Starting phenix.real_space_refine on Sat Dec 28 06:15:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sat_24956/12_2024/7sat_24956.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sat_24956/12_2024/7sat_24956.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7sat_24956/12_2024/7sat_24956.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sat_24956/12_2024/7sat_24956.map" model { file = "/net/cci-nas-00/data/ceres_data/7sat_24956/12_2024/7sat_24956.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sat_24956/12_2024/7sat_24956.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1811 atoms to isotropic. 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 41 5.16 5 C 4255 2.51 5 N 1111 2.21 5 O 1174 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 6581 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1704 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 3, 'TRANS': 215} Chain: "B" Number of atoms: 1688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1688 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 3, 'TRANS': 214} Chain: "C" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 638 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "D" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 612 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "E" Number of atoms: 663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 663 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "F" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 638 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "G" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 638 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Time building chain proxies: 4.37, per 1000 atoms: 0.66 Number of scatterers: 6581 At special positions: 0 Unit cell: (86.508, 84.372, 130.296, 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 41 16.00 O 1174 8.00 N 1111 7.00 C 4255 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.69 Conformation dependent library (CDL) restraints added in 1.0 seconds 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1534 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 0 sheets defined 74.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 10 through 26 Processing helix chain 'A' and resid 31 through 70 removed outlier: 3.610A pdb=" N SER A 44 " --> pdb=" O LYS A 40 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N SER A 61 " --> pdb=" O ASN A 57 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLU A 62 " --> pdb=" O LEU A 58 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU A 63 " --> pdb=" O VAL A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 107 Processing helix chain 'A' and resid 125 through 130 Processing helix chain 'A' and resid 135 through 148 removed outlier: 4.317A pdb=" N THR A 139 " --> pdb=" O GLY A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 155 removed outlier: 3.665A pdb=" N MET A 155 " --> pdb=" O ALA A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 167 removed outlier: 4.626A pdb=" N GLN A 166 " --> pdb=" O LYS A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 223 Processing helix chain 'B' and resid 10 through 31 removed outlier: 4.024A pdb=" N MET B 14 " --> pdb=" O ASN B 10 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N LEU B 20 " --> pdb=" O ASN B 16 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL B 21 " --> pdb=" O LEU B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 70 removed outlier: 3.932A pdb=" N LYS B 40 " --> pdb=" O ASP B 36 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL B 41 " --> pdb=" O GLY B 37 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N THR B 69 " --> pdb=" O THR B 65 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASN B 70 " --> pdb=" O ALA B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 98 Processing helix chain 'B' and resid 100 through 105 removed outlier: 4.037A pdb=" N GLU B 105 " --> pdb=" O ALA B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 130 Processing helix chain 'B' and resid 136 through 154 removed outlier: 4.219A pdb=" N LYS B 146 " --> pdb=" O LYS B 142 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE B 147 " --> pdb=" O GLU B 143 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU B 154 " --> pdb=" O LEU B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 168 Processing helix chain 'B' and resid 178 through 183 Processing helix chain 'B' and resid 188 through 221 Processing helix chain 'C' and resid 3 through 16 removed outlier: 3.577A pdb=" N ALA C 16 " --> pdb=" O GLU C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 45 removed outlier: 3.897A pdb=" N LEU C 23 " --> pdb=" O LYS C 19 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASN C 25 " --> pdb=" O ARG C 21 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE C 26 " --> pdb=" O ARG C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 67 removed outlier: 3.659A pdb=" N MET C 52 " --> pdb=" O MET C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 70 No H-bonds generated for 'chain 'C' and resid 68 through 70' Processing helix chain 'D' and resid 8 through 17 Processing helix chain 'D' and resid 19 through 43 removed outlier: 3.903A pdb=" N LEU D 23 " --> pdb=" O LYS D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 68 removed outlier: 3.964A pdb=" N MET D 52 " --> pdb=" O MET D 48 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU D 53 " --> pdb=" O GLY D 49 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N PHE D 54 " --> pdb=" O ASN D 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 17 removed outlier: 3.735A pdb=" N MET E 13 " --> pdb=" O ASN E 9 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TYR E 14 " --> pdb=" O ILE E 10 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU E 15 " --> pdb=" O LEU E 11 " (cutoff:3.500A) Processing helix chain 'E' and resid 17 through 44 Processing helix chain 'E' and resid 49 through 67 removed outlier: 3.951A pdb=" N VAL E 55 " --> pdb=" O GLU E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 70 No H-bonds generated for 'chain 'E' and resid 68 through 70' Processing helix chain 'F' and resid 3 through 15 removed outlier: 3.669A pdb=" N TYR F 7 " --> pdb=" O HIS F 3 " (cutoff:3.500A) Processing helix chain 'F' and resid 17 through 44 removed outlier: 3.998A pdb=" N ALA F 32 " --> pdb=" O TYR F 28 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 67 removed outlier: 3.594A pdb=" N PHE F 54 " --> pdb=" O ASN F 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 11 through 16 removed outlier: 3.562A pdb=" N ALA G 16 " --> pdb=" O GLU G 12 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 45 removed outlier: 3.526A pdb=" N LEU G 23 " --> pdb=" O LYS G 19 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 67 441 hydrogen bonds defined for protein. 1314 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.81 Time building geometry restraints manager: 1.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2077 1.34 - 1.46: 1008 1.46 - 1.57: 3545 1.57 - 1.69: 0 1.69 - 1.81: 80 Bond restraints: 6710 Sorted by residual: bond pdb=" CG GLU B 209 " pdb=" CD GLU B 209 " ideal model delta sigma weight residual 1.516 1.489 0.027 2.50e-02 1.60e+03 1.21e+00 bond pdb=" CG1 ILE B 15 " pdb=" CD1 ILE B 15 " ideal model delta sigma weight residual 1.513 1.471 0.042 3.90e-02 6.57e+02 1.14e+00 bond pdb=" CA VAL B 151 " pdb=" C VAL B 151 " ideal model delta sigma weight residual 1.518 1.530 -0.012 1.13e-02 7.83e+03 1.10e+00 bond pdb=" CB VAL D 63 " pdb=" CG1 VAL D 63 " ideal model delta sigma weight residual 1.521 1.487 0.034 3.30e-02 9.18e+02 1.05e+00 bond pdb=" CB VAL C 35 " pdb=" CG1 VAL C 35 " ideal model delta sigma weight residual 1.521 1.488 0.033 3.30e-02 9.18e+02 9.97e-01 ... (remaining 6705 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 8814 2.09 - 4.19: 184 4.19 - 6.28: 27 6.28 - 8.37: 8 8.37 - 10.46: 1 Bond angle restraints: 9034 Sorted by residual: angle pdb=" N TRP G 30 " pdb=" CA TRP G 30 " pdb=" CB TRP G 30 " ideal model delta sigma weight residual 110.39 116.53 -6.14 1.66e+00 3.63e-01 1.37e+01 angle pdb=" C ARG A 148 " pdb=" N GLU A 149 " pdb=" CA GLU A 149 " ideal model delta sigma weight residual 121.54 128.46 -6.92 1.91e+00 2.74e-01 1.31e+01 angle pdb=" C SER G 29 " pdb=" N TRP G 30 " pdb=" CA TRP G 30 " ideal model delta sigma weight residual 120.72 114.85 5.87 1.67e+00 3.59e-01 1.24e+01 angle pdb=" N ARG B 117 " pdb=" CA ARG B 117 " pdb=" C ARG B 117 " ideal model delta sigma weight residual 113.43 109.25 4.18 1.26e+00 6.30e-01 1.10e+01 angle pdb=" N ASP A 115 " pdb=" CA ASP A 115 " pdb=" C ASP A 115 " ideal model delta sigma weight residual 114.64 109.78 4.86 1.52e+00 4.33e-01 1.02e+01 ... (remaining 9029 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.04: 3380 14.04 - 28.08: 450 28.08 - 42.12: 151 42.12 - 56.16: 23 56.16 - 70.20: 10 Dihedral angle restraints: 4014 sinusoidal: 1632 harmonic: 2382 Sorted by residual: dihedral pdb=" CA LYS B 99 " pdb=" C LYS B 99 " pdb=" N LEU B 100 " pdb=" CA LEU B 100 " ideal model delta harmonic sigma weight residual 180.00 157.88 22.12 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" CA TRP A 179 " pdb=" C TRP A 179 " pdb=" N GLU A 180 " pdb=" CA GLU A 180 " ideal model delta harmonic sigma weight residual 180.00 161.09 18.91 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA LEU B 161 " pdb=" C LEU B 161 " pdb=" N LYS B 162 " pdb=" CA LYS B 162 " ideal model delta harmonic sigma weight residual -180.00 -161.84 -18.16 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 4011 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 818 0.048 - 0.097: 169 0.097 - 0.145: 21 0.145 - 0.194: 3 0.194 - 0.242: 1 Chirality restraints: 1012 Sorted by residual: chirality pdb=" CA TRP G 30 " pdb=" N TRP G 30 " pdb=" C TRP G 30 " pdb=" CB TRP G 30 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA GLU A 87 " pdb=" N GLU A 87 " pdb=" C GLU A 87 " pdb=" CB GLU A 87 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.71e-01 chirality pdb=" CB ILE A 15 " pdb=" CA ILE A 15 " pdb=" CG1 ILE A 15 " pdb=" CG2 ILE A 15 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.35e-01 ... (remaining 1009 not shown) Planarity restraints: 1122 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP G 30 " 0.039 2.00e-02 2.50e+03 3.50e-02 3.07e+01 pdb=" CG TRP G 30 " -0.094 2.00e-02 2.50e+03 pdb=" CD1 TRP G 30 " 0.041 2.00e-02 2.50e+03 pdb=" CD2 TRP G 30 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP G 30 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP G 30 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP G 30 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 30 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 30 " 0.013 2.00e-02 2.50e+03 pdb=" CH2 TRP G 30 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU E 46 " -0.053 5.00e-02 4.00e+02 8.06e-02 1.04e+01 pdb=" N PRO E 47 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO E 47 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO E 47 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 83 " -0.012 2.00e-02 2.50e+03 2.43e-02 5.89e+00 pdb=" C VAL A 83 " 0.042 2.00e-02 2.50e+03 pdb=" O VAL A 83 " -0.016 2.00e-02 2.50e+03 pdb=" N LEU A 84 " -0.014 2.00e-02 2.50e+03 ... (remaining 1119 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 111 2.64 - 3.21: 6605 3.21 - 3.77: 10371 3.77 - 4.34: 13204 4.34 - 4.90: 21473 Nonbonded interactions: 51764 Sorted by model distance: nonbonded pdb=" OG SER A 181 " pdb=" OE1 GLU A 185 " model vdw 2.080 3.040 nonbonded pdb=" OD1 ASN A 64 " pdb=" OH TYR A 78 " model vdw 2.151 3.040 nonbonded pdb=" O VAL F 63 " pdb=" OG SER F 67 " model vdw 2.208 3.040 nonbonded pdb=" NZ LYS A 99 " pdb=" OE1 GLN A 200 " model vdw 2.250 3.120 nonbonded pdb=" O ASP B 89 " pdb=" OG1 THR B 93 " model vdw 2.264 3.040 ... (remaining 51759 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' and resid 5 through 221) selection = (chain 'B' and resid 5 through 221) } ncs_group { reference = (chain 'C' and resid 5 through 78) selection = chain 'D' selection = (chain 'E' and resid 5 through 78) selection = (chain 'F' and resid 5 through 78) selection = (chain 'G' and resid 5 through 78) } 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: 0.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.460 Find NCS groups from input model: 0.250 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6710 Z= 0.254 Angle : 0.755 10.464 9034 Z= 0.409 Chirality : 0.040 0.242 1012 Planarity : 0.004 0.081 1122 Dihedral : 14.441 70.198 2480 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 0.28 % Allowed : 0.14 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.30), residues: 808 helix: 1.09 (0.22), residues: 573 sheet: None (None), residues: 0 loop : -2.67 (0.39), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.094 0.003 TRP G 30 HIS 0.009 0.001 HIS C 18 PHE 0.019 0.001 PHE D 61 TYR 0.025 0.002 TYR D 7 ARG 0.009 0.001 ARG D 21 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 281 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ASP cc_start: 0.8054 (p0) cc_final: 0.7736 (p0) REVERT: A 194 THR cc_start: 0.8510 (m) cc_final: 0.7855 (m) REVERT: A 204 ARG cc_start: 0.8811 (mmt-90) cc_final: 0.8458 (tpp-160) REVERT: C 12 GLU cc_start: 0.7437 (tm-30) cc_final: 0.7126 (tm-30) REVERT: C 13 MET cc_start: 0.7482 (ptp) cc_final: 0.7097 (ptp) REVERT: D 48 MET cc_start: 0.6970 (ptt) cc_final: 0.6593 (ptt) REVERT: G 51 GLU cc_start: 0.8387 (mp0) cc_final: 0.8174 (mp0) outliers start: 2 outliers final: 0 residues processed: 281 average time/residue: 0.1944 time to fit residues: 70.3318 Evaluate side-chains 235 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 10.0000 chunk 59 optimal weight: 3.9990 chunk 32 optimal weight: 9.9990 chunk 20 optimal weight: 6.9990 chunk 39 optimal weight: 0.0970 chunk 31 optimal weight: 4.9990 chunk 61 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 37 optimal weight: 0.0270 chunk 45 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 overall best weight: 0.5636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 ASN ** B 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 29 ASN ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6710 Z= 0.194 Angle : 0.705 11.984 9034 Z= 0.357 Chirality : 0.039 0.154 1012 Planarity : 0.004 0.055 1122 Dihedral : 4.558 20.021 888 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 2.39 % Allowed : 14.08 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.30), residues: 808 helix: 1.25 (0.21), residues: 595 sheet: None (None), residues: 0 loop : -2.83 (0.42), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP G 30 HIS 0.005 0.001 HIS C 18 PHE 0.022 0.002 PHE D 54 TYR 0.017 0.002 TYR B 205 ARG 0.006 0.001 ARG B 80 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 262 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 204 ARG cc_start: 0.8766 (mmt-90) cc_final: 0.7793 (tpp-160) REVERT: B 78 TYR cc_start: 0.6836 (t80) cc_final: 0.6573 (t80) REVERT: B 155 MET cc_start: 0.1482 (mmt) cc_final: 0.0804 (mmt) REVERT: C 12 GLU cc_start: 0.7409 (tm-30) cc_final: 0.7185 (tm-30) REVERT: C 13 MET cc_start: 0.7495 (ptp) cc_final: 0.7076 (ptp) REVERT: C 24 LEU cc_start: 0.9018 (mt) cc_final: 0.8391 (tp) REVERT: C 60 GLU cc_start: 0.8518 (pp20) cc_final: 0.8031 (pp20) REVERT: D 48 MET cc_start: 0.6908 (ptt) cc_final: 0.6673 (ptt) REVERT: E 17 SER cc_start: 0.7286 (m) cc_final: 0.6968 (p) REVERT: E 22 ARG cc_start: 0.7918 (ttt-90) cc_final: 0.7646 (tpt-90) REVERT: G 14 TYR cc_start: 0.8038 (t80) cc_final: 0.7830 (t80) REVERT: G 30 TRP cc_start: 0.8385 (m-90) cc_final: 0.8063 (m-90) REVERT: G 74 MET cc_start: 0.7261 (mmm) cc_final: 0.7045 (mmm) outliers start: 17 outliers final: 13 residues processed: 269 average time/residue: 0.1932 time to fit residues: 67.3439 Evaluate side-chains 247 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 234 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain F residue 57 MET Chi-restraints excluded: chain G residue 26 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 1.9990 chunk 21 optimal weight: 10.0000 chunk 58 optimal weight: 0.8980 chunk 48 optimal weight: 4.9990 chunk 19 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 63 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6710 Z= 0.216 Angle : 0.698 11.478 9034 Z= 0.349 Chirality : 0.039 0.143 1012 Planarity : 0.004 0.052 1122 Dihedral : 4.413 19.470 888 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 3.66 % Allowed : 16.34 % Favored : 80.00 % 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: 0.51 (0.30), residues: 808 helix: 1.46 (0.21), residues: 589 sheet: None (None), residues: 0 loop : -2.91 (0.40), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP G 30 HIS 0.003 0.001 HIS E 77 PHE 0.023 0.002 PHE D 61 TYR 0.019 0.002 TYR A 78 ARG 0.006 0.000 ARG G 21 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 256 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 ASN cc_start: 0.8712 (p0) cc_final: 0.8485 (p0) REVERT: A 194 THR cc_start: 0.8416 (m) cc_final: 0.8127 (m) REVERT: B 78 TYR cc_start: 0.6835 (t80) cc_final: 0.6623 (t80) REVERT: B 80 ARG cc_start: 0.7687 (OUTLIER) cc_final: 0.6884 (ptt90) REVERT: B 155 MET cc_start: 0.1302 (mmt) cc_final: 0.0641 (mmt) REVERT: C 12 GLU cc_start: 0.7453 (tm-30) cc_final: 0.7199 (tm-30) REVERT: C 13 MET cc_start: 0.7572 (ptp) cc_final: 0.7169 (ptp) REVERT: C 60 GLU cc_start: 0.8456 (pp20) cc_final: 0.8016 (pp20) REVERT: D 37 LEU cc_start: 0.9217 (tt) cc_final: 0.8982 (tt) REVERT: E 17 SER cc_start: 0.7258 (m) cc_final: 0.7005 (p) REVERT: E 22 ARG cc_start: 0.7894 (ttt-90) cc_final: 0.7611 (tpt-90) REVERT: E 74 MET cc_start: 0.7778 (tpp) cc_final: 0.7549 (tpp) outliers start: 26 outliers final: 18 residues processed: 268 average time/residue: 0.1893 time to fit residues: 65.7374 Evaluate side-chains 248 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 229 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 80 ARG Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain F residue 57 MET Chi-restraints excluded: chain G residue 53 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 0.0570 chunk 7 optimal weight: 0.9980 chunk 33 optimal weight: 9.9990 chunk 47 optimal weight: 3.9990 chunk 71 optimal weight: 0.3980 chunk 75 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 GLN ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6710 Z= 0.184 Angle : 0.698 12.461 9034 Z= 0.347 Chirality : 0.039 0.182 1012 Planarity : 0.004 0.047 1122 Dihedral : 4.312 19.300 888 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 3.24 % Allowed : 19.72 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.30), residues: 808 helix: 1.43 (0.21), residues: 591 sheet: None (None), residues: 0 loop : -2.81 (0.41), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP G 30 HIS 0.002 0.000 HIS D 77 PHE 0.025 0.002 PHE D 61 TYR 0.027 0.002 TYR C 4 ARG 0.006 0.000 ARG E 21 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 267 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 VAL cc_start: 0.8596 (m) cc_final: 0.7916 (t) REVERT: A 204 ARG cc_start: 0.8800 (mmt-90) cc_final: 0.7882 (tpp-160) REVERT: B 117 ARG cc_start: 0.7488 (ptm-80) cc_final: 0.7014 (ttp-110) REVERT: C 12 GLU cc_start: 0.7534 (tm-30) cc_final: 0.7233 (tm-30) REVERT: C 13 MET cc_start: 0.7516 (ptp) cc_final: 0.7128 (ptp) REVERT: C 25 ASN cc_start: 0.9067 (t0) cc_final: 0.8813 (m-40) REVERT: C 60 GLU cc_start: 0.8291 (pp20) cc_final: 0.8004 (pp20) REVERT: D 37 LEU cc_start: 0.9120 (tt) cc_final: 0.8805 (tt) REVERT: E 17 SER cc_start: 0.7191 (m) cc_final: 0.6939 (p) REVERT: E 22 ARG cc_start: 0.7927 (ttt-90) cc_final: 0.7546 (tpt-90) REVERT: E 67 SER cc_start: 0.8861 (t) cc_final: 0.8550 (p) REVERT: F 28 TYR cc_start: 0.6709 (OUTLIER) cc_final: 0.6356 (m-80) REVERT: F 37 LEU cc_start: 0.9014 (tp) cc_final: 0.8533 (tp) REVERT: F 70 GLU cc_start: 0.6926 (pm20) cc_final: 0.6410 (mp0) outliers start: 23 outliers final: 17 residues processed: 279 average time/residue: 0.1940 time to fit residues: 70.1584 Evaluate side-chains 256 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 238 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain F residue 28 TYR Chi-restraints excluded: chain F residue 57 MET Chi-restraints excluded: chain G residue 19 LYS Chi-restraints excluded: chain G residue 53 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 0.9990 chunk 56 optimal weight: 0.0570 chunk 31 optimal weight: 0.0670 chunk 64 optimal weight: 9.9990 chunk 52 optimal weight: 4.9990 chunk 0 optimal weight: 0.9980 chunk 38 optimal weight: 0.0980 chunk 67 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 25 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 overall best weight: 0.3036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 ASN ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 25 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6710 Z= 0.178 Angle : 0.705 12.531 9034 Z= 0.354 Chirality : 0.040 0.184 1012 Planarity : 0.003 0.045 1122 Dihedral : 4.260 18.735 888 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 3.38 % Allowed : 22.25 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.30), residues: 808 helix: 1.50 (0.21), residues: 590 sheet: None (None), residues: 0 loop : -2.78 (0.40), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP G 30 HIS 0.002 0.000 HIS D 77 PHE 0.020 0.002 PHE D 61 TYR 0.040 0.002 TYR B 78 ARG 0.007 0.001 ARG G 21 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 264 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 LYS cc_start: 0.8252 (tttt) cc_final: 0.7880 (mtpt) REVERT: A 204 ARG cc_start: 0.8795 (mmt-90) cc_final: 0.7835 (tpp-160) REVERT: B 14 MET cc_start: 0.8675 (OUTLIER) cc_final: 0.8364 (tpt) REVERT: B 78 TYR cc_start: 0.7096 (t80) cc_final: 0.6632 (t80) REVERT: B 117 ARG cc_start: 0.7466 (ptm-80) cc_final: 0.7074 (ttm110) REVERT: B 198 LYS cc_start: 0.8349 (OUTLIER) cc_final: 0.7998 (pttp) REVERT: C 12 GLU cc_start: 0.7484 (tm-30) cc_final: 0.7209 (tm-30) REVERT: C 13 MET cc_start: 0.7611 (ptp) cc_final: 0.7219 (ptp) REVERT: C 25 ASN cc_start: 0.8995 (t0) cc_final: 0.8759 (m-40) REVERT: C 75 GLU cc_start: 0.7943 (pt0) cc_final: 0.7726 (pt0) REVERT: D 37 LEU cc_start: 0.9116 (tt) cc_final: 0.8845 (tt) REVERT: E 17 SER cc_start: 0.7158 (m) cc_final: 0.6908 (p) REVERT: E 22 ARG cc_start: 0.7885 (ttt-90) cc_final: 0.7508 (tpt-90) REVERT: E 30 TRP cc_start: 0.8672 (m100) cc_final: 0.8367 (m100) REVERT: E 67 SER cc_start: 0.8841 (t) cc_final: 0.8535 (p) REVERT: G 21 ARG cc_start: 0.8938 (mtp85) cc_final: 0.8662 (mtp85) outliers start: 24 outliers final: 13 residues processed: 276 average time/residue: 0.1986 time to fit residues: 70.6173 Evaluate side-chains 265 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 250 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 67 TYR Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain B residue 6 ASN Chi-restraints excluded: chain B residue 14 MET Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 198 LYS Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain F residue 57 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 0.7980 chunk 18 optimal weight: 4.9990 chunk 75 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 6 optimal weight: 7.9990 chunk 24 optimal weight: 0.9980 chunk 39 optimal weight: 0.0170 chunk 72 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 42 optimal weight: 8.9990 overall best weight: 1.1220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 25 ASN F 18 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6710 Z= 0.215 Angle : 0.734 14.874 9034 Z= 0.365 Chirality : 0.040 0.159 1012 Planarity : 0.004 0.044 1122 Dihedral : 4.294 18.598 888 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 3.66 % Allowed : 22.54 % Favored : 73.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.30), residues: 808 helix: 1.50 (0.21), residues: 591 sheet: None (None), residues: 0 loop : -2.76 (0.40), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.002 TRP G 30 HIS 0.003 0.001 HIS D 77 PHE 0.025 0.002 PHE D 61 TYR 0.021 0.002 TYR B 78 ARG 0.007 0.000 ARG E 21 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 259 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 14 MET cc_start: 0.8703 (OUTLIER) cc_final: 0.8401 (tpt) REVERT: B 117 ARG cc_start: 0.7514 (ptm-80) cc_final: 0.7035 (ttm110) REVERT: B 198 LYS cc_start: 0.8348 (OUTLIER) cc_final: 0.8003 (pttp) REVERT: C 12 GLU cc_start: 0.7537 (tm-30) cc_final: 0.7263 (tm-30) REVERT: C 13 MET cc_start: 0.7556 (ptp) cc_final: 0.7136 (ptp) REVERT: C 25 ASN cc_start: 0.9018 (t0) cc_final: 0.8731 (m-40) REVERT: D 37 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8935 (tt) REVERT: E 17 SER cc_start: 0.7175 (m) cc_final: 0.6958 (p) REVERT: E 22 ARG cc_start: 0.7913 (ttt-90) cc_final: 0.7555 (tpt-90) REVERT: E 30 TRP cc_start: 0.8689 (m100) cc_final: 0.8477 (m100) REVERT: E 67 SER cc_start: 0.8917 (t) cc_final: 0.8571 (p) REVERT: F 37 LEU cc_start: 0.9074 (tp) cc_final: 0.8763 (tp) REVERT: F 70 GLU cc_start: 0.7133 (OUTLIER) cc_final: 0.6919 (mp0) REVERT: G 21 ARG cc_start: 0.9010 (mtp85) cc_final: 0.8739 (mtp85) outliers start: 26 outliers final: 16 residues processed: 271 average time/residue: 0.1958 time to fit residues: 68.5473 Evaluate side-chains 266 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 246 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 67 TYR Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain B residue 14 MET Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 198 LYS Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain F residue 57 MET Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain G residue 34 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 0.0040 chunk 42 optimal weight: 6.9990 chunk 63 optimal weight: 8.9990 chunk 75 optimal weight: 0.3980 chunk 47 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 30 optimal weight: 0.3980 chunk 44 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 ASN ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 25 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.3516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6710 Z= 0.192 Angle : 0.739 13.024 9034 Z= 0.369 Chirality : 0.041 0.209 1012 Planarity : 0.004 0.043 1122 Dihedral : 4.279 18.472 888 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 2.82 % Allowed : 24.65 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.30), residues: 808 helix: 1.49 (0.21), residues: 590 sheet: None (None), residues: 0 loop : -2.70 (0.40), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.001 TRP G 30 HIS 0.002 0.000 HIS D 77 PHE 0.023 0.002 PHE D 61 TYR 0.020 0.001 TYR E 28 ARG 0.007 0.001 ARG D 21 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 263 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 LYS cc_start: 0.8188 (tttt) cc_final: 0.7943 (mtpt) REVERT: B 85 GLN cc_start: 0.8622 (tm-30) cc_final: 0.8397 (tm-30) REVERT: B 117 ARG cc_start: 0.7524 (ptm-80) cc_final: 0.7017 (ttm110) REVERT: B 139 THR cc_start: 0.8792 (p) cc_final: 0.8451 (t) REVERT: B 198 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7764 (pttp) REVERT: B 215 VAL cc_start: 0.9116 (m) cc_final: 0.8889 (p) REVERT: C 12 GLU cc_start: 0.7551 (tm-30) cc_final: 0.7273 (tm-30) REVERT: C 13 MET cc_start: 0.7545 (ptp) cc_final: 0.7141 (ptp) REVERT: C 25 ASN cc_start: 0.8933 (t0) cc_final: 0.8719 (m-40) REVERT: C 75 GLU cc_start: 0.7887 (pt0) cc_final: 0.7674 (pt0) REVERT: D 37 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8962 (tt) REVERT: E 22 ARG cc_start: 0.7839 (ttt-90) cc_final: 0.7472 (tpt-90) REVERT: E 67 SER cc_start: 0.8852 (t) cc_final: 0.8510 (p) REVERT: F 37 LEU cc_start: 0.9021 (tp) cc_final: 0.8795 (tp) REVERT: G 30 TRP cc_start: 0.8271 (m-90) cc_final: 0.7823 (m100) outliers start: 20 outliers final: 11 residues processed: 272 average time/residue: 0.2003 time to fit residues: 69.7940 Evaluate side-chains 259 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 246 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain B residue 6 ASN Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 198 LYS Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain F residue 57 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 4.9990 chunk 47 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 72 optimal weight: 0.0040 chunk 65 optimal weight: 1.9990 chunk 70 optimal weight: 0.0030 chunk 42 optimal weight: 6.9990 overall best weight: 0.7206 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.3657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6710 Z= 0.205 Angle : 0.754 13.315 9034 Z= 0.376 Chirality : 0.041 0.223 1012 Planarity : 0.004 0.043 1122 Dihedral : 4.301 18.211 888 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 1.83 % Allowed : 26.62 % Favored : 71.55 % 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: 0.67 (0.30), residues: 808 helix: 1.45 (0.21), residues: 598 sheet: None (None), residues: 0 loop : -2.60 (0.40), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP G 30 HIS 0.002 0.000 HIS D 77 PHE 0.028 0.001 PHE D 61 TYR 0.019 0.001 TYR A 78 ARG 0.007 0.000 ARG E 21 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 254 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 LYS cc_start: 0.8226 (tttt) cc_final: 0.7964 (mtpt) REVERT: B 78 TYR cc_start: 0.7187 (t80) cc_final: 0.6524 (t80) REVERT: B 117 ARG cc_start: 0.7478 (ptm-80) cc_final: 0.6981 (ttm110) REVERT: B 139 THR cc_start: 0.8827 (p) cc_final: 0.8473 (t) REVERT: B 198 LYS cc_start: 0.8321 (OUTLIER) cc_final: 0.8030 (pttp) REVERT: B 215 VAL cc_start: 0.9093 (m) cc_final: 0.8891 (p) REVERT: C 12 GLU cc_start: 0.7560 (tm-30) cc_final: 0.7300 (tm-30) REVERT: C 13 MET cc_start: 0.7529 (ptp) cc_final: 0.7271 (ptp) REVERT: C 25 ASN cc_start: 0.8928 (t0) cc_final: 0.8685 (m-40) REVERT: C 75 GLU cc_start: 0.7942 (pt0) cc_final: 0.7721 (pt0) REVERT: D 37 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8959 (tt) REVERT: E 22 ARG cc_start: 0.7795 (ttt-90) cc_final: 0.7493 (tpt-90) REVERT: E 30 TRP cc_start: 0.8630 (m100) cc_final: 0.8264 (m100) REVERT: E 67 SER cc_start: 0.8835 (t) cc_final: 0.8230 (p) REVERT: F 70 GLU cc_start: 0.6982 (mp0) cc_final: 0.6773 (mp0) outliers start: 13 outliers final: 9 residues processed: 262 average time/residue: 0.2008 time to fit residues: 67.4576 Evaluate side-chains 252 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 241 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 67 TYR Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 198 LYS Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain F residue 57 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 0.0030 chunk 55 optimal weight: 3.9990 chunk 21 optimal weight: 0.0970 chunk 63 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 46 optimal weight: 0.4980 chunk 74 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 overall best weight: 0.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 25 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.3843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6710 Z= 0.195 Angle : 0.789 17.740 9034 Z= 0.384 Chirality : 0.041 0.190 1012 Planarity : 0.004 0.045 1122 Dihedral : 4.297 20.260 888 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.39 % Allowed : 26.62 % Favored : 70.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.30), residues: 808 helix: 1.49 (0.21), residues: 598 sheet: None (None), residues: 0 loop : -2.60 (0.40), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP G 30 HIS 0.002 0.000 HIS F 45 PHE 0.026 0.001 PHE D 61 TYR 0.019 0.001 TYR D 28 ARG 0.008 0.001 ARG B 148 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 262 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 LYS cc_start: 0.8087 (tttt) cc_final: 0.7620 (mtpp) REVERT: A 204 ARG cc_start: 0.8723 (mmt180) cc_final: 0.7483 (tpp-160) REVERT: B 78 TYR cc_start: 0.7214 (t80) cc_final: 0.6564 (t80) REVERT: B 94 PHE cc_start: 0.8684 (t80) cc_final: 0.8446 (t80) REVERT: B 117 ARG cc_start: 0.7503 (ptm-80) cc_final: 0.7150 (ttm110) REVERT: B 139 THR cc_start: 0.8771 (p) cc_final: 0.8432 (t) REVERT: C 12 GLU cc_start: 0.7543 (tm-30) cc_final: 0.7330 (tm-30) REVERT: C 13 MET cc_start: 0.7496 (ptp) cc_final: 0.7229 (ptp) REVERT: D 37 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8949 (tt) REVERT: E 22 ARG cc_start: 0.7790 (ttt-90) cc_final: 0.7454 (tpt-90) REVERT: E 30 TRP cc_start: 0.8579 (m100) cc_final: 0.8346 (m100) REVERT: E 67 SER cc_start: 0.8735 (t) cc_final: 0.8402 (p) REVERT: E 70 GLU cc_start: 0.8288 (pt0) cc_final: 0.8067 (pt0) REVERT: F 14 TYR cc_start: 0.5505 (t80) cc_final: 0.5302 (t80) REVERT: F 37 LEU cc_start: 0.8952 (tp) cc_final: 0.8633 (tp) REVERT: F 70 GLU cc_start: 0.6981 (mp0) cc_final: 0.6780 (mp0) REVERT: F 76 TYR cc_start: 0.7383 (t80) cc_final: 0.6955 (t80) outliers start: 17 outliers final: 9 residues processed: 272 average time/residue: 0.2011 time to fit residues: 70.1468 Evaluate side-chains 259 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 249 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 67 TYR Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain E residue 15 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 0.9980 chunk 71 optimal weight: 0.0670 chunk 61 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 47 optimal weight: 0.6980 chunk 37 optimal weight: 0.4980 chunk 49 optimal weight: 5.9990 chunk 65 optimal weight: 10.0000 chunk 18 optimal weight: 0.0870 chunk 57 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 overall best weight: 0.4696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 ASN ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.4048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6710 Z= 0.219 Angle : 0.828 17.295 9034 Z= 0.404 Chirality : 0.042 0.247 1012 Planarity : 0.004 0.047 1122 Dihedral : 4.352 17.894 888 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 1.69 % Allowed : 27.46 % Favored : 70.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.30), residues: 808 helix: 1.42 (0.21), residues: 597 sheet: None (None), residues: 0 loop : -2.49 (0.40), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP G 30 HIS 0.002 0.000 HIS D 77 PHE 0.027 0.001 PHE D 61 TYR 0.015 0.001 TYR B 78 ARG 0.008 0.001 ARG G 21 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 255 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 6 ASN cc_start: 0.6845 (OUTLIER) cc_final: 0.6594 (p0) REVERT: B 78 TYR cc_start: 0.7103 (t80) cc_final: 0.6466 (t80) REVERT: B 94 PHE cc_start: 0.8691 (t80) cc_final: 0.8457 (t80) REVERT: B 117 ARG cc_start: 0.7543 (ptm-80) cc_final: 0.7180 (ttm110) REVERT: C 12 GLU cc_start: 0.7539 (tm-30) cc_final: 0.7337 (tm-30) REVERT: C 13 MET cc_start: 0.7489 (ptp) cc_final: 0.7252 (ptp) REVERT: D 37 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8965 (tt) REVERT: E 22 ARG cc_start: 0.7772 (ttt-90) cc_final: 0.7471 (tpt-90) REVERT: E 67 SER cc_start: 0.8750 (t) cc_final: 0.8415 (p) REVERT: E 70 GLU cc_start: 0.8300 (pt0) cc_final: 0.8044 (pt0) REVERT: F 70 GLU cc_start: 0.7067 (mp0) cc_final: 0.6846 (mp0) outliers start: 12 outliers final: 10 residues processed: 263 average time/residue: 0.1881 time to fit residues: 64.2022 Evaluate side-chains 258 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 246 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 67 TYR Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain B residue 6 ASN Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain E residue 15 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 63 optimal weight: 9.9990 chunk 7 optimal weight: 0.8980 chunk 11 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 70 optimal weight: 5.9990 chunk 41 optimal weight: 0.6980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.126179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.100347 restraints weight = 13445.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.102943 restraints weight = 8388.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.104739 restraints weight = 6110.076| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.3951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 6710 Z= 0.252 Angle : 0.845 17.453 9034 Z= 0.412 Chirality : 0.043 0.256 1012 Planarity : 0.004 0.049 1122 Dihedral : 4.381 17.379 888 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 1.69 % Allowed : 27.75 % Favored : 70.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.30), residues: 808 helix: 1.42 (0.21), residues: 587 sheet: None (None), residues: 0 loop : -2.50 (0.39), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP G 30 HIS 0.002 0.000 HIS D 77 PHE 0.026 0.002 PHE D 61 TYR 0.018 0.001 TYR D 28 ARG 0.008 0.001 ARG G 21 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1879.38 seconds wall clock time: 34 minutes 53.76 seconds (2093.76 seconds total)