Starting phenix.real_space_refine on Thu Feb 15 11:56:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fq5_4297/02_2024/6fq5_4297.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fq5_4297/02_2024/6fq5_4297.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fq5_4297/02_2024/6fq5_4297.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fq5_4297/02_2024/6fq5_4297.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fq5_4297/02_2024/6fq5_4297.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fq5_4297/02_2024/6fq5_4297.pdb" } resolution = 3.8 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= 0.003 sd= 0.031 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 294 5.49 5 S 12 5.16 5 C 6741 2.51 5 N 2303 2.21 5 O 2843 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 12193 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 811 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "B" Number of atoms: 678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 678 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "C" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 850 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "D" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 746 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 683 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "G" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 850 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "H" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 746 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3031 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Time building chain proxies: 6.63, per 1000 atoms: 0.54 Number of scatterers: 12193 At special positions: 0 Unit cell: (78.4, 120.4, 113.4, 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 12 16.00 P 294 15.00 O 2843 8.00 N 2303 7.00 C 6741 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: 6.71 Conformation dependent library (CDL) restraints added in 1.1 seconds 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1454 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 71.8% alpha, 2.8% beta 146 base pairs and 255 stacking pairs defined. Time for finding SS restraints: 6.12 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 4.214A 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 132 removed outlier: 3.524A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.561A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.519A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.530A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.457A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.725A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) 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 Processing helix chain 'D' and resid 101 through 120 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 77 removed outlier: 4.271A 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 24 through 29 removed outlier: 3.566A pdb=" N GLN F 27 " --> pdb=" O ASP F 24 " (cutoff:3.500A) removed outlier: 3.669A 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: 3.688A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.515A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) 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 72 removed outlier: 4.437A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 removed outlier: 3.728A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) 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 removed outlier: 3.606A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 121 removed outlier: 3.605A pdb=" N ALA H 104 " --> pdb=" O PRO H 100 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER H 120 " --> pdb=" O THR H 116 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.916A 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 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 42 through 43 removed outlier: 7.379A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.964A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.336A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 403 hydrogen bonds defined for protein. 1188 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 375 hydrogen bonds 750 hydrogen bond angles 0 basepair planarities 146 basepair parallelities 255 stacking parallelities Total time for adding SS restraints: 4.34 Time building geometry restraints manager: 7.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.32: 1746 1.32 - 1.44: 4620 1.44 - 1.56: 6033 1.56 - 1.68: 587 1.68 - 1.80: 22 Bond restraints: 13008 Sorted by residual: bond pdb=" C ILE C 79 " pdb=" N PRO C 80 " ideal model delta sigma weight residual 1.334 1.405 -0.071 2.34e-02 1.83e+03 9.30e+00 bond pdb=" C ILE G 79 " pdb=" N PRO G 80 " ideal model delta sigma weight residual 1.334 1.400 -0.066 2.34e-02 1.83e+03 7.92e+00 bond pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " ideal model delta sigma weight residual 1.422 1.499 -0.077 3.00e-02 1.11e+03 6.57e+00 bond pdb=" C LEU E 65 " pdb=" N PRO E 66 " ideal model delta sigma weight residual 1.334 1.370 -0.036 1.51e-02 4.39e+03 5.70e+00 bond pdb=" C LEU A 65 " pdb=" N PRO A 66 " ideal model delta sigma weight residual 1.334 1.370 -0.036 1.51e-02 4.39e+03 5.69e+00 ... (remaining 13003 not shown) Histogram of bond angle deviations from ideal: 97.22 - 104.34: 1155 104.34 - 111.46: 6354 111.46 - 118.59: 4108 118.59 - 125.71: 6237 125.71 - 132.83: 968 Bond angle restraints: 18822 Sorted by residual: angle pdb=" CA ARG C 88 " pdb=" CB ARG C 88 " pdb=" CG ARG C 88 " ideal model delta sigma weight residual 114.10 124.18 -10.08 2.00e+00 2.50e-01 2.54e+01 angle pdb=" C ARG C 77 " pdb=" CA ARG C 77 " pdb=" CB ARG C 77 " ideal model delta sigma weight residual 109.72 117.90 -8.18 1.73e+00 3.34e-01 2.24e+01 angle pdb=" CA ARG G 88 " pdb=" CB ARG G 88 " pdb=" CG ARG G 88 " ideal model delta sigma weight residual 114.10 123.51 -9.41 2.00e+00 2.50e-01 2.21e+01 angle pdb=" N PRO C 80 " pdb=" CA PRO C 80 " pdb=" C PRO C 80 " ideal model delta sigma weight residual 112.47 122.09 -9.62 2.06e+00 2.36e-01 2.18e+01 angle pdb=" N GLY H 101 " pdb=" CA GLY H 101 " pdb=" C GLY H 101 " ideal model delta sigma weight residual 113.18 123.65 -10.47 2.37e+00 1.78e-01 1.95e+01 ... (remaining 18817 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.26: 5478 34.26 - 68.51: 1560 68.51 - 102.77: 37 102.77 - 137.02: 3 137.02 - 171.28: 3 Dihedral angle restraints: 7081 sinusoidal: 4831 harmonic: 2250 Sorted by residual: dihedral pdb=" C4' DT I -59 " pdb=" C3' DT I -59 " pdb=" O3' DT I -59 " pdb=" P DC I -58 " ideal model delta sinusoidal sigma weight residual 220.00 48.72 171.28 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DG I 20 " pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " pdb=" P DG I 21 " ideal model delta sinusoidal sigma weight residual 220.00 54.95 165.05 1 3.50e+01 8.16e-04 1.54e+01 dihedral pdb=" CA ARG D 27 " pdb=" C ARG D 27 " pdb=" N LYS D 28 " pdb=" CA LYS D 28 " ideal model delta harmonic sigma weight residual 180.00 -161.24 -18.76 0 5.00e+00 4.00e-02 1.41e+01 ... (remaining 7078 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1647 0.065 - 0.130: 424 0.130 - 0.194: 63 0.194 - 0.259: 6 0.259 - 0.324: 3 Chirality restraints: 2143 Sorted by residual: chirality pdb=" CA PRO C 80 " pdb=" N PRO C 80 " pdb=" C PRO C 80 " pdb=" CB PRO C 80 " both_signs ideal model delta sigma weight residual False 2.72 2.39 0.32 2.00e-01 2.50e+01 2.62e+00 chirality pdb=" CA PRO G 80 " pdb=" N PRO G 80 " pdb=" C PRO G 80 " pdb=" CB PRO G 80 " both_signs ideal model delta sigma weight residual False 2.72 2.43 0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" CG LEU B 22 " pdb=" CB LEU B 22 " pdb=" CD1 LEU B 22 " pdb=" CD2 LEU B 22 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 2.01e+00 ... (remaining 2140 not shown) Planarity restraints: 1360 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 64 " -0.021 2.00e-02 2.50e+03 4.25e-02 1.81e+01 pdb=" C ASN B 64 " 0.074 2.00e-02 2.50e+03 pdb=" O ASN B 64 " -0.028 2.00e-02 2.50e+03 pdb=" N VAL B 65 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS D 105 " -0.019 2.00e-02 2.50e+03 3.85e-02 1.48e+01 pdb=" C LYS D 105 " 0.067 2.00e-02 2.50e+03 pdb=" O LYS D 105 " -0.025 2.00e-02 2.50e+03 pdb=" N HIS D 106 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR F 72 " -0.018 2.00e-02 2.50e+03 3.67e-02 1.35e+01 pdb=" C TYR F 72 " 0.063 2.00e-02 2.50e+03 pdb=" O TYR F 72 " -0.024 2.00e-02 2.50e+03 pdb=" N THR F 73 " -0.021 2.00e-02 2.50e+03 ... (remaining 1357 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2276 2.78 - 3.31: 10754 3.31 - 3.84: 25082 3.84 - 4.37: 27703 4.37 - 4.90: 39345 Nonbonded interactions: 105160 Sorted by model distance: nonbonded pdb=" O THR C 16 " pdb=" OG SER C 19 " model vdw 2.253 2.440 nonbonded pdb=" OG1 THR H 29 " pdb=" OP1 DT J 30 " model vdw 2.299 2.440 nonbonded pdb=" O THR G 16 " pdb=" OG SER G 19 " model vdw 2.329 2.440 nonbonded pdb=" OH TYR B 98 " pdb=" OD2 ASP H 65 " model vdw 2.340 2.440 nonbonded pdb=" OE2 GLU E 133 " pdb=" NH2 ARG F 95 " model vdw 2.341 2.520 ... (remaining 105155 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' and resid 38 through 134) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 18 through 101) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.830 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: 0.020 Extract box with map and model: 1.790 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 39.450 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.060 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 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 : 0.008 0.077 13008 Z= 0.470 Angle : 1.088 11.893 18822 Z= 0.642 Chirality : 0.058 0.324 2143 Planarity : 0.008 0.042 1360 Dihedral : 28.680 171.275 5627 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.31 % Allowed : 1.55 % Favored : 98.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.25), residues: 758 helix: -0.74 (0.18), residues: 544 sheet: None (None), residues: 0 loop : -1.39 (0.36), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.018 0.003 HIS H 46 PHE 0.037 0.005 PHE G 25 TYR 0.029 0.004 TYR A 54 ARG 0.004 0.001 ARG H 30 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 647 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 390 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 PRO cc_start: 0.6958 (Cg_exo) cc_final: 0.6722 (Cg_endo) REVERT: A 51 ILE cc_start: 0.9322 (mt) cc_final: 0.9023 (mt) REVERT: A 56 LYS cc_start: 0.8721 (tttt) cc_final: 0.8483 (tttp) REVERT: A 58 THR cc_start: 0.7519 (p) cc_final: 0.7243 (t) REVERT: B 24 ASP cc_start: 0.6823 (m-30) cc_final: 0.6023 (p0) REVERT: B 59 LYS cc_start: 0.8788 (ttpt) cc_final: 0.8404 (ttpp) REVERT: B 60 VAL cc_start: 0.9172 (t) cc_final: 0.8795 (t) REVERT: B 63 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7621 (mt-10) REVERT: C 84 GLN cc_start: 0.7358 (tp40) cc_final: 0.7001 (tp40) REVERT: C 113 SER cc_start: 0.9098 (m) cc_final: 0.8848 (p) REVERT: D 31 LYS cc_start: 0.7934 (mttt) cc_final: 0.7571 (pptt) REVERT: D 40 LYS cc_start: 0.8872 (mttt) cc_final: 0.8516 (mtpt) REVERT: D 43 LYS cc_start: 0.8986 (mmtt) cc_final: 0.8764 (mmmt) REVERT: D 76 ARG cc_start: 0.8594 (mtt90) cc_final: 0.8239 (ttm110) REVERT: D 80 TYR cc_start: 0.7159 (m-10) cc_final: 0.6911 (m-10) REVERT: D 106 HIS cc_start: 0.8580 (m-70) cc_final: 0.7411 (m-70) REVERT: D 109 SER cc_start: 0.9321 (t) cc_final: 0.8809 (p) REVERT: E 51 ILE cc_start: 0.9352 (mt) cc_final: 0.8928 (mt) REVERT: E 58 THR cc_start: 0.7748 (p) cc_final: 0.7533 (t) REVERT: E 67 PHE cc_start: 0.8391 (t80) cc_final: 0.7800 (t80) REVERT: F 59 LYS cc_start: 0.8703 (tttm) cc_final: 0.8160 (ttpp) REVERT: F 63 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7458 (mt-10) REVERT: F 82 THR cc_start: 0.8478 (p) cc_final: 0.8265 (p) REVERT: F 90 LEU cc_start: 0.9224 (mt) cc_final: 0.8892 (mp) REVERT: F 100 PHE cc_start: 0.7196 (m-80) cc_final: 0.6343 (m-80) REVERT: G 84 GLN cc_start: 0.7459 (tp40) cc_final: 0.6757 (tp40) REVERT: G 113 SER cc_start: 0.8966 (m) cc_final: 0.8642 (p) REVERT: H 40 LYS cc_start: 0.8837 (mttt) cc_final: 0.8610 (mtpt) REVERT: H 73 GLU cc_start: 0.8827 (mm-30) cc_final: 0.8521 (mm-30) REVERT: H 86 ILE cc_start: 0.8867 (mt) cc_final: 0.8609 (tp) REVERT: H 106 HIS cc_start: 0.9053 (m-70) cc_final: 0.7622 (m170) REVERT: H 109 SER cc_start: 0.9317 (m) cc_final: 0.8825 (p) outliers start: 2 outliers final: 0 residues processed: 392 average time/residue: 0.3085 time to fit residues: 159.2006 Evaluate side-chains 216 residues out of total 647 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 216 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 10.0000 chunk 77 optimal weight: 7.9990 chunk 42 optimal weight: 7.9990 chunk 26 optimal weight: 0.0870 chunk 52 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 79 optimal weight: 8.9990 chunk 30 optimal weight: 10.0000 chunk 48 optimal weight: 6.9990 chunk 59 optimal weight: 0.9980 chunk 92 optimal weight: 8.9990 overall best weight: 2.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS A 108 ASN A 113 HIS ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN D 60 ASN ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 HIS E 108 ASN E 113 HIS ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN G 73 ASN G 104 GLN G 110 ASN H 44 GLN ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 106 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13008 Z= 0.258 Angle : 0.678 6.806 18822 Z= 0.401 Chirality : 0.039 0.228 2143 Planarity : 0.005 0.065 1360 Dihedral : 32.062 165.774 4077 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 5.87 % Allowed : 19.32 % Favored : 74.81 % 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: 1.34 (0.29), residues: 758 helix: 1.51 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -0.67 (0.38), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 75 PHE 0.017 0.002 PHE F 61 TYR 0.016 0.002 TYR E 54 ARG 0.006 0.001 ARG B 45 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 647 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 253 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LEU cc_start: 0.7498 (OUTLIER) cc_final: 0.6838 (mm) REVERT: A 67 PHE cc_start: 0.8414 (t80) cc_final: 0.8201 (t80) REVERT: B 59 LYS cc_start: 0.8723 (ttpt) cc_final: 0.7851 (ttpp) REVERT: B 60 VAL cc_start: 0.9143 (t) cc_final: 0.8537 (p) REVERT: B 63 GLU cc_start: 0.7824 (mt-10) cc_final: 0.7280 (mt-10) REVERT: B 90 LEU cc_start: 0.9252 (mt) cc_final: 0.8960 (mp) REVERT: C 57 TYR cc_start: 0.8410 (t80) cc_final: 0.7950 (t80) REVERT: C 84 GLN cc_start: 0.8106 (tp40) cc_final: 0.7861 (tp40) REVERT: C 113 SER cc_start: 0.8784 (m) cc_final: 0.8583 (p) REVERT: D 31 LYS cc_start: 0.7728 (mttt) cc_final: 0.7450 (pptt) REVERT: D 40 LYS cc_start: 0.8922 (mttt) cc_final: 0.8652 (mtpt) REVERT: D 73 GLU cc_start: 0.8687 (mm-30) cc_final: 0.8432 (mm-30) REVERT: D 76 ARG cc_start: 0.8639 (mtt90) cc_final: 0.8420 (ttm110) REVERT: D 80 TYR cc_start: 0.7082 (m-10) cc_final: 0.6698 (m-80) REVERT: D 106 HIS cc_start: 0.8901 (m90) cc_final: 0.7484 (m170) REVERT: D 109 SER cc_start: 0.9127 (t) cc_final: 0.8819 (p) REVERT: E 58 THR cc_start: 0.7781 (p) cc_final: 0.7547 (t) REVERT: E 78 PHE cc_start: 0.8292 (m-80) cc_final: 0.8078 (m-80) REVERT: E 133 GLU cc_start: 0.7970 (mp0) cc_final: 0.6412 (mt-10) REVERT: F 59 LYS cc_start: 0.8611 (tttm) cc_final: 0.8350 (ttpp) REVERT: F 60 VAL cc_start: 0.8832 (t) cc_final: 0.8454 (p) REVERT: F 63 GLU cc_start: 0.7720 (mt-10) cc_final: 0.7333 (mt-10) REVERT: F 90 LEU cc_start: 0.9182 (mt) cc_final: 0.8924 (mp) REVERT: G 84 GLN cc_start: 0.8018 (tp40) cc_final: 0.7810 (tp40) REVERT: H 73 GLU cc_start: 0.8846 (mm-30) cc_final: 0.8437 (mm-30) REVERT: H 80 TYR cc_start: 0.7652 (m-10) cc_final: 0.7446 (m-80) REVERT: H 86 ILE cc_start: 0.8953 (mt) cc_final: 0.8710 (tp) REVERT: H 106 HIS cc_start: 0.8931 (m90) cc_final: 0.7929 (m90) REVERT: H 109 SER cc_start: 0.9435 (m) cc_final: 0.8909 (p) REVERT: H 110 GLU cc_start: 0.8477 (mm-30) cc_final: 0.7962 (mm-30) outliers start: 38 outliers final: 19 residues processed: 270 average time/residue: 0.2215 time to fit residues: 85.6182 Evaluate side-chains 218 residues out of total 647 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 198 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain D residue 28 LYS Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 65 ASP Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 81 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 0.3980 chunk 28 optimal weight: 8.9990 chunk 77 optimal weight: 7.9990 chunk 63 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 92 optimal weight: 10.0000 chunk 100 optimal weight: 10.0000 chunk 82 optimal weight: 10.0000 chunk 31 optimal weight: 0.6980 chunk 74 optimal weight: 10.0000 chunk 91 optimal weight: 8.9990 overall best weight: 4.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 ASN C 110 ASN ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN E 125 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 89 ASN G 110 ASN ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 60 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.4614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 13008 Z= 0.322 Angle : 0.694 6.847 18822 Z= 0.411 Chirality : 0.039 0.152 2143 Planarity : 0.006 0.050 1360 Dihedral : 31.769 167.258 4077 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 19.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 6.18 % Allowed : 21.33 % Favored : 72.49 % 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: 1.26 (0.28), residues: 758 helix: 1.46 (0.21), residues: 542 sheet: None (None), residues: 0 loop : -0.68 (0.37), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS F 75 PHE 0.019 0.002 PHE E 67 TYR 0.021 0.003 TYR H 37 ARG 0.006 0.001 ARG D 27 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 647 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 207 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 PHE cc_start: 0.8386 (t80) cc_final: 0.8165 (t80) REVERT: B 59 LYS cc_start: 0.8829 (ttpt) cc_final: 0.8087 (ttpp) REVERT: B 60 VAL cc_start: 0.8963 (t) cc_final: 0.8344 (m) REVERT: B 63 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7306 (mt-10) REVERT: B 90 LEU cc_start: 0.9218 (mt) cc_final: 0.8918 (mp) REVERT: C 113 SER cc_start: 0.8965 (m) cc_final: 0.8678 (p) REVERT: D 31 LYS cc_start: 0.7871 (mttt) cc_final: 0.7430 (pptt) REVERT: D 40 LYS cc_start: 0.9084 (mttt) cc_final: 0.8771 (mtpt) REVERT: D 73 GLU cc_start: 0.8888 (mm-30) cc_final: 0.8388 (mm-30) REVERT: D 76 ARG cc_start: 0.8376 (mtt90) cc_final: 0.7876 (ttm110) REVERT: E 58 THR cc_start: 0.8003 (p) cc_final: 0.7783 (t) REVERT: E 93 GLN cc_start: 0.8219 (tp-100) cc_final: 0.8017 (tp40) REVERT: E 123 ASP cc_start: 0.8155 (t70) cc_final: 0.7731 (t70) REVERT: F 60 VAL cc_start: 0.8746 (t) cc_final: 0.8428 (p) REVERT: F 63 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7568 (mt-10) REVERT: F 90 LEU cc_start: 0.9015 (mt) cc_final: 0.8750 (mp) REVERT: G 84 GLN cc_start: 0.8107 (tp40) cc_final: 0.7822 (tp40) REVERT: G 113 SER cc_start: 0.8720 (m) cc_final: 0.8401 (p) REVERT: H 31 LYS cc_start: 0.7801 (tptp) cc_final: 0.7423 (tmmt) REVERT: H 37 TYR cc_start: 0.8983 (m-80) cc_final: 0.8621 (m-80) REVERT: H 73 GLU cc_start: 0.8966 (mm-30) cc_final: 0.8633 (mm-30) REVERT: H 106 HIS cc_start: 0.9054 (m90) cc_final: 0.8012 (m90) REVERT: H 109 SER cc_start: 0.9472 (m) cc_final: 0.9036 (p) REVERT: H 110 GLU cc_start: 0.8712 (mm-30) cc_final: 0.8453 (mm-30) outliers start: 40 outliers final: 30 residues processed: 230 average time/residue: 0.2124 time to fit residues: 71.0155 Evaluate side-chains 206 residues out of total 647 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 176 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 28 LYS Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 64 ASN Chi-restraints excluded: chain H residue 65 ASP Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 81 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 6.9990 chunk 48 optimal weight: 9.9990 chunk 10 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 93 optimal weight: 10.0000 chunk 98 optimal weight: 8.9990 chunk 88 optimal weight: 10.0000 chunk 26 optimal weight: 8.9990 chunk 82 optimal weight: 10.0000 chunk 55 optimal weight: 4.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- 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** C 110 ASN ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN E 85 GLN G 110 ASN ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 60 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.5200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13008 Z= 0.297 Angle : 0.667 7.847 18822 Z= 0.394 Chirality : 0.039 0.215 2143 Planarity : 0.005 0.044 1360 Dihedral : 31.652 172.848 4077 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 18.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 6.49 % Allowed : 23.96 % Favored : 69.55 % 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: 1.40 (0.29), residues: 758 helix: 1.59 (0.22), residues: 539 sheet: None (None), residues: 0 loop : -0.68 (0.37), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 75 PHE 0.020 0.002 PHE B 61 TYR 0.017 0.002 TYR H 37 ARG 0.005 0.000 ARG D 27 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 647 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 191 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 LYS cc_start: 0.8815 (ttpt) cc_final: 0.8015 (ttpp) REVERT: B 60 VAL cc_start: 0.8987 (t) cc_final: 0.8304 (p) REVERT: B 63 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7258 (mt-10) REVERT: B 90 LEU cc_start: 0.9266 (mt) cc_final: 0.8958 (mp) REVERT: C 9 LYS cc_start: 0.6482 (mttt) cc_final: 0.5541 (tmtt) REVERT: C 113 SER cc_start: 0.8867 (m) cc_final: 0.8556 (p) REVERT: D 31 LYS cc_start: 0.7947 (mttt) cc_final: 0.7679 (pptt) REVERT: D 40 LYS cc_start: 0.9017 (mttt) cc_final: 0.8656 (mtpt) REVERT: D 73 GLU cc_start: 0.8849 (mm-30) cc_final: 0.8402 (mm-30) REVERT: D 76 ARG cc_start: 0.8400 (mtt90) cc_final: 0.7973 (ttm110) REVERT: D 90 GLU cc_start: 0.8194 (mp0) cc_final: 0.7819 (mp0) REVERT: E 58 THR cc_start: 0.8071 (p) cc_final: 0.7867 (t) REVERT: E 93 GLN cc_start: 0.7995 (tp-100) cc_final: 0.7715 (tp-100) REVERT: E 123 ASP cc_start: 0.8157 (t70) cc_final: 0.7842 (t70) REVERT: F 90 LEU cc_start: 0.9092 (mt) cc_final: 0.8864 (mp) REVERT: G 50 TYR cc_start: 0.8135 (OUTLIER) cc_final: 0.7741 (t80) REVERT: G 113 SER cc_start: 0.8757 (m) cc_final: 0.8400 (p) REVERT: H 31 LYS cc_start: 0.7636 (tptp) cc_final: 0.7254 (tmmt) REVERT: H 73 GLU cc_start: 0.8903 (mm-30) cc_final: 0.8293 (mm-30) REVERT: H 77 LEU cc_start: 0.9474 (OUTLIER) cc_final: 0.9224 (tp) REVERT: H 106 HIS cc_start: 0.9113 (m90) cc_final: 0.7865 (m170) REVERT: H 109 SER cc_start: 0.9425 (m) cc_final: 0.8934 (p) REVERT: H 110 GLU cc_start: 0.8774 (mm-30) cc_final: 0.8466 (mm-30) outliers start: 42 outliers final: 29 residues processed: 216 average time/residue: 0.2137 time to fit residues: 67.9737 Evaluate side-chains 211 residues out of total 647 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 180 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain D residue 28 LYS Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 64 ASN Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 50 TYR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 64 ASN Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 81 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 84 optimal weight: 10.0000 chunk 68 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 50 optimal weight: 2.9990 chunk 88 optimal weight: 10.0000 chunk 24 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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** C 89 ASN ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 60 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.5484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13008 Z= 0.204 Angle : 0.608 9.555 18822 Z= 0.362 Chirality : 0.037 0.184 2143 Planarity : 0.004 0.044 1360 Dihedral : 31.400 176.797 4077 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.71 % Allowed : 24.57 % Favored : 71.72 % 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: 1.75 (0.30), residues: 758 helix: 1.84 (0.22), residues: 541 sheet: None (None), residues: 0 loop : -0.56 (0.37), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS G 82 PHE 0.017 0.002 PHE B 61 TYR 0.019 0.002 TYR A 99 ARG 0.004 0.000 ARG B 45 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 647 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 219 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 LYS cc_start: 0.8783 (ttpt) cc_final: 0.8078 (ttpp) REVERT: B 60 VAL cc_start: 0.9027 (t) cc_final: 0.8364 (p) REVERT: B 63 GLU cc_start: 0.7774 (mt-10) cc_final: 0.7135 (mt-10) REVERT: B 90 LEU cc_start: 0.9173 (mt) cc_final: 0.8843 (mp) REVERT: C 9 LYS cc_start: 0.6284 (mttt) cc_final: 0.5241 (tmtt) REVERT: C 113 SER cc_start: 0.8773 (m) cc_final: 0.8536 (p) REVERT: D 31 LYS cc_start: 0.7841 (mttt) cc_final: 0.7438 (pptt) REVERT: D 40 LYS cc_start: 0.8879 (mttt) cc_final: 0.8615 (mtmt) REVERT: D 73 GLU cc_start: 0.8772 (mm-30) cc_final: 0.8451 (mm-30) REVERT: D 76 ARG cc_start: 0.8291 (mtt90) cc_final: 0.7943 (ttm110) REVERT: D 81 ASN cc_start: 0.9026 (m-40) cc_final: 0.8803 (m-40) REVERT: D 90 GLU cc_start: 0.8182 (mp0) cc_final: 0.7800 (mp0) REVERT: E 60 LEU cc_start: 0.8072 (mt) cc_final: 0.7679 (mt) REVERT: E 67 PHE cc_start: 0.8298 (t80) cc_final: 0.8039 (t80) REVERT: E 93 GLN cc_start: 0.7763 (tp-100) cc_final: 0.7413 (tp-100) REVERT: G 50 TYR cc_start: 0.8025 (OUTLIER) cc_final: 0.7655 (t80) REVERT: G 115 LEU cc_start: 0.8832 (mt) cc_final: 0.8586 (mm) REVERT: H 31 LYS cc_start: 0.7548 (tptp) cc_final: 0.7243 (tmmt) REVERT: H 37 TYR cc_start: 0.8799 (m-80) cc_final: 0.8444 (m-80) REVERT: H 77 LEU cc_start: 0.9346 (mm) cc_final: 0.9072 (tp) REVERT: H 80 TYR cc_start: 0.7879 (m-10) cc_final: 0.7073 (m-80) REVERT: H 97 LEU cc_start: 0.8541 (mt) cc_final: 0.8284 (mt) outliers start: 24 outliers final: 18 residues processed: 230 average time/residue: 0.2202 time to fit residues: 73.7483 Evaluate side-chains 194 residues out of total 647 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 175 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain C residue 11 ARG Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 28 LYS Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 64 ASN Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 50 TYR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 64 ASN Chi-restraints excluded: chain H residue 81 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 98 optimal weight: 10.0000 chunk 81 optimal weight: 10.0000 chunk 45 optimal weight: 0.9980 chunk 8 optimal weight: 8.9990 chunk 32 optimal weight: 0.9990 chunk 51 optimal weight: 10.0000 chunk 95 optimal weight: 8.9990 chunk 11 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 60 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.5767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13008 Z= 0.252 Angle : 0.633 9.921 18822 Z= 0.374 Chirality : 0.038 0.203 2143 Planarity : 0.004 0.041 1360 Dihedral : 31.315 177.586 4077 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 16.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 4.48 % Allowed : 24.57 % Favored : 70.94 % 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: 1.63 (0.29), residues: 758 helix: 1.73 (0.22), residues: 541 sheet: None (None), residues: 0 loop : -0.51 (0.37), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.022 0.002 PHE A 67 TYR 0.023 0.002 TYR D 37 ARG 0.006 0.000 ARG F 92 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 647 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 187 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 LEU cc_start: 0.9145 (tp) cc_final: 0.8943 (mm) REVERT: B 59 LYS cc_start: 0.8839 (ttpt) cc_final: 0.8119 (ttpp) REVERT: B 63 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7336 (mt-10) REVERT: C 9 LYS cc_start: 0.6585 (mttt) cc_final: 0.5487 (tmtt) REVERT: C 41 GLU cc_start: 0.8538 (pp20) cc_final: 0.8321 (pp20) REVERT: C 95 LYS cc_start: 0.9329 (mmmm) cc_final: 0.9117 (mmmm) REVERT: C 113 SER cc_start: 0.8855 (m) cc_final: 0.8644 (p) REVERT: D 31 LYS cc_start: 0.7742 (mttt) cc_final: 0.7439 (pptt) REVERT: D 40 LYS cc_start: 0.8890 (mttt) cc_final: 0.8569 (mtpt) REVERT: D 81 ASN cc_start: 0.9091 (m-40) cc_final: 0.8833 (m-40) REVERT: E 67 PHE cc_start: 0.8407 (t80) cc_final: 0.8151 (t80) REVERT: E 93 GLN cc_start: 0.7759 (tp-100) cc_final: 0.7550 (tp40) REVERT: F 19 ARG cc_start: 0.6449 (mtm-85) cc_final: 0.5226 (tpt170) REVERT: G 50 TYR cc_start: 0.8129 (OUTLIER) cc_final: 0.7796 (t80) REVERT: G 84 GLN cc_start: 0.8176 (tp40) cc_final: 0.7779 (tp40) REVERT: H 31 LYS cc_start: 0.7521 (tptp) cc_final: 0.7263 (tmmt) REVERT: H 37 TYR cc_start: 0.8783 (m-80) cc_final: 0.8433 (m-80) outliers start: 29 outliers final: 24 residues processed: 205 average time/residue: 0.2325 time to fit residues: 68.9919 Evaluate side-chains 197 residues out of total 647 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 172 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain D residue 28 LYS Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 50 TYR Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 64 ASN Chi-restraints excluded: chain H residue 81 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 7.9990 chunk 55 optimal weight: 0.4980 chunk 83 optimal weight: 8.9990 chunk 98 optimal weight: 10.0000 chunk 61 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 45 optimal weight: 8.9990 chunk 60 optimal weight: 10.0000 chunk 39 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 60 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.6056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13008 Z= 0.199 Angle : 0.623 15.864 18822 Z= 0.362 Chirality : 0.037 0.230 2143 Planarity : 0.004 0.066 1360 Dihedral : 31.182 179.481 4077 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.55 % Allowed : 26.58 % Favored : 69.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.29), residues: 758 helix: 1.80 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.37 (0.38), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 46 PHE 0.008 0.001 PHE F 100 TYR 0.032 0.002 TYR D 80 ARG 0.004 0.000 ARG F 92 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 647 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 191 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7538 (mm-30) cc_final: 0.7294 (mm-30) REVERT: A 73 GLU cc_start: 0.8064 (pp20) cc_final: 0.7761 (pp20) REVERT: A 99 TYR cc_start: 0.8094 (t80) cc_final: 0.7820 (t80) REVERT: B 59 LYS cc_start: 0.8814 (ttpt) cc_final: 0.7965 (ttpp) REVERT: B 63 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7153 (mt-10) REVERT: C 9 LYS cc_start: 0.6808 (mttt) cc_final: 0.5594 (tmtt) REVERT: C 41 GLU cc_start: 0.8574 (pp20) cc_final: 0.8300 (pp20) REVERT: D 31 LYS cc_start: 0.7805 (mttt) cc_final: 0.7503 (pptt) REVERT: D 40 LYS cc_start: 0.8881 (mttt) cc_final: 0.8567 (mtpt) REVERT: D 76 ARG cc_start: 0.8795 (mtm-85) cc_final: 0.8420 (mtm180) REVERT: D 81 ASN cc_start: 0.8948 (m-40) cc_final: 0.8649 (m-40) REVERT: E 67 PHE cc_start: 0.8378 (t80) cc_final: 0.8061 (t80) REVERT: E 124 ILE cc_start: 0.9242 (mp) cc_final: 0.8999 (tp) REVERT: F 19 ARG cc_start: 0.6489 (mtm-85) cc_final: 0.5291 (tpt90) REVERT: G 50 TYR cc_start: 0.8040 (OUTLIER) cc_final: 0.7712 (t80) REVERT: H 31 LYS cc_start: 0.7537 (tptp) cc_final: 0.7259 (tmmt) REVERT: H 37 TYR cc_start: 0.8646 (m-80) cc_final: 0.8300 (m-80) outliers start: 23 outliers final: 16 residues processed: 206 average time/residue: 0.2311 time to fit residues: 68.6283 Evaluate side-chains 189 residues out of total 647 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 172 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain D residue 28 LYS Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 50 TYR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 64 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 66 optimal weight: 8.9990 chunk 48 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 77 optimal weight: 8.9990 chunk 89 optimal weight: 10.0000 chunk 94 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 chunk 91 optimal weight: 9.9990 chunk 55 optimal weight: 0.8980 overall best weight: 4.9586 ------------------------------------------------------------------------------- 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** C 89 ASN C 104 GLN ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.6308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 13008 Z= 0.347 Angle : 0.707 9.901 18822 Z= 0.411 Chirality : 0.040 0.180 2143 Planarity : 0.005 0.069 1360 Dihedral : 31.339 179.264 4077 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 21.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 5.26 % Allowed : 26.58 % Favored : 68.16 % 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: 1.22 (0.29), residues: 758 helix: 1.35 (0.21), residues: 544 sheet: None (None), residues: 0 loop : -0.47 (0.39), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS B 75 PHE 0.025 0.002 PHE A 67 TYR 0.042 0.003 TYR D 80 ARG 0.008 0.001 ARG D 27 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 647 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 170 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8205 (pp20) cc_final: 0.7869 (pp20) REVERT: B 59 LYS cc_start: 0.8897 (ttpt) cc_final: 0.8625 (ttpp) REVERT: C 9 LYS cc_start: 0.6585 (mttt) cc_final: 0.5440 (tmtt) REVERT: D 31 LYS cc_start: 0.7732 (mttt) cc_final: 0.7510 (pptt) REVERT: D 40 LYS cc_start: 0.9092 (mttt) cc_final: 0.8761 (mtpt) REVERT: E 67 PHE cc_start: 0.8544 (t80) cc_final: 0.8162 (t80) REVERT: F 19 ARG cc_start: 0.6698 (mtm-85) cc_final: 0.5485 (tpt170) REVERT: F 63 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7753 (mt-10) REVERT: G 50 TYR cc_start: 0.8219 (OUTLIER) cc_final: 0.7867 (t80) REVERT: G 84 GLN cc_start: 0.8215 (tp40) cc_final: 0.7355 (tp40) REVERT: G 113 SER cc_start: 0.8871 (m) cc_final: 0.8550 (p) REVERT: H 37 TYR cc_start: 0.8845 (m-80) cc_final: 0.8466 (m-80) outliers start: 34 outliers final: 24 residues processed: 193 average time/residue: 0.2162 time to fit residues: 61.1114 Evaluate side-chains 185 residues out of total 647 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 160 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain D residue 28 LYS Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 50 TYR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 64 ASN Chi-restraints excluded: chain H residue 86 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 0.0010 chunk 71 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 82 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 60 optimal weight: 0.0980 chunk 96 optimal weight: 9.9990 chunk 59 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 overall best weight: 1.0188 ------------------------------------------------------------------------------- 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** C 89 ASN ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 60 ASN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.6450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13008 Z= 0.197 Angle : 0.648 14.179 18822 Z= 0.374 Chirality : 0.038 0.199 2143 Planarity : 0.004 0.059 1360 Dihedral : 31.176 179.982 4077 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.40 % Allowed : 29.52 % Favored : 67.08 % 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: 1.56 (0.30), residues: 758 helix: 1.62 (0.22), residues: 540 sheet: None (None), residues: 0 loop : -0.35 (0.39), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 75 PHE 0.008 0.001 PHE B 61 TYR 0.043 0.003 TYR D 80 ARG 0.004 0.000 ARG B 40 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 647 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 183 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7607 (mm-30) cc_final: 0.7362 (mm-30) REVERT: A 73 GLU cc_start: 0.8132 (pp20) cc_final: 0.7863 (pp20) REVERT: B 59 LYS cc_start: 0.8828 (ttpt) cc_final: 0.8479 (ttpp) REVERT: B 84 MET cc_start: 0.7013 (mmm) cc_final: 0.6504 (tmm) REVERT: C 9 LYS cc_start: 0.6625 (mttt) cc_final: 0.5310 (tmtt) REVERT: D 31 LYS cc_start: 0.7774 (mttt) cc_final: 0.7442 (pptt) REVERT: D 40 LYS cc_start: 0.8954 (mttt) cc_final: 0.8661 (mtpt) REVERT: E 67 PHE cc_start: 0.8407 (t80) cc_final: 0.7993 (t80) REVERT: F 19 ARG cc_start: 0.6676 (mtm-85) cc_final: 0.5362 (tpt170) REVERT: G 50 TYR cc_start: 0.8068 (OUTLIER) cc_final: 0.7741 (t80) REVERT: G 84 GLN cc_start: 0.8189 (tp40) cc_final: 0.7382 (tp40) REVERT: G 115 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8439 (mt) REVERT: H 37 TYR cc_start: 0.8757 (m-80) cc_final: 0.8403 (m-80) outliers start: 22 outliers final: 17 residues processed: 198 average time/residue: 0.2208 time to fit residues: 63.2947 Evaluate side-chains 181 residues out of total 647 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 162 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain D residue 28 LYS Chi-restraints excluded: chain D residue 64 ASN Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 50 TYR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 57 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 10.0000 chunk 93 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 64 optimal weight: 0.4980 chunk 86 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 74 optimal weight: 10.0000 chunk 11 optimal weight: 7.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- 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 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 60 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.6585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13008 Z= 0.239 Angle : 0.667 13.543 18822 Z= 0.386 Chirality : 0.038 0.195 2143 Planarity : 0.004 0.059 1360 Dihedral : 31.086 179.388 4077 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 17.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.55 % Allowed : 29.68 % Favored : 66.77 % 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: 1.31 (0.30), residues: 758 helix: 1.41 (0.22), residues: 540 sheet: None (None), residues: 0 loop : -0.39 (0.39), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 75 PHE 0.027 0.002 PHE H 67 TYR 0.046 0.003 TYR D 80 ARG 0.005 0.000 ARG F 45 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 647 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 164 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8176 (pp20) cc_final: 0.7901 (pp20) REVERT: B 59 LYS cc_start: 0.8886 (ttpt) cc_final: 0.8529 (ttpp) REVERT: B 84 MET cc_start: 0.7015 (mmm) cc_final: 0.6656 (tmm) REVERT: C 9 LYS cc_start: 0.6618 (mttt) cc_final: 0.5239 (tmtt) REVERT: D 31 LYS cc_start: 0.7756 (mttt) cc_final: 0.7470 (pptt) REVERT: D 40 LYS cc_start: 0.8963 (mttt) cc_final: 0.8667 (mtpt) REVERT: D 108 VAL cc_start: 0.8838 (p) cc_final: 0.8615 (p) REVERT: E 67 PHE cc_start: 0.8466 (t80) cc_final: 0.8093 (t80) REVERT: F 19 ARG cc_start: 0.6649 (mtm-85) cc_final: 0.5310 (tpt170) REVERT: G 50 TYR cc_start: 0.8125 (OUTLIER) cc_final: 0.7798 (t80) REVERT: G 84 GLN cc_start: 0.8178 (tp40) cc_final: 0.7379 (tp40) REVERT: G 115 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8465 (mt) REVERT: H 37 TYR cc_start: 0.8830 (m-80) cc_final: 0.8449 (m-80) outliers start: 23 outliers final: 19 residues processed: 180 average time/residue: 0.2202 time to fit residues: 57.6653 Evaluate side-chains 181 residues out of total 647 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 160 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain D residue 28 LYS Chi-restraints excluded: chain D residue 64 ASN Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 50 TYR Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 64 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 0.9990 chunk 81 optimal weight: 10.0000 chunk 33 optimal weight: 9.9990 chunk 83 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 9.9990 chunk 71 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 92 optimal weight: 10.0000 chunk 54 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 60 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.064618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.055826 restraints weight = 66869.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.057354 restraints weight = 34212.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.058382 restraints weight = 21009.044| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.6720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13008 Z= 0.234 Angle : 0.668 13.187 18822 Z= 0.385 Chirality : 0.038 0.191 2143 Planarity : 0.004 0.054 1360 Dihedral : 31.049 179.533 4077 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 17.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.71 % Allowed : 30.29 % Favored : 66.00 % 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: 1.25 (0.30), residues: 758 helix: 1.34 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -0.34 (0.40), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 75 PHE 0.024 0.002 PHE H 67 TYR 0.043 0.003 TYR D 80 ARG 0.004 0.000 ARG F 45 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2086.03 seconds wall clock time: 39 minutes 6.29 seconds (2346.29 seconds total)