Starting phenix.real_space_refine on Fri Jan 19 22:00:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xzy_33534/01_2024/7xzy_33534.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xzy_33534/01_2024/7xzy_33534.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xzy_33534/01_2024/7xzy_33534.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xzy_33534/01_2024/7xzy_33534.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xzy_33534/01_2024/7xzy_33534.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xzy_33534/01_2024/7xzy_33534.pdb" } resolution = 3.97 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 330 5.49 5 S 14 5.16 5 C 7015 2.51 5 N 2417 2.21 5 O 3045 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 97": "OE1" <-> "OE2" Residue "A GLU 105": "OE1" <-> "OE2" Residue "A ASP 106": "OD1" <-> "OD2" Residue "A ASP 123": "OD1" <-> "OD2" Residue "B ASP 24": "OD1" <-> "OD2" Residue "B PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 68": "OD1" <-> "OD2" Residue "C ASP 72": "OD1" <-> "OD2" Residue "C ASP 90": "OD1" <-> "OD2" Residue "D GLU 32": "OE1" <-> "OE2" Residue "D ASP 48": "OD1" <-> "OD2" Residue "D ASP 65": "OD1" <-> "OD2" Residue "D GLU 68": "OE1" <-> "OE2" Residue "D GLU 73": "OE1" <-> "OE2" Residue "E GLU 50": "OE1" <-> "OE2" Residue "E PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 94": "OE1" <-> "OE2" Residue "E GLU 97": "OE1" <-> "OE2" Residue "E GLU 105": "OE1" <-> "OE2" Residue "E ASP 106": "OD1" <-> "OD2" Residue "E ASP 123": "OD1" <-> "OD2" Residue "F ASP 24": "OD1" <-> "OD2" Residue "F GLU 63": "OE1" <-> "OE2" Residue "F ASP 85": "OD1" <-> "OD2" Residue "F TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 110": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 12821 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 844 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "F" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 819 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 746 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 3372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 3372 Classifications: {'DNA': 165} Link IDs: {'rna3p': 164} Chain: "J" Number of atoms: 3393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 3393 Classifications: {'DNA': 165} Link IDs: {'rna3p': 164} Time building chain proxies: 6.98, per 1000 atoms: 0.54 Number of scatterers: 12821 At special positions: 0 Unit cell: (127.6, 151.8, 105.6, 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 14 16.00 P 330 15.00 O 3045 8.00 N 2417 7.00 C 7015 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: 7.55 Conformation dependent library (CDL) restraints added in 1.3 seconds 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1420 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 9 sheets defined 73.5% alpha, 2.4% beta 163 base pairs and 262 stacking pairs defined. Time for finding SS restraints: 6.62 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.654A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.345A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.175A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 removed outlier: 4.127A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 121 removed outlier: 3.536A pdb=" N ALA D 121 " --> pdb=" O LYS D 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.519A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 23 through 29 removed outlier: 4.152A pdb=" N ILE F 26 " --> pdb=" O ARG F 23 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.723A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.306A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 122 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.699A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 removed outlier: 3.602A pdb=" N ILE A 119 " --> pdb=" O ARG B 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 78 removed outlier: 4.222A pdb=" N ILE C 78 " --> pdb=" O GLY D 50 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 101 removed outlier: 3.639A pdb=" N THR C 101 " --> pdb=" O THR F 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.771A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.555A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78 removed outlier: 3.735A pdb=" N ILE G 78 " --> pdb=" O GLY H 50 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 410 hydrogen bonds defined for protein. 1206 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 423 hydrogen bonds 842 hydrogen bond angles 0 basepair planarities 163 basepair parallelities 262 stacking parallelities Total time for adding SS restraints: 4.96 Time building geometry restraints manager: 7.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2094 1.33 - 1.45: 4796 1.45 - 1.57: 6152 1.57 - 1.69: 658 1.69 - 1.81: 24 Bond restraints: 13724 Sorted by residual: bond pdb=" N ILE H 66 " pdb=" CA ILE H 66 " ideal model delta sigma weight residual 1.461 1.499 -0.038 1.17e-02 7.31e+03 1.04e+01 bond pdb=" N ASN H 81 " pdb=" CA ASN H 81 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.26e-02 6.30e+03 8.21e+00 bond pdb=" N ILE G 87 " pdb=" CA ILE G 87 " ideal model delta sigma weight residual 1.460 1.491 -0.031 1.21e-02 6.83e+03 6.56e+00 bond pdb=" N ILE D 66 " pdb=" CA ILE D 66 " ideal model delta sigma weight residual 1.461 1.490 -0.029 1.17e-02 7.31e+03 6.21e+00 bond pdb=" N LYS C 118 " pdb=" CA LYS C 118 " ideal model delta sigma weight residual 1.454 1.480 -0.026 1.23e-02 6.61e+03 4.51e+00 ... (remaining 13719 not shown) Histogram of bond angle deviations from ideal: 98.46 - 105.32: 1425 105.32 - 112.18: 7550 112.18 - 119.04: 3616 119.04 - 125.90: 6289 125.90 - 132.76: 1068 Bond angle restraints: 19948 Sorted by residual: angle pdb=" CA ILE D 66 " pdb=" C ILE D 66 " pdb=" O ILE D 66 " ideal model delta sigma weight residual 121.17 117.11 4.06 1.06e+00 8.90e-01 1.47e+01 angle pdb=" N ILE D 66 " pdb=" CA ILE D 66 " pdb=" C ILE D 66 " ideal model delta sigma weight residual 110.42 107.00 3.42 9.60e-01 1.09e+00 1.27e+01 angle pdb=" C THR A 80 " pdb=" N ASP A 81 " pdb=" CA ASP A 81 " ideal model delta sigma weight residual 121.54 128.31 -6.77 1.91e+00 2.74e-01 1.26e+01 angle pdb=" CA GLU A 73 " pdb=" CB GLU A 73 " pdb=" CG GLU A 73 " ideal model delta sigma weight residual 114.10 121.03 -6.93 2.00e+00 2.50e-01 1.20e+01 angle pdb=" C ALA C 86 " pdb=" N ILE C 87 " pdb=" CA ILE C 87 " ideal model delta sigma weight residual 120.56 116.25 4.31 1.28e+00 6.10e-01 1.14e+01 ... (remaining 19943 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 4731 17.96 - 35.91: 1186 35.91 - 53.87: 1116 53.87 - 71.82: 317 71.82 - 89.78: 23 Dihedral angle restraints: 7373 sinusoidal: 5169 harmonic: 2204 Sorted by residual: dihedral pdb=" CA ILE B 29 " pdb=" C ILE B 29 " pdb=" N THR B 30 " pdb=" CA THR B 30 " ideal model delta harmonic sigma weight residual -180.00 -163.93 -16.07 0 5.00e+00 4.00e-02 1.03e+01 dihedral pdb=" CA ILE G 87 " pdb=" CB ILE G 87 " pdb=" CG1 ILE G 87 " pdb=" CD1 ILE G 87 " ideal model delta sinusoidal sigma weight residual 180.00 124.96 55.04 3 1.50e+01 4.44e-03 9.32e+00 dihedral pdb=" CG ARG E 128 " pdb=" CD ARG E 128 " pdb=" NE ARG E 128 " pdb=" CZ ARG E 128 " ideal model delta sinusoidal sigma weight residual -180.00 -138.82 -41.18 2 1.50e+01 4.44e-03 9.25e+00 ... (remaining 7370 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 2042 0.061 - 0.123: 209 0.123 - 0.184: 10 0.184 - 0.245: 1 0.245 - 0.306: 2 Chirality restraints: 2264 Sorted by residual: chirality pdb=" CB ILE B 29 " pdb=" CA ILE B 29 " pdb=" CG1 ILE B 29 " pdb=" CG2 ILE B 29 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" CB ILE F 29 " pdb=" CA ILE F 29 " pdb=" CG1 ILE F 29 " pdb=" CG2 ILE F 29 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CA ILE C 87 " pdb=" N ILE C 87 " pdb=" C ILE C 87 " pdb=" CB ILE C 87 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 2261 not shown) Planarity restraints: 1381 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 64 " 0.016 2.00e-02 2.50e+03 3.15e-02 9.90e+00 pdb=" C ASN B 64 " -0.054 2.00e-02 2.50e+03 pdb=" O ASN B 64 " 0.020 2.00e-02 2.50e+03 pdb=" N VAL B 65 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 62 " -0.014 2.00e-02 2.50e+03 2.79e-02 7.76e+00 pdb=" C LEU B 62 " 0.048 2.00e-02 2.50e+03 pdb=" O LEU B 62 " -0.018 2.00e-02 2.50e+03 pdb=" N GLU B 63 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 69 " -0.012 2.00e-02 2.50e+03 2.38e-02 5.67e+00 pdb=" C ALA B 69 " 0.041 2.00e-02 2.50e+03 pdb=" O ALA B 69 " -0.015 2.00e-02 2.50e+03 pdb=" N VAL B 70 " -0.014 2.00e-02 2.50e+03 ... (remaining 1378 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 199 2.63 - 3.20: 10916 3.20 - 3.76: 24685 3.76 - 4.33: 30688 4.33 - 4.90: 43141 Nonbonded interactions: 109629 Sorted by model distance: nonbonded pdb=" OH TYR C 39 " pdb=" OE1 GLU D 68 " model vdw 2.062 2.440 nonbonded pdb=" O ARG C 20 " pdb=" NZ LYS D 117 " model vdw 2.080 2.520 nonbonded pdb=" OG SER B 47 " pdb=" OP1 DC J 105 " model vdw 2.136 2.440 nonbonded pdb=" O2 DC I 73 " pdb=" N2 DG J 121 " model vdw 2.162 2.496 nonbonded pdb=" NH2 ARG H 30 " pdb=" OP2 DA I 146 " model vdw 2.222 2.520 ... (remaining 109624 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 'E' and resid 38 through 134) } ncs_group { reference = (chain 'B' and resid 23 through 102) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 13 through 118) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 28 through 121) selection = (chain 'H' and resid 28 through 121) } 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=0.00 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: 0.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.890 Check model and map are aligned: 0.210 Set scattering table: 0.140 Process input model: 43.660 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.050 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:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6874 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 : 0.004 0.041 13724 Z= 0.227 Angle : 0.688 8.112 19948 Z= 0.424 Chirality : 0.039 0.306 2264 Planarity : 0.005 0.039 1381 Dihedral : 27.844 89.778 5953 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.16 % Allowed : 0.79 % Favored : 99.06 % 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: 1.04 (0.28), residues: 746 helix: 1.20 (0.20), residues: 542 sheet: None (None), residues: 0 loop : -0.54 (0.41), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS E 113 PHE 0.018 0.002 PHE G 25 TYR 0.023 0.002 TYR C 50 ARG 0.005 0.001 ARG F 92 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 182 time to evaluate : 0.989 Fit side-chains REVERT: A 60 LEU cc_start: 0.9316 (mp) cc_final: 0.9116 (mp) REVERT: B 59 LYS cc_start: 0.8792 (tttm) cc_final: 0.8221 (tttm) REVERT: B 63 GLU cc_start: 0.8233 (mt-10) cc_final: 0.7947 (mp0) REVERT: C 64 GLU cc_start: 0.8587 (mm-30) cc_final: 0.8299 (mm-30) REVERT: C 92 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7633 (mt-10) REVERT: G 39 TYR cc_start: 0.7474 (m-10) cc_final: 0.7231 (m-80) REVERT: G 92 GLU cc_start: 0.8786 (mp0) cc_final: 0.8585 (mp0) REVERT: H 31 LYS cc_start: 0.8302 (mmmm) cc_final: 0.7980 (mmmt) REVERT: H 73 GLU cc_start: 0.8204 (tp30) cc_final: 0.7912 (tp30) outliers start: 1 outliers final: 0 residues processed: 182 average time/residue: 0.2351 time to fit residues: 61.6836 Evaluate side-chains 144 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 20.0000 chunk 78 optimal weight: 8.9990 chunk 43 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 53 optimal weight: 10.0000 chunk 42 optimal weight: 2.9990 chunk 81 optimal weight: 8.9990 chunk 31 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN E 93 GLN H 81 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13724 Z= 0.205 Angle : 0.600 9.392 19948 Z= 0.353 Chirality : 0.035 0.175 2264 Planarity : 0.005 0.050 1381 Dihedral : 31.337 88.337 4432 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.99 % Allowed : 9.76 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.27 (0.30), residues: 746 helix: 2.20 (0.21), residues: 549 sheet: None (None), residues: 0 loop : -0.50 (0.40), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS C 31 PHE 0.022 0.002 PHE E 67 TYR 0.031 0.002 TYR F 88 ARG 0.008 0.001 ARG B 40 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 171 time to evaluate : 0.913 Fit side-chains revert: symmetry clash REVERT: B 50 ILE cc_start: 0.8645 (mm) cc_final: 0.8358 (mm) REVERT: B 53 GLU cc_start: 0.8426 (mp0) cc_final: 0.8207 (mp0) REVERT: B 73 THR cc_start: 0.9376 (m) cc_final: 0.9106 (t) REVERT: E 50 GLU cc_start: 0.8744 (pt0) cc_final: 0.8508 (pt0) REVERT: E 123 ASP cc_start: 0.9110 (m-30) cc_final: 0.8904 (m-30) REVERT: F 93 GLN cc_start: 0.8727 (tp40) cc_final: 0.8431 (tp40) REVERT: G 92 GLU cc_start: 0.8875 (mp0) cc_final: 0.8600 (mp0) REVERT: H 42 LEU cc_start: 0.9607 (tp) cc_final: 0.9299 (tp) REVERT: H 65 ASP cc_start: 0.8745 (t70) cc_final: 0.8380 (t0) outliers start: 19 outliers final: 5 residues processed: 180 average time/residue: 0.2137 time to fit residues: 56.8807 Evaluate side-chains 140 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 135 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain G residue 79 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 52 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 78 optimal weight: 9.9990 chunk 64 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 94 optimal weight: 8.9990 chunk 102 optimal weight: 10.0000 chunk 84 optimal weight: 8.9990 chunk 93 optimal weight: 8.9990 chunk 32 optimal weight: 7.9990 chunk 75 optimal weight: 10.0000 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 60 ASN E 93 GLN E 113 HIS G 24 GLN H 81 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.9048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 13724 Z= 0.354 Angle : 0.793 14.811 19948 Z= 0.458 Chirality : 0.042 0.303 2264 Planarity : 0.007 0.056 1381 Dihedral : 31.968 99.141 4432 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 4.88 % Allowed : 15.43 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.29), residues: 746 helix: 1.68 (0.21), residues: 549 sheet: None (None), residues: 0 loop : -1.42 (0.38), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS D 46 PHE 0.014 0.002 PHE A 78 TYR 0.034 0.003 TYR F 88 ARG 0.008 0.001 ARG F 40 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 144 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 PHE cc_start: 0.7240 (m-10) cc_final: 0.6905 (m-10) REVERT: B 59 LYS cc_start: 0.9136 (OUTLIER) cc_final: 0.8826 (tttm) REVERT: B 88 TYR cc_start: 0.8859 (m-10) cc_final: 0.8638 (m-10) REVERT: E 57 SER cc_start: 0.9122 (p) cc_final: 0.8791 (p) REVERT: E 59 GLU cc_start: 0.8095 (pm20) cc_final: 0.7678 (pm20) REVERT: E 79 LYS cc_start: 0.8640 (tptp) cc_final: 0.8100 (tttp) REVERT: G 101 THR cc_start: 0.9384 (m) cc_final: 0.9068 (t) REVERT: H 81 ASN cc_start: 0.9144 (OUTLIER) cc_final: 0.8573 (t0) outliers start: 31 outliers final: 15 residues processed: 164 average time/residue: 0.2859 time to fit residues: 64.6542 Evaluate side-chains 131 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 114 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 50 TYR Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 50 TYR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain H residue 81 ASN Chi-restraints excluded: chain H residue 95 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 93 optimal weight: 10.0000 chunk 71 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 45 optimal weight: 6.9990 chunk 63 optimal weight: 7.9990 chunk 94 optimal weight: 10.0000 chunk 100 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 chunk 27 optimal weight: 0.0050 chunk 83 optimal weight: 8.9990 overall best weight: 2.1598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 HIS G 38 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.9466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13724 Z= 0.217 Angle : 0.617 11.289 19948 Z= 0.362 Chirality : 0.035 0.136 2264 Planarity : 0.005 0.073 1381 Dihedral : 31.432 90.380 4432 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.73 % Allowed : 20.31 % Favored : 77.95 % 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: 2.35 (0.31), residues: 746 helix: 2.53 (0.22), residues: 545 sheet: None (None), residues: 0 loop : -1.32 (0.39), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 113 PHE 0.011 0.001 PHE A 78 TYR 0.012 0.001 TYR D 37 ARG 0.004 0.000 ARG F 40 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 118 time to evaluate : 0.931 Fit side-chains revert: symmetry clash REVERT: B 53 GLU cc_start: 0.8601 (mp0) cc_final: 0.8292 (mp0) REVERT: B 88 TYR cc_start: 0.8874 (m-10) cc_final: 0.8501 (m-10) REVERT: C 50 TYR cc_start: 0.8747 (OUTLIER) cc_final: 0.8522 (m-80) REVERT: E 59 GLU cc_start: 0.7936 (pm20) cc_final: 0.7600 (pm20) REVERT: E 79 LYS cc_start: 0.8681 (tptp) cc_final: 0.8293 (tttp) REVERT: H 54 LYS cc_start: 0.9100 (mmtp) cc_final: 0.8781 (mmmm) outliers start: 11 outliers final: 7 residues processed: 125 average time/residue: 0.2691 time to fit residues: 47.2935 Evaluate side-chains 114 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 106 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 50 TYR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain G residue 79 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 57 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 74 optimal weight: 10.0000 chunk 41 optimal weight: 1.9990 chunk 85 optimal weight: 10.0000 chunk 69 optimal weight: 0.7980 chunk 0 optimal weight: 9.9990 chunk 51 optimal weight: 0.9980 chunk 90 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 33 optimal weight: 4.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 1.0185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13724 Z= 0.215 Angle : 0.604 13.751 19948 Z= 0.352 Chirality : 0.033 0.169 2264 Planarity : 0.004 0.048 1381 Dihedral : 31.175 88.445 4432 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.62 % Allowed : 20.63 % Favored : 75.75 % 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: 2.54 (0.31), residues: 746 helix: 2.64 (0.22), residues: 547 sheet: None (None), residues: 0 loop : -1.22 (0.41), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 113 PHE 0.018 0.001 PHE C 25 TYR 0.015 0.001 TYR D 37 ARG 0.014 0.000 ARG E 40 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 119 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 53 GLU cc_start: 0.8564 (mp0) cc_final: 0.8300 (mp0) REVERT: B 88 TYR cc_start: 0.8907 (m-10) cc_final: 0.8612 (m-10) REVERT: E 79 LYS cc_start: 0.8531 (tptp) cc_final: 0.8078 (tttp) REVERT: F 53 GLU cc_start: 0.8525 (mp0) cc_final: 0.8244 (mp0) outliers start: 23 outliers final: 13 residues processed: 134 average time/residue: 0.2730 time to fit residues: 52.2349 Evaluate side-chains 119 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 106 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 23 ARG Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain G residue 50 TYR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 80 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 90 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 100 optimal weight: 10.0000 chunk 83 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 97 optimal weight: 10.0000 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 1.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13724 Z= 0.230 Angle : 0.631 13.803 19948 Z= 0.364 Chirality : 0.034 0.178 2264 Planarity : 0.004 0.050 1381 Dihedral : 31.070 88.126 4432 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.20 % Allowed : 21.73 % Favored : 76.06 % 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: 2.60 (0.31), residues: 746 helix: 2.73 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -1.31 (0.41), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 113 PHE 0.028 0.002 PHE A 78 TYR 0.016 0.001 TYR H 80 ARG 0.005 0.000 ARG A 134 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 122 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 53 GLU cc_start: 0.8597 (mp0) cc_final: 0.8368 (mp0) REVERT: B 88 TYR cc_start: 0.8868 (m-10) cc_final: 0.8495 (m-10) REVERT: E 79 LYS cc_start: 0.8436 (tptp) cc_final: 0.8095 (tttp) REVERT: H 51 ILE cc_start: 0.8573 (mm) cc_final: 0.8101 (tp) outliers start: 14 outliers final: 10 residues processed: 130 average time/residue: 0.2619 time to fit residues: 48.3299 Evaluate side-chains 120 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 110 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 50 TYR Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 50 TYR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 80 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 6.9990 chunk 57 optimal weight: 7.9990 chunk 73 optimal weight: 20.0000 chunk 56 optimal weight: 5.9990 chunk 84 optimal weight: 10.0000 chunk 100 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 chunk 61 optimal weight: 10.0000 chunk 46 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 59 optimal weight: 0.4980 overall best weight: 4.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 ASN F 25 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 1.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 13724 Z= 0.323 Angle : 0.699 12.109 19948 Z= 0.403 Chirality : 0.037 0.177 2264 Planarity : 0.005 0.047 1381 Dihedral : 31.165 89.210 4432 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.31 % Allowed : 23.31 % Favored : 73.39 % 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: 2.05 (0.31), residues: 746 helix: 2.35 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -1.58 (0.42), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS F 75 PHE 0.030 0.002 PHE A 78 TYR 0.013 0.001 TYR D 37 ARG 0.009 0.001 ARG E 40 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 107 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8374 (pm20) cc_final: 0.8097 (pm20) REVERT: B 88 TYR cc_start: 0.8914 (m-10) cc_final: 0.8641 (m-80) REVERT: H 56 MET cc_start: 0.9311 (mmm) cc_final: 0.9044 (tpp) outliers start: 21 outliers final: 12 residues processed: 124 average time/residue: 0.2527 time to fit residues: 44.1636 Evaluate side-chains 111 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 99 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 50 TYR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 80 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 30 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 68 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 chunk 9 optimal weight: 8.9990 chunk 78 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 chunk 87 optimal weight: 20.0000 chunk 93 optimal weight: 9.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 1.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13724 Z= 0.244 Angle : 0.631 10.120 19948 Z= 0.369 Chirality : 0.034 0.184 2264 Planarity : 0.004 0.049 1381 Dihedral : 30.957 88.936 4432 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.73 % Allowed : 25.04 % Favored : 73.23 % 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: 2.47 (0.32), residues: 746 helix: 2.73 (0.22), residues: 543 sheet: None (None), residues: 0 loop : -1.62 (0.43), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 113 PHE 0.007 0.001 PHE E 67 TYR 0.011 0.001 TYR H 80 ARG 0.005 0.000 ARG E 40 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 107 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 88 TYR cc_start: 0.8922 (m-10) cc_final: 0.8501 (m-10) REVERT: C 56 GLU cc_start: 0.8694 (mm-30) cc_final: 0.8487 (mm-30) REVERT: H 56 MET cc_start: 0.9232 (mmm) cc_final: 0.9026 (tpp) outliers start: 11 outliers final: 8 residues processed: 113 average time/residue: 0.2584 time to fit residues: 41.6609 Evaluate side-chains 111 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 103 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 50 TYR Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 80 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 96 optimal weight: 10.0000 chunk 56 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 73 optimal weight: 20.0000 chunk 28 optimal weight: 0.9990 chunk 84 optimal weight: 10.0000 chunk 88 optimal weight: 20.0000 chunk 93 optimal weight: 10.0000 chunk 61 optimal weight: 1.9990 chunk 98 optimal weight: 10.0000 chunk 60 optimal weight: 0.8980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 1.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13724 Z= 0.215 Angle : 0.618 13.060 19948 Z= 0.359 Chirality : 0.033 0.176 2264 Planarity : 0.004 0.049 1381 Dihedral : 30.796 89.420 4432 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.36 % Allowed : 23.94 % Favored : 73.70 % 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: 2.59 (0.32), residues: 746 helix: 2.82 (0.22), residues: 543 sheet: None (None), residues: 0 loop : -1.57 (0.43), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 113 PHE 0.008 0.001 PHE D 62 TYR 0.014 0.001 TYR F 88 ARG 0.005 0.000 ARG E 40 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 109 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 88 TYR cc_start: 0.8878 (m-10) cc_final: 0.7870 (m-10) REVERT: C 56 GLU cc_start: 0.8679 (mm-30) cc_final: 0.8396 (mm-30) REVERT: D 80 TYR cc_start: 0.7404 (m-10) cc_final: 0.6995 (m-10) outliers start: 15 outliers final: 8 residues processed: 119 average time/residue: 0.2534 time to fit residues: 43.1174 Evaluate side-chains 113 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 105 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 50 TYR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 80 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 46 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 103 optimal weight: 20.0000 chunk 95 optimal weight: 10.0000 chunk 82 optimal weight: 10.0000 chunk 8 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 chunk 50 optimal weight: 0.4980 chunk 65 optimal weight: 4.9990 chunk 87 optimal weight: 20.0000 chunk 25 optimal weight: 3.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 ASN E 125 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 1.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 13724 Z= 0.279 Angle : 0.670 17.349 19948 Z= 0.384 Chirality : 0.035 0.184 2264 Planarity : 0.004 0.047 1381 Dihedral : 30.858 89.729 4432 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.73 % Allowed : 24.88 % Favored : 73.39 % 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: 2.28 (0.32), residues: 746 helix: 2.58 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -1.70 (0.44), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS F 75 PHE 0.011 0.001 PHE A 78 TYR 0.016 0.001 TYR H 80 ARG 0.008 0.000 ARG F 92 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 103 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8410 (pm20) cc_final: 0.8130 (pm20) REVERT: A 73 GLU cc_start: 0.7929 (tt0) cc_final: 0.7665 (tt0) REVERT: B 88 TYR cc_start: 0.8882 (m-10) cc_final: 0.8479 (m-10) REVERT: C 56 GLU cc_start: 0.8704 (mm-30) cc_final: 0.8449 (mm-30) outliers start: 11 outliers final: 8 residues processed: 110 average time/residue: 0.2537 time to fit residues: 39.7772 Evaluate side-chains 110 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 102 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 50 TYR Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 80 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 76 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 82 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 chunk 84 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 72 optimal weight: 30.0000 chunk 4 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.060865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.038405 restraints weight = 84244.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.039239 restraints weight = 45222.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.039864 restraints weight = 31122.067| |-----------------------------------------------------------------------------| r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 1.3541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.109 13724 Z= 0.262 Angle : 0.863 59.199 19948 Z= 0.526 Chirality : 0.034 0.187 2264 Planarity : 0.004 0.047 1381 Dihedral : 30.864 89.699 4432 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.89 % Allowed : 24.72 % Favored : 73.39 % Cbeta Deviations : 0.14 % 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: 2.23 (0.32), residues: 746 helix: 2.54 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -1.70 (0.44), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 75 PHE 0.010 0.001 PHE A 78 TYR 0.016 0.001 TYR H 80 ARG 0.004 0.000 ARG E 40 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2022.71 seconds wall clock time: 37 minutes 34.80 seconds (2254.80 seconds total)