: 96 loop : -1.17 (0.48), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 111 HIS 0.005 0.001 HIS D 96 PHE 0.011 0.002 PHE D 25 TYR 0.008 0.002 TYR D 95 ARG 0.003 0.000 ARG D 152 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 114 time to evaluate : 0.589 Fit side-chains REVERT: A 17 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8609 (pp) REVERT: A 68 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7990 (pt0) REVERT: B 93 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8052 (mt-10) REVERT: D 17 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8580 (pp) outliers start: 27 outliers final: 15 residues processed: 128 average time/residue: 0.1674 time to fit residues: 27.4106 Evaluate side-chains 136 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 117 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain B residue 3 ASP Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 140 CYS Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 140 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 3.9990 chunk 43 optimal weight: 10.0000 chunk 23 optimal weight: 0.0670 chunk 49 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 14 optimal weight: 0.0670 chunk 19 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 overall best weight: 0.4856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5036 Z= 0.172 Angle : 0.517 6.142 6832 Z= 0.253 Chirality : 0.033 0.175 728 Planarity : 0.004 0.035 896 Dihedral : 3.309 14.803 692 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 5.19 % Allowed : 17.50 % Favored : 77.31 % 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: 2.72 (0.34), residues: 608 helix: 3.18 (0.27), residues: 356 sheet: 0.92 (0.46), residues: 96 loop : -1.06 (0.48), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 111 HIS 0.004 0.001 HIS B 96 PHE 0.004 0.001 PHE D 151 TYR 0.014 0.001 TYR B 11 ARG 0.003 0.000 ARG C 152 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 110 time to evaluate : 0.594 Fit side-chains REVERT: A 17 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8510 (pp) REVERT: B 17 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8546 (pp) REVERT: B 93 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.8159 (mt-10) REVERT: C 17 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8508 (pp) REVERT: D 17 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8510 (pp) outliers start: 27 outliers final: 13 residues processed: 126 average time/residue: 0.1537 time to fit residues: 24.8740 Evaluate side-chains 123 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 105 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 140 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 0.3980 chunk 55 optimal weight: 0.0670 chunk 6 optimal weight: 5.9990 chunk 33 optimal weight: 0.0370 chunk 42 optimal weight: 1.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5036 Z= 0.194 Angle : 0.530 5.347 6832 Z= 0.258 Chirality : 0.033 0.180 728 Planarity : 0.004 0.035 896 Dihedral : 3.215 14.690 692 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 5.38 % Allowed : 17.31 % Favored : 77.31 % 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: 2.82 (0.34), residues: 608 helix: 3.25 (0.26), residues: 356 sheet: 0.87 (0.45), residues: 96 loop : -0.93 (0.48), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 21 HIS 0.003 0.001 HIS B 96 PHE 0.005 0.001 PHE A 78 TYR 0.010 0.001 TYR B 11 ARG 0.003 0.000 ARG D 152 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 111 time to evaluate : 0.598 Fit side-chains REVERT: A 17 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8528 (pp) REVERT: B 17 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8547 (pp) REVERT: B 93 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.8141 (mt-10) REVERT: C 17 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8523 (pp) REVERT: D 17 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8489 (pp) outliers start: 28 outliers final: 17 residues processed: 128 average time/residue: 0.1594 time to fit residues: 26.4520 Evaluate side-chains 131 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 109 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 140 CYS Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 140 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 30 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5036 Z= 0.219 Angle : 0.530 7.252 6832 Z= 0.258 Chirality : 0.033 0.183 728 Planarity : 0.004 0.035 896 Dihedral : 3.210 14.679 692 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 5.38 % Allowed : 17.88 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.88 (0.34), residues: 608 helix: 3.30 (0.27), residues: 356 sheet: 0.84 (0.45), residues: 96 loop : -0.87 (0.48), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 21 HIS 0.003 0.001 HIS B 79 PHE 0.006 0.001 PHE B 78 TYR 0.009 0.001 TYR D 11 ARG 0.005 0.000 ARG D 152 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 109 time to evaluate : 0.589 Fit side-chains REVERT: A 17 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8521 (pp) REVERT: B 17 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8562 (pp) REVERT: B 93 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8160 (mt-10) REVERT: C 17 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8523 (pp) REVERT: D 17 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8501 (pp) outliers start: 28 outliers final: 20 residues processed: 126 average time/residue: 0.1606 time to fit residues: 26.1397 Evaluate side-chains 132 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 107 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain B residue 3 ASP Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 140 CYS Chi-restraints excluded: chain D residue 3 ASP Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 140 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5036 Z= 0.204 Angle : 0.536 7.873 6832 Z= 0.258 Chirality : 0.033 0.184 728 Planarity : 0.004 0.035 896 Dihedral : 3.182 14.324 692 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 5.38 % Allowed : 17.50 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.90 (0.34), residues: 608 helix: 3.30 (0.27), residues: 356 sheet: 0.85 (0.45), residues: 96 loop : -0.83 (0.48), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 21 HIS 0.003 0.001 HIS B 96 PHE 0.004 0.001 PHE B 25 TYR 0.009 0.001 TYR D 11 ARG 0.003 0.000 ARG C 152 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 111 time to evaluate : 0.616 Fit side-chains REVERT: A 17 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8528 (pp) REVERT: A 33 MET cc_start: 0.6467 (mmt) cc_final: 0.6159 (mtt) REVERT: B 17 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8559 (pp) REVERT: B 93 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8161 (mt-10) REVERT: C 15 GLN cc_start: 0.8868 (tp40) cc_final: 0.8536 (tp40) REVERT: C 17 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8573 (pp) REVERT: C 152 ARG cc_start: 0.8719 (tpp80) cc_final: 0.8221 (mtt90) REVERT: D 17 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8488 (pp) outliers start: 28 outliers final: 17 residues processed: 129 average time/residue: 0.1563 time to fit residues: 26.0474 Evaluate side-chains 131 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 109 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 140 CYS Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 140 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 chunk 56 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 55 optimal weight: 0.0770 chunk 47 optimal weight: 0.5980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 14 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5036 Z= 0.189 Angle : 0.540 8.032 6832 Z= 0.258 Chirality : 0.033 0.180 728 Planarity : 0.004 0.035 896 Dihedral : 3.148 14.439 692 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 5.00 % Allowed : 18.46 % Favored : 76.54 % 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: 2.97 (0.34), residues: 608 helix: 3.34 (0.27), residues: 356 sheet: 0.92 (0.45), residues: 96 loop : -0.76 (0.47), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 21 HIS 0.003 0.001 HIS B 96 PHE 0.005 0.001 PHE C 44 TYR 0.009 0.001 TYR D 11 ARG 0.004 0.000 ARG D 152 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 110 time to evaluate : 0.589 Fit side-chains REVERT: A 17 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8495 (pp) REVERT: A 33 MET cc_start: 0.6588 (mmt) cc_final: 0.6202 (mtt) REVERT: B 17 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8522 (pp) REVERT: B 93 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.8148 (mt-10) REVERT: C 17 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8554 (pp) REVERT: C 152 ARG cc_start: 0.8763 (tpp80) cc_final: 0.8249 (mtt90) REVERT: D 17 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8478 (pp) outliers start: 26 outliers final: 16 residues processed: 128 average time/residue: 0.1538 time to fit residues: 25.4947 Evaluate side-chains 133 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 112 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 140 CYS Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 140 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 0.9980 chunk 36 optimal weight: 7.9990 chunk 29 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 13 optimal weight: 10.0000 chunk 47 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5036 Z= 0.239 Angle : 0.573 8.087 6832 Z= 0.275 Chirality : 0.034 0.175 728 Planarity : 0.004 0.034 896 Dihedral : 3.193 14.670 692 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 4.62 % Allowed : 19.23 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.00 (0.34), residues: 608 helix: 3.35 (0.27), residues: 356 sheet: 0.95 (0.45), residues: 96 loop : -0.73 (0.47), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 111 HIS 0.003 0.001 HIS B 79 PHE 0.007 0.001 PHE D 25 TYR 0.007 0.001 TYR D 11 ARG 0.004 0.000 ARG D 152 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 108 time to evaluate : 0.610 Fit side-chains REVERT: A 17 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8529 (pp) REVERT: A 33 MET cc_start: 0.6573 (mmt) cc_final: 0.6193 (mtt) REVERT: B 17 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8590 (pp) REVERT: B 93 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.8121 (mt-10) REVERT: C 17 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8588 (pp) REVERT: C 33 MET cc_start: 0.6335 (mmt) cc_final: 0.5908 (mtt) REVERT: C 152 ARG cc_start: 0.8723 (tpp80) cc_final: 0.8202 (mtt90) REVERT: D 17 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8519 (pp) outliers start: 24 outliers final: 18 residues processed: 125 average time/residue: 0.1606 time to fit residues: 26.1051 Evaluate side-chains 133 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 110 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 140 CYS Chi-restraints excluded: chain D residue 3 ASP Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 140 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 34 optimal weight: 0.8980 chunk 54 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 40 optimal weight: 0.0570 chunk 1 optimal weight: 0.9980 chunk 38 optimal weight: 0.0770 overall best weight: 0.4656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.159126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.115462 restraints weight = 6710.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.117994 restraints weight = 5526.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.119781 restraints weight = 4856.988| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5036 Z= 0.180 Angle : 0.556 8.685 6832 Z= 0.264 Chirality : 0.033 0.179 728 Planarity : 0.004 0.035 896 Dihedral : 3.144 14.179 692 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 4.04 % Allowed : 19.81 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.03 (0.34), residues: 608 helix: 3.38 (0.27), residues: 356 sheet: 0.96 (0.45), residues: 96 loop : -0.74 (0.47), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP D 21 HIS 0.003 0.001 HIS B 96 PHE 0.003 0.001 PHE B 44 TYR 0.009 0.001 TYR C 11 ARG 0.004 0.000 ARG D 152 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1309.87 seconds wall clock time: 24 minutes 22.76 seconds (1462.76 seconds total)