Starting phenix.real_space_refine on Sat Aug 3 09:58:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xh7_38343/08_2024/8xh7_38343.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xh7_38343/08_2024/8xh7_38343.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xh7_38343/08_2024/8xh7_38343.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xh7_38343/08_2024/8xh7_38343.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xh7_38343/08_2024/8xh7_38343.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xh7_38343/08_2024/8xh7_38343.cif" } resolution = 3.52 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 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 42 5.16 5 C 5610 2.51 5 N 1134 2.21 5 O 1116 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 7902 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 1317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1317 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 1, 'TRANS': 159} Chain: "E" Number of atoms: 1317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1317 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 1, 'TRANS': 159} Chain: "F" Number of atoms: 1317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1317 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 1, 'TRANS': 159} Chain: "A" Number of atoms: 1317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1317 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 1, 'TRANS': 159} Chain: "B" Number of atoms: 1317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1317 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 1, 'TRANS': 159} Chain: "D" Number of atoms: 1317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1317 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 1, 'TRANS': 159} Time building chain proxies: 7.47, per 1000 atoms: 0.95 Number of scatterers: 7902 At special positions: 0 Unit cell: (125.32, 109.2, 60.32, 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 42 16.00 O 1116 8.00 N 1134 7.00 C 5610 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: 3.29 Conformation dependent library (CDL) restraints added in 1.5 seconds 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1800 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 0 sheets defined 90.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'C' and resid 24 through 45 Processing helix chain 'C' and resid 51 through 72 removed outlier: 3.932A pdb=" N LEU C 55 " --> pdb=" O ALA C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 77 Processing helix chain 'C' and resid 78 through 99 removed outlier: 4.659A pdb=" N ASN C 99 " --> pdb=" O ILE C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 134 Processing helix chain 'C' and resid 136 through 160 Processing helix chain 'C' and resid 162 through 180 removed outlier: 3.612A pdb=" N LEU C 168 " --> pdb=" O TRP C 164 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE C 180 " --> pdb=" O LEU C 176 " (cutoff:3.500A) Processing helix chain 'E' and resid 25 through 44 removed outlier: 3.826A pdb=" N MET E 44 " --> pdb=" O LEU E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 72 removed outlier: 3.926A pdb=" N VAL E 54 " --> pdb=" O GLY E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 98 removed outlier: 3.793A pdb=" N LEU E 83 " --> pdb=" O PRO E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 134 removed outlier: 3.636A pdb=" N LEU E 107 " --> pdb=" O GLN E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 160 removed outlier: 3.550A pdb=" N TYR E 159 " --> pdb=" O ILE E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 184 removed outlier: 3.545A pdb=" N LEU E 168 " --> pdb=" O TRP E 164 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N MET E 184 " --> pdb=" O ILE E 180 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 44 removed outlier: 3.757A pdb=" N MET F 44 " --> pdb=" O LEU F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 73 removed outlier: 3.800A pdb=" N VAL F 54 " --> pdb=" O GLY F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 77 removed outlier: 3.898A pdb=" N LEU F 77 " --> pdb=" O ARG F 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 74 through 77' Processing helix chain 'F' and resid 78 through 100 removed outlier: 3.535A pdb=" N GLY F 82 " --> pdb=" O CYS F 78 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ASN F 99 " --> pdb=" O ILE F 95 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU F 100 " --> pdb=" O ALA F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 134 Processing helix chain 'F' and resid 136 through 160 Processing helix chain 'F' and resid 162 through 180 Processing helix chain 'A' and resid 25 through 44 removed outlier: 3.852A pdb=" N MET A 44 " --> pdb=" O LEU A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 72 removed outlier: 3.926A pdb=" N VAL A 54 " --> pdb=" O GLY A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 98 removed outlier: 3.774A pdb=" N LEU A 83 " --> pdb=" O PRO A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 134 removed outlier: 3.665A pdb=" N LEU A 107 " --> pdb=" O GLN A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 160 removed outlier: 3.557A pdb=" N TYR A 159 " --> pdb=" O ILE A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 184 removed outlier: 3.552A pdb=" N LEU A 168 " --> pdb=" O TRP A 164 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N MET A 184 " --> pdb=" O ILE A 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 44 removed outlier: 3.502A pdb=" N MET B 44 " --> pdb=" O LEU B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 73 removed outlier: 3.808A pdb=" N VAL B 54 " --> pdb=" O GLY B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 77 removed outlier: 3.883A pdb=" N LEU B 77 " --> pdb=" O ARG B 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 74 through 77' Processing helix chain 'B' and resid 78 through 100 removed outlier: 3.540A pdb=" N GLY B 82 " --> pdb=" O CYS B 78 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ASN B 99 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU B 100 " --> pdb=" O ALA B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 134 Processing helix chain 'B' and resid 136 through 160 Processing helix chain 'B' and resid 162 through 180 Processing helix chain 'D' and resid 25 through 45 Processing helix chain 'D' and resid 51 through 72 removed outlier: 3.869A pdb=" N LEU D 55 " --> pdb=" O ALA D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 77 Processing helix chain 'D' and resid 78 through 99 removed outlier: 4.645A pdb=" N ASN D 99 " --> pdb=" O ILE D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 134 Processing helix chain 'D' and resid 136 through 160 Processing helix chain 'D' and resid 162 through 180 removed outlier: 3.655A pdb=" N LEU D 168 " --> pdb=" O TRP D 164 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE D 180 " --> pdb=" O LEU D 176 " (cutoff:3.500A) 683 hydrogen bonds defined for protein. 2037 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.20 Time building geometry restraints manager: 3.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1044 1.29 - 1.43: 2259 1.43 - 1.57: 4749 1.57 - 1.70: 0 1.70 - 1.84: 72 Bond restraints: 8124 Sorted by residual: bond pdb=" C MET A 61 " pdb=" O MET A 61 " ideal model delta sigma weight residual 1.237 1.157 0.080 1.17e-02 7.31e+03 4.66e+01 bond pdb=" N ILE E 64 " pdb=" CA ILE E 64 " ideal model delta sigma weight residual 1.461 1.500 -0.039 1.17e-02 7.31e+03 1.10e+01 bond pdb=" N ILE A 64 " pdb=" CA ILE A 64 " ideal model delta sigma weight residual 1.461 1.500 -0.039 1.17e-02 7.31e+03 1.09e+01 bond pdb=" N LEU B 181 " pdb=" CA LEU B 181 " ideal model delta sigma weight residual 1.457 1.499 -0.042 1.29e-02 6.01e+03 1.06e+01 bond pdb=" N ILE D 69 " pdb=" CA ILE D 69 " ideal model delta sigma weight residual 1.461 1.499 -0.038 1.19e-02 7.06e+03 1.04e+01 ... (remaining 8119 not shown) Histogram of bond angle deviations from ideal: 97.05 - 104.69: 43 104.69 - 112.32: 4523 112.32 - 119.96: 3001 119.96 - 127.59: 3422 127.59 - 135.23: 135 Bond angle restraints: 11124 Sorted by residual: angle pdb=" CA MET A 61 " pdb=" C MET A 61 " pdb=" O MET A 61 " ideal model delta sigma weight residual 120.55 113.26 7.29 1.06e+00 8.90e-01 4.72e+01 angle pdb=" CA ILE C 180 " pdb=" C ILE C 180 " pdb=" O ILE C 180 " ideal model delta sigma weight residual 122.13 116.43 5.70 1.11e+00 8.12e-01 2.64e+01 angle pdb=" C ALA F 59 " pdb=" N LEU F 60 " pdb=" CA LEU F 60 " ideal model delta sigma weight residual 120.31 113.36 6.95 1.52e+00 4.33e-01 2.09e+01 angle pdb=" O LEU C 60 " pdb=" C LEU C 60 " pdb=" N MET C 61 " ideal model delta sigma weight residual 122.12 126.81 -4.69 1.06e+00 8.90e-01 1.96e+01 angle pdb=" N MET A 61 " pdb=" CA MET A 61 " pdb=" C MET A 61 " ideal model delta sigma weight residual 111.28 106.48 4.80 1.09e+00 8.42e-01 1.94e+01 ... (remaining 11119 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.11: 3883 16.11 - 32.22: 436 32.22 - 48.33: 139 48.33 - 64.44: 22 64.44 - 80.55: 2 Dihedral angle restraints: 4482 sinusoidal: 1692 harmonic: 2790 Sorted by residual: dihedral pdb=" C ILE A 71 " pdb=" N ILE A 71 " pdb=" CA ILE A 71 " pdb=" CB ILE A 71 " ideal model delta harmonic sigma weight residual -122.00 -130.43 8.43 0 2.50e+00 1.60e-01 1.14e+01 dihedral pdb=" CA ASP B 75 " pdb=" CB ASP B 75 " pdb=" CG ASP B 75 " pdb=" OD1 ASP B 75 " ideal model delta sinusoidal sigma weight residual -30.00 -86.90 56.90 1 2.00e+01 2.50e-03 1.09e+01 dihedral pdb=" CA ASP F 75 " pdb=" CB ASP F 75 " pdb=" CG ASP F 75 " pdb=" OD1 ASP F 75 " ideal model delta sinusoidal sigma weight residual -30.00 -86.88 56.88 1 2.00e+01 2.50e-03 1.09e+01 ... (remaining 4479 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1180 0.067 - 0.134: 146 0.134 - 0.201: 61 0.201 - 0.268: 28 0.268 - 0.335: 7 Chirality restraints: 1422 Sorted by residual: chirality pdb=" CA ILE E 64 " pdb=" N ILE E 64 " pdb=" C ILE E 64 " pdb=" CB ILE E 64 " both_signs ideal model delta sigma weight residual False 2.43 2.77 -0.34 2.00e-01 2.50e+01 2.81e+00 chirality pdb=" CA ILE A 64 " pdb=" N ILE A 64 " pdb=" C ILE A 64 " pdb=" CB ILE A 64 " both_signs ideal model delta sigma weight residual False 2.43 2.74 -0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CA LEU B 88 " pdb=" N LEU B 88 " pdb=" C LEU B 88 " pdb=" CB LEU B 88 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.98e+00 ... (remaining 1419 not shown) Planarity restraints: 1206 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 47 " -0.019 2.00e-02 2.50e+03 1.19e-02 3.53e+00 pdb=" CG TRP A 47 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 TRP A 47 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TRP A 47 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 47 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 47 " -0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP A 47 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 47 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 47 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 47 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU E 153 " -0.009 2.00e-02 2.50e+03 1.86e-02 3.47e+00 pdb=" C LEU E 153 " 0.032 2.00e-02 2.50e+03 pdb=" O LEU E 153 " -0.012 2.00e-02 2.50e+03 pdb=" N LEU E 154 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 62 " -0.008 2.00e-02 2.50e+03 1.74e-02 3.02e+00 pdb=" C LEU A 62 " 0.030 2.00e-02 2.50e+03 pdb=" O LEU A 62 " -0.011 2.00e-02 2.50e+03 pdb=" N ILE A 63 " -0.010 2.00e-02 2.50e+03 ... (remaining 1203 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 2753 2.88 - 3.39: 8491 3.39 - 3.89: 13348 3.89 - 4.40: 14230 4.40 - 4.90: 23282 Nonbonded interactions: 62104 Sorted by model distance: nonbonded pdb=" O TRP C 47 " pdb=" OG1 THR C 48 " model vdw 2.376 3.040 nonbonded pdb=" O TRP D 47 " pdb=" OG1 THR D 48 " model vdw 2.393 3.040 nonbonded pdb=" NH1 ARG F 73 " pdb=" O MET F 184 " model vdw 2.397 3.120 nonbonded pdb=" O LEU F 154 " pdb=" CD1 LEU F 158 " model vdw 2.414 3.460 nonbonded pdb=" O TRP F 47 " pdb=" OG1 THR F 48 " model vdw 2.460 3.040 ... (remaining 62099 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 11.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 27.840 Find NCS groups from input model: 0.280 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:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 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 : 0.005 0.080 8124 Z= 0.345 Angle : 0.913 7.286 11124 Z= 0.631 Chirality : 0.065 0.335 1422 Planarity : 0.003 0.021 1206 Dihedral : 14.929 80.553 2682 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.17 % Allowed : 4.59 % Favored : 93.24 % 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: 2.45 (0.27), residues: 954 helix: 2.03 (0.17), residues: 864 sheet: None (None), residues: 0 loop : -2.55 (0.55), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 47 HIS 0.000 0.000 HIS D 101 PHE 0.018 0.001 PHE D 58 TYR 0.010 0.001 TYR D 41 ARG 0.002 0.000 ARG B 73 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 197 time to evaluate : 1.148 Fit side-chains REVERT: C 40 LEU cc_start: 0.8526 (tp) cc_final: 0.8214 (tp) REVERT: C 44 MET cc_start: 0.8426 (OUTLIER) cc_final: 0.7694 (mpp) REVERT: F 140 LEU cc_start: 0.7254 (OUTLIER) cc_final: 0.7018 (mp) REVERT: A 178 MET cc_start: 0.6683 (tpp) cc_final: 0.6433 (mmt) REVERT: B 165 TRP cc_start: 0.7807 (t-100) cc_final: 0.7548 (t-100) outliers start: 18 outliers final: 7 residues processed: 206 average time/residue: 0.1526 time to fit residues: 46.2468 Evaluate side-chains 165 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 156 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain F residue 129 ILE Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 158 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 75 optimal weight: 10.0000 chunk 29 optimal weight: 4.9990 chunk 45 optimal weight: 0.0470 chunk 56 optimal weight: 0.9990 chunk 87 optimal weight: 0.5980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 101 HIS B 101 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 8124 Z= 0.185 Angle : 0.578 10.803 11124 Z= 0.271 Chirality : 0.035 0.161 1422 Planarity : 0.003 0.023 1206 Dihedral : 5.104 47.970 1027 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.05 % Allowed : 16.79 % Favored : 81.16 % 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: 3.22 (0.27), residues: 954 helix: 2.52 (0.17), residues: 876 sheet: None (None), residues: 0 loop : -2.91 (0.58), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 164 HIS 0.007 0.002 HIS F 101 PHE 0.010 0.001 PHE D 112 TYR 0.010 0.001 TYR C 41 ARG 0.002 0.000 ARG B 73 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 158 time to evaluate : 0.903 Fit side-chains REVERT: C 44 MET cc_start: 0.8306 (OUTLIER) cc_final: 0.7690 (mtp) REVERT: B 165 TRP cc_start: 0.7871 (t-100) cc_final: 0.7380 (t-100) outliers start: 17 outliers final: 8 residues processed: 170 average time/residue: 0.1391 time to fit residues: 35.4794 Evaluate side-chains 156 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 147 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 143 PHE Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 144 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 72 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 70 optimal weight: 0.5980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 101 HIS B 101 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8124 Z= 0.212 Angle : 0.576 11.032 11124 Z= 0.269 Chirality : 0.034 0.162 1422 Planarity : 0.002 0.024 1206 Dihedral : 4.606 53.649 1013 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.14 % Allowed : 18.36 % Favored : 78.50 % 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: 3.32 (0.27), residues: 954 helix: 2.58 (0.17), residues: 876 sheet: None (None), residues: 0 loop : -2.84 (0.61), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 131 HIS 0.005 0.001 HIS F 101 PHE 0.010 0.001 PHE E 112 TYR 0.010 0.001 TYR D 41 ARG 0.002 0.000 ARG A 132 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 154 time to evaluate : 0.783 Fit side-chains REVERT: F 155 ILE cc_start: 0.9039 (OUTLIER) cc_final: 0.8743 (mt) REVERT: B 113 ILE cc_start: 0.8120 (tp) cc_final: 0.7720 (pt) REVERT: B 155 ILE cc_start: 0.9034 (OUTLIER) cc_final: 0.8737 (mt) REVERT: D 113 ILE cc_start: 0.8878 (OUTLIER) cc_final: 0.8629 (mp) outliers start: 26 outliers final: 17 residues processed: 167 average time/residue: 0.1421 time to fit residues: 34.9729 Evaluate side-chains 167 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 147 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 89 MET Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 143 PHE Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain F residue 164 TRP Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 148 PHE Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 164 TRP Chi-restraints excluded: chain D residue 89 MET Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 144 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 0.5980 chunk 65 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 87 optimal weight: 0.9980 chunk 92 optimal weight: 0.9980 chunk 83 optimal weight: 0.5980 chunk 25 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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: 0.7573 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8124 Z= 0.199 Angle : 0.572 10.798 11124 Z= 0.265 Chirality : 0.034 0.168 1422 Planarity : 0.002 0.023 1206 Dihedral : 4.638 54.036 1013 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.99 % Allowed : 20.53 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.42 (0.27), residues: 954 helix: 2.64 (0.17), residues: 876 sheet: None (None), residues: 0 loop : -2.68 (0.65), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 131 HIS 0.001 0.000 HIS C 101 PHE 0.009 0.001 PHE E 112 TYR 0.010 0.001 TYR D 41 ARG 0.001 0.000 ARG A 132 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 153 time to evaluate : 0.794 Fit side-chains REVERT: C 113 ILE cc_start: 0.8834 (OUTLIER) cc_final: 0.8620 (mp) REVERT: F 113 ILE cc_start: 0.8168 (tp) cc_final: 0.7765 (pt) REVERT: F 155 ILE cc_start: 0.9068 (OUTLIER) cc_final: 0.8741 (mt) REVERT: B 113 ILE cc_start: 0.8059 (tp) cc_final: 0.7699 (pt) REVERT: B 155 ILE cc_start: 0.9066 (OUTLIER) cc_final: 0.8750 (mt) REVERT: D 113 ILE cc_start: 0.8857 (OUTLIER) cc_final: 0.8601 (mp) outliers start: 33 outliers final: 21 residues processed: 171 average time/residue: 0.1463 time to fit residues: 36.9352 Evaluate side-chains 175 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 150 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 89 MET Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 143 PHE Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 148 PHE Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain F residue 164 TRP Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 148 PHE Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 164 TRP Chi-restraints excluded: chain D residue 89 MET Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 144 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 69 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 79 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 83 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 101 HIS B 101 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8124 Z= 0.175 Angle : 0.549 10.312 11124 Z= 0.257 Chirality : 0.034 0.174 1422 Planarity : 0.002 0.022 1206 Dihedral : 4.586 54.433 1013 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 4.35 % Allowed : 21.26 % Favored : 74.40 % 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: 3.53 (0.27), residues: 954 helix: 2.71 (0.17), residues: 876 sheet: None (None), residues: 0 loop : -2.60 (0.67), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 131 HIS 0.005 0.001 HIS F 101 PHE 0.008 0.001 PHE E 112 TYR 0.010 0.001 TYR D 41 ARG 0.002 0.000 ARG F 73 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 157 time to evaluate : 0.901 Fit side-chains REVERT: C 113 ILE cc_start: 0.8757 (OUTLIER) cc_final: 0.8497 (mp) REVERT: F 113 ILE cc_start: 0.8092 (tp) cc_final: 0.7721 (pt) REVERT: F 155 ILE cc_start: 0.9075 (OUTLIER) cc_final: 0.8758 (mt) REVERT: B 113 ILE cc_start: 0.7998 (tp) cc_final: 0.7666 (pt) REVERT: B 155 ILE cc_start: 0.9064 (OUTLIER) cc_final: 0.8761 (mt) REVERT: D 44 MET cc_start: 0.8470 (OUTLIER) cc_final: 0.7327 (mpp) REVERT: D 113 ILE cc_start: 0.8803 (OUTLIER) cc_final: 0.8539 (mp) outliers start: 36 outliers final: 24 residues processed: 175 average time/residue: 0.1390 time to fit residues: 36.3683 Evaluate side-chains 181 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 152 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 89 MET Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 143 PHE Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 148 PHE Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain F residue 164 TRP Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 143 PHE Chi-restraints excluded: chain B residue 148 PHE Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 164 TRP Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 89 MET Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 144 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 0.8980 chunk 18 optimal weight: 0.0670 chunk 54 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 43 optimal weight: 10.0000 chunk 7 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 48 optimal weight: 6.9990 chunk 89 optimal weight: 0.6980 overall best weight: 0.6118 ------------------------------------------------------------------------------- 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: 0.7552 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8124 Z= 0.169 Angle : 0.562 10.143 11124 Z= 0.259 Chirality : 0.034 0.168 1422 Planarity : 0.002 0.022 1206 Dihedral : 4.525 53.887 1013 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 4.23 % Allowed : 22.10 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.58 (0.27), residues: 954 helix: 2.74 (0.17), residues: 876 sheet: None (None), residues: 0 loop : -2.61 (0.67), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 164 HIS 0.001 0.000 HIS C 101 PHE 0.008 0.001 PHE D 58 TYR 0.017 0.001 TYR E 125 ARG 0.002 0.000 ARG F 73 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 164 time to evaluate : 0.865 Fit side-chains REVERT: C 113 ILE cc_start: 0.8726 (OUTLIER) cc_final: 0.8477 (mp) REVERT: C 158 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7628 (mm) REVERT: F 113 ILE cc_start: 0.8049 (tp) cc_final: 0.7701 (pt) REVERT: F 155 ILE cc_start: 0.9081 (OUTLIER) cc_final: 0.8757 (mt) REVERT: B 113 ILE cc_start: 0.8004 (tp) cc_final: 0.7673 (pt) REVERT: B 155 ILE cc_start: 0.9068 (OUTLIER) cc_final: 0.8759 (mt) REVERT: D 44 MET cc_start: 0.8477 (OUTLIER) cc_final: 0.7408 (mpp) REVERT: D 113 ILE cc_start: 0.8778 (OUTLIER) cc_final: 0.8530 (mp) REVERT: D 158 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7597 (mm) outliers start: 35 outliers final: 21 residues processed: 180 average time/residue: 0.1453 time to fit residues: 39.2995 Evaluate side-chains 188 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 160 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 89 MET Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 143 PHE Chi-restraints excluded: chain F residue 148 PHE Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain F residue 164 TRP Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 143 PHE Chi-restraints excluded: chain B residue 148 PHE Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 164 TRP Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 89 MET Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 158 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 92 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 42 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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: 0.7583 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8124 Z= 0.202 Angle : 0.581 9.871 11124 Z= 0.269 Chirality : 0.034 0.178 1422 Planarity : 0.002 0.023 1206 Dihedral : 4.513 51.325 1013 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 4.47 % Allowed : 22.34 % Favored : 73.19 % 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: 3.56 (0.27), residues: 954 helix: 2.73 (0.17), residues: 876 sheet: None (None), residues: 0 loop : -2.59 (0.67), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 39 HIS 0.001 0.000 HIS C 101 PHE 0.010 0.001 PHE E 112 TYR 0.020 0.001 TYR E 125 ARG 0.002 0.000 ARG F 73 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 160 time to evaluate : 0.866 Fit side-chains REVERT: C 113 ILE cc_start: 0.8757 (OUTLIER) cc_final: 0.8509 (mp) REVERT: C 158 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7643 (mm) REVERT: F 113 ILE cc_start: 0.8029 (tp) cc_final: 0.7692 (pt) REVERT: F 155 ILE cc_start: 0.9065 (OUTLIER) cc_final: 0.8748 (mt) REVERT: B 113 ILE cc_start: 0.8012 (tp) cc_final: 0.7681 (pt) REVERT: B 155 ILE cc_start: 0.9067 (OUTLIER) cc_final: 0.8781 (mt) REVERT: D 44 MET cc_start: 0.8562 (OUTLIER) cc_final: 0.7531 (mpp) REVERT: D 113 ILE cc_start: 0.8804 (OUTLIER) cc_final: 0.8565 (mp) REVERT: D 158 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7618 (mm) outliers start: 37 outliers final: 22 residues processed: 179 average time/residue: 0.1386 time to fit residues: 36.9267 Evaluate side-chains 187 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 158 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 89 MET Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 143 PHE Chi-restraints excluded: chain F residue 148 PHE Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain F residue 164 TRP Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 98 TRP Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 143 PHE Chi-restraints excluded: chain B residue 148 PHE Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 164 TRP Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 158 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 chunk 45 optimal weight: 0.4980 chunk 8 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 84 optimal weight: 0.6980 chunk 88 optimal weight: 0.7980 chunk 80 optimal weight: 4.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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: 0.7581 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8124 Z= 0.194 Angle : 0.582 9.867 11124 Z= 0.268 Chirality : 0.034 0.199 1422 Planarity : 0.002 0.021 1206 Dihedral : 4.508 51.385 1013 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.99 % Allowed : 23.55 % Favored : 72.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.57 (0.27), residues: 954 helix: 2.73 (0.17), residues: 876 sheet: None (None), residues: 0 loop : -2.60 (0.69), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 39 HIS 0.001 0.000 HIS D 101 PHE 0.009 0.001 PHE E 112 TYR 0.020 0.001 TYR A 125 ARG 0.002 0.000 ARG F 73 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 163 time to evaluate : 0.827 Fit side-chains REVERT: C 113 ILE cc_start: 0.8742 (OUTLIER) cc_final: 0.8499 (mp) REVERT: C 158 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7650 (mm) REVERT: F 113 ILE cc_start: 0.8019 (tp) cc_final: 0.7705 (pt) REVERT: F 155 ILE cc_start: 0.9071 (OUTLIER) cc_final: 0.8814 (mt) REVERT: B 113 ILE cc_start: 0.7992 (tp) cc_final: 0.7682 (pt) REVERT: B 155 ILE cc_start: 0.9060 (OUTLIER) cc_final: 0.8773 (mt) REVERT: D 44 MET cc_start: 0.8540 (OUTLIER) cc_final: 0.7543 (mpp) REVERT: D 113 ILE cc_start: 0.8817 (OUTLIER) cc_final: 0.8567 (mp) REVERT: D 158 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7623 (mm) outliers start: 33 outliers final: 24 residues processed: 175 average time/residue: 0.1500 time to fit residues: 39.5488 Evaluate side-chains 191 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 160 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 89 MET Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 143 PHE Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 148 PHE Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain F residue 164 TRP Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 98 TRP Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 148 PHE Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 164 TRP Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 89 MET Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 158 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 0.5980 chunk 88 optimal weight: 0.5980 chunk 51 optimal weight: 0.6980 chunk 37 optimal weight: 0.0070 chunk 67 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 81 optimal weight: 0.5980 chunk 85 optimal weight: 9.9990 chunk 56 optimal weight: 0.9990 chunk 91 optimal weight: 0.0170 overall best weight: 0.3636 ------------------------------------------------------------------------------- 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: 0.7503 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8124 Z= 0.144 Angle : 0.575 10.687 11124 Z= 0.260 Chirality : 0.034 0.202 1422 Planarity : 0.002 0.022 1206 Dihedral : 4.390 49.976 1013 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.14 % Allowed : 25.12 % Favored : 71.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.73 (0.27), residues: 954 helix: 2.84 (0.17), residues: 876 sheet: None (None), residues: 0 loop : -2.60 (0.67), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 131 HIS 0.001 0.000 HIS E 101 PHE 0.008 0.001 PHE D 58 TYR 0.019 0.001 TYR A 125 ARG 0.003 0.000 ARG F 73 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 160 time to evaluate : 0.841 Fit side-chains REVERT: C 113 ILE cc_start: 0.8615 (OUTLIER) cc_final: 0.8390 (mp) REVERT: C 158 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7609 (mm) REVERT: F 113 ILE cc_start: 0.7972 (tp) cc_final: 0.7651 (pt) REVERT: F 155 ILE cc_start: 0.9066 (OUTLIER) cc_final: 0.8795 (mt) REVERT: B 113 ILE cc_start: 0.7969 (tp) cc_final: 0.7655 (pt) REVERT: B 155 ILE cc_start: 0.9065 (OUTLIER) cc_final: 0.8757 (mt) REVERT: D 113 ILE cc_start: 0.8736 (OUTLIER) cc_final: 0.8487 (mp) REVERT: D 158 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7568 (mm) outliers start: 26 outliers final: 17 residues processed: 171 average time/residue: 0.1417 time to fit residues: 35.9276 Evaluate side-chains 176 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 153 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 89 MET Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 143 PHE Chi-restraints excluded: chain F residue 148 PHE Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain F residue 164 TRP Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 148 PHE Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain D residue 89 MET Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 158 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 0.0040 chunk 43 optimal weight: 9.9990 chunk 63 optimal weight: 0.4980 chunk 95 optimal weight: 4.9990 chunk 88 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 chunk 46 optimal weight: 0.4980 chunk 60 optimal weight: 0.9990 chunk 81 optimal weight: 0.6980 overall best weight: 0.4992 ------------------------------------------------------------------------------- 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: 0.7522 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8124 Z= 0.160 Angle : 0.596 10.228 11124 Z= 0.268 Chirality : 0.034 0.190 1422 Planarity : 0.002 0.022 1206 Dihedral : 4.170 50.334 1011 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 3.02 % Allowed : 25.00 % Favored : 71.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.67 (0.27), residues: 954 helix: 2.80 (0.17), residues: 876 sheet: None (None), residues: 0 loop : -2.62 (0.67), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 131 HIS 0.001 0.000 HIS C 101 PHE 0.009 0.001 PHE D 58 TYR 0.019 0.001 TYR A 125 ARG 0.002 0.000 ARG F 73 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 154 time to evaluate : 0.832 Fit side-chains REVERT: C 113 ILE cc_start: 0.8644 (OUTLIER) cc_final: 0.8415 (mp) REVERT: C 158 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7629 (mm) REVERT: E 178 MET cc_start: 0.6780 (tpp) cc_final: 0.6530 (mmt) REVERT: F 113 ILE cc_start: 0.7992 (tp) cc_final: 0.7668 (pt) REVERT: F 155 ILE cc_start: 0.9071 (OUTLIER) cc_final: 0.8796 (mt) REVERT: B 113 ILE cc_start: 0.7988 (tp) cc_final: 0.7667 (pt) REVERT: B 155 ILE cc_start: 0.9062 (OUTLIER) cc_final: 0.8762 (mt) REVERT: D 113 ILE cc_start: 0.8745 (OUTLIER) cc_final: 0.8480 (mp) REVERT: D 158 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7599 (mm) outliers start: 25 outliers final: 18 residues processed: 167 average time/residue: 0.1416 time to fit residues: 35.2218 Evaluate side-chains 176 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 152 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 89 MET Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 143 PHE Chi-restraints excluded: chain F residue 148 PHE Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain F residue 164 TRP Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 98 TRP Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 148 PHE Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain D residue 89 MET Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 158 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 0.7980 chunk 70 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 21 optimal weight: 8.9990 chunk 76 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 78 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4636 r_free = 0.4636 target = 0.214492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.176208 restraints weight = 9695.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.179663 restraints weight = 6564.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.181761 restraints weight = 5209.669| |-----------------------------------------------------------------------------| r_work (final): 0.4292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8124 Z= 0.196 Angle : 0.623 10.149 11124 Z= 0.280 Chirality : 0.035 0.185 1422 Planarity : 0.002 0.022 1206 Dihedral : 4.244 51.447 1011 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.38 % Allowed : 25.36 % Favored : 71.26 % 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: 3.55 (0.27), residues: 954 helix: 2.72 (0.17), residues: 876 sheet: None (None), residues: 0 loop : -2.63 (0.68), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 131 HIS 0.001 0.000 HIS D 101 PHE 0.009 0.001 PHE E 112 TYR 0.019 0.001 TYR A 125 ARG 0.001 0.000 ARG F 73 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2222.01 seconds wall clock time: 40 minutes 9.36 seconds (2409.36 seconds total)