Starting phenix.real_space_refine on Wed Feb 14 01:53:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sat_24956/02_2024/7sat_24956.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sat_24956/02_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sat_24956/02_2024/7sat_24956.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sat_24956/02_2024/7sat_24956.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sat_24956/02_2024/7sat_24956.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sat_24956/02_2024/7sat_24956.pdb" } 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 Residue "A GLU 62": "OE1" <-> "OE2" Residue "A TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 105": "OE1" <-> "OE2" Residue "A ARG 117": "NH1" <-> "NH2" Residue "A ARG 148": "NH1" <-> "NH2" Residue "A ARG 204": "NH1" <-> "NH2" Residue "B GLU 33": "OE1" <-> "OE2" Residue "B TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 97": "OD1" <-> "OD2" Residue "B ARG 104": "NH1" <-> "NH2" Residue "B GLU 105": "OE1" <-> "OE2" Residue "B ARG 118": "NH1" <-> "NH2" Residue "B PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 185": "OE1" <-> "OE2" Residue "B TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 60": "OE1" <-> "OE2" Residue "D PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 12": "OE1" <-> "OE2" Residue "F TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 21": "NH1" <-> "NH2" Residue "G GLU 60": "OE1" <-> "OE2" Residue "G PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 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: 3.97, per 1000 atoms: 0.60 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 - 3.50 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: 2.63 Conformation dependent library (CDL) restraints added in 1.4 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: 0.52 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: 1.59 Time building geometry restraints manager: 2.82 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: 97.43 - 104.76: 83 104.76 - 112.08: 3301 112.08 - 119.40: 2228 119.40 - 126.73: 3335 126.73 - 134.05: 87 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 2.440 nonbonded pdb=" OD1 ASN A 64 " pdb=" OH TYR A 78 " model vdw 2.151 2.440 nonbonded pdb=" O VAL F 63 " pdb=" OG SER F 67 " model vdw 2.208 2.440 nonbonded pdb=" NZ LYS A 99 " pdb=" OE1 GLN A 200 " model vdw 2.250 2.520 nonbonded pdb=" O ASP B 89 " pdb=" OG1 THR B 93 " model vdw 2.264 2.440 ... (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 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: 0.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 2.040 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 21.090 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.020 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.030 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 2 poor density : 281 time to evaluate : 0.843 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: 0.1897 time to fit residues: 68.5922 Evaluate side-chains 235 residues out of total 710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 235 time to evaluate : 0.793 ------------------------------------------------------------------------------- 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: 9.9990 chunk 59 optimal weight: 4.9990 chunk 32 optimal weight: 0.0970 chunk 20 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7780 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6710 Z= 0.209 Angle : 0.688 11.966 9034 Z= 0.348 Chirality : 0.038 0.155 1012 Planarity : 0.004 0.056 1122 Dihedral : 4.591 19.761 888 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 3.52 % Allowed : 12.54 % Favored : 83.94 % 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: 0.35 (0.30), residues: 808 helix: 1.33 (0.21), residues: 590 sheet: None (None), residues: 0 loop : -2.96 (0.40), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP G 30 HIS 0.005 0.001 HIS C 18 PHE 0.020 0.002 PHE D 54 TYR 0.018 0.002 TYR F 28 ARG 0.005 0.000 ARG G 21 *********************** 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 284 residues out of total 710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 259 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 ARG cc_start: 0.5833 (ptt-90) cc_final: 0.5369 (ptt-90) REVERT: A 204 ARG cc_start: 0.8738 (mmt-90) cc_final: 0.8398 (tpp-160) REVERT: B 78 TYR cc_start: 0.6823 (t80) cc_final: 0.6602 (t80) REVERT: C 12 GLU cc_start: 0.7390 (tm-30) cc_final: 0.7175 (tm-30) REVERT: C 13 MET cc_start: 0.7596 (ptp) cc_final: 0.7203 (ptp) REVERT: C 60 GLU cc_start: 0.8480 (pp20) cc_final: 0.7989 (pp20) REVERT: D 48 MET cc_start: 0.6959 (ptt) cc_final: 0.6719 (ptt) REVERT: E 17 SER cc_start: 0.7294 (m) cc_final: 0.6992 (p) REVERT: E 74 MET cc_start: 0.7629 (tpp) cc_final: 0.6789 (tpp) REVERT: G 14 TYR cc_start: 0.8076 (t80) cc_final: 0.7850 (t80) REVERT: G 30 TRP cc_start: 0.8512 (m-90) cc_final: 0.8157 (m-90) REVERT: G 51 GLU cc_start: 0.8339 (mp0) cc_final: 0.8132 (mp0) outliers start: 25 outliers final: 22 residues processed: 270 average time/residue: 0.1931 time to fit residues: 67.0509 Evaluate side-chains 255 residues out of total 710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 233 time to evaluate : 0.783 ------------------------------------------------------------------------------- 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 93 THR Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 114 ASN Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain F residue 57 MET Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 52 MET Chi-restraints excluded: chain G residue 53 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 0.1980 chunk 21 optimal weight: 10.0000 chunk 58 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 19 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 63 optimal weight: 8.9990 chunk 24 optimal weight: 0.8980 chunk 56 optimal weight: 9.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7787 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6710 Z= 0.201 Angle : 0.671 11.760 9034 Z= 0.332 Chirality : 0.038 0.148 1012 Planarity : 0.003 0.049 1122 Dihedral : 4.440 19.668 888 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 3.80 % Allowed : 16.62 % Favored : 79.58 % 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: 0.61 (0.30), residues: 808 helix: 1.55 (0.21), residues: 590 sheet: None (None), residues: 0 loop : -2.95 (0.40), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP G 30 HIS 0.002 0.001 HIS E 77 PHE 0.024 0.002 PHE D 61 TYR 0.018 0.001 TYR D 28 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 289 residues out of total 710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 262 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 ARG cc_start: 0.5900 (ptt-90) cc_final: 0.5575 (ptt-90) REVERT: B 78 TYR cc_start: 0.6780 (t80) cc_final: 0.6540 (t80) REVERT: B 155 MET cc_start: 0.1171 (mmt) cc_final: 0.0548 (mmt) REVERT: C 12 GLU cc_start: 0.7486 (tm-30) cc_final: 0.7197 (tm-30) REVERT: C 13 MET cc_start: 0.7579 (ptp) cc_final: 0.7177 (ptp) REVERT: C 60 GLU cc_start: 0.8438 (pp20) cc_final: 0.8004 (pp20) REVERT: D 37 LEU cc_start: 0.9200 (tt) cc_final: 0.8981 (tt) REVERT: E 17 SER cc_start: 0.7268 (m) cc_final: 0.7020 (p) REVERT: F 28 TYR cc_start: 0.6715 (OUTLIER) cc_final: 0.6226 (m-80) REVERT: G 48 MET cc_start: 0.7070 (tpt) cc_final: 0.6701 (tpt) outliers start: 27 outliers final: 17 residues processed: 273 average time/residue: 0.1954 time to fit residues: 68.4434 Evaluate side-chains 255 residues out of total 710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 237 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU 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 197 THR Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 114 ASN Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain D residue 35 VAL 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 0.0570 chunk 7 optimal weight: 0.8980 chunk 33 optimal weight: 0.0370 chunk 47 optimal weight: 0.9990 chunk 71 optimal weight: 8.9990 chunk 75 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.5376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 12 GLN B 29 ASN ** B 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7744 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6710 Z= 0.173 Angle : 0.678 12.241 9034 Z= 0.338 Chirality : 0.038 0.189 1012 Planarity : 0.003 0.047 1122 Dihedral : 4.312 18.687 888 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 3.94 % Allowed : 19.58 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.30), residues: 808 helix: 1.51 (0.21), residues: 591 sheet: None (None), residues: 0 loop : -2.93 (0.40), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP G 30 HIS 0.002 0.000 HIS D 77 PHE 0.025 0.001 PHE D 61 TYR 0.026 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 296 residues out of total 710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 268 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 ARG cc_start: 0.5662 (ptt-90) cc_final: 0.5237 (ptt-90) REVERT: A 118 ARG cc_start: 0.8112 (ppt170) cc_final: 0.7868 (ppt170) REVERT: A 204 ARG cc_start: 0.8783 (mmt-90) cc_final: 0.7824 (tpp-160) REVERT: B 155 MET cc_start: 0.0915 (mmt) cc_final: 0.0413 (mmt) REVERT: B 198 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.8288 (pttt) REVERT: C 12 GLU cc_start: 0.7462 (tm-30) cc_final: 0.7218 (tm-30) REVERT: C 13 MET cc_start: 0.7553 (ptp) cc_final: 0.7171 (ptp) REVERT: C 60 GLU cc_start: 0.8296 (pp20) cc_final: 0.7969 (pp20) REVERT: D 37 LEU cc_start: 0.9129 (tt) cc_final: 0.8803 (tt) REVERT: E 17 SER cc_start: 0.7197 (m) cc_final: 0.6944 (p) REVERT: E 61 PHE cc_start: 0.9246 (t80) cc_final: 0.9030 (t80) REVERT: F 28 TYR cc_start: 0.6583 (OUTLIER) cc_final: 0.6163 (m-80) REVERT: F 37 LEU cc_start: 0.8984 (tp) cc_final: 0.8578 (tp) outliers start: 28 outliers final: 19 residues processed: 281 average time/residue: 0.1970 time to fit residues: 70.9704 Evaluate side-chains 261 residues out of total 710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 240 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain B residue 14 MET Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 114 ASN Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 198 LYS Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain D residue 59 THR 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 F residue 70 GLU 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: 0.8980 chunk 56 optimal weight: 6.9990 chunk 31 optimal weight: 0.9980 chunk 64 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 38 optimal weight: 8.9990 chunk 67 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 ASN B 6 ASN ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 25 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6710 Z= 0.209 Angle : 0.707 11.800 9034 Z= 0.352 Chirality : 0.039 0.206 1012 Planarity : 0.003 0.047 1122 Dihedral : 4.335 18.477 888 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 4.23 % Allowed : 21.55 % Favored : 74.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.30), residues: 808 helix: 1.48 (0.21), residues: 591 sheet: None (None), residues: 0 loop : -2.89 (0.39), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP G 30 HIS 0.003 0.001 HIS D 77 PHE 0.019 0.002 PHE D 61 TYR 0.042 0.002 TYR B 78 ARG 0.006 0.000 ARG E 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 290 residues out of total 710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 260 time to evaluate : 0.847 Fit side-chains revert: symmetry clash REVERT: A 13 LYS cc_start: 0.8271 (tttt) cc_final: 0.7978 (mtpt) REVERT: A 117 ARG cc_start: 0.5737 (ptt-90) cc_final: 0.5279 (ptt-90) REVERT: B 78 TYR cc_start: 0.7198 (t80) cc_final: 0.6660 (t80) REVERT: B 80 ARG cc_start: 0.7704 (ttt90) cc_final: 0.7344 (ptt90) REVERT: B 117 ARG cc_start: 0.7743 (ptt90) cc_final: 0.7322 (ttp-110) REVERT: B 198 LYS cc_start: 0.8449 (OUTLIER) cc_final: 0.8084 (pttp) REVERT: C 12 GLU cc_start: 0.7564 (tm-30) cc_final: 0.7298 (tm-30) REVERT: C 13 MET cc_start: 0.7561 (ptp) cc_final: 0.7147 (ptp) REVERT: C 60 GLU cc_start: 0.8265 (pp20) cc_final: 0.8004 (pp20) REVERT: D 37 LEU cc_start: 0.9154 (tt) cc_final: 0.8867 (tt) REVERT: D 70 GLU cc_start: 0.8117 (pt0) cc_final: 0.7891 (pt0) REVERT: E 17 SER cc_start: 0.7190 (m) cc_final: 0.6920 (p) REVERT: E 30 TRP cc_start: 0.8690 (m100) cc_final: 0.8378 (m100) REVERT: E 61 PHE cc_start: 0.9276 (t80) cc_final: 0.9068 (t80) outliers start: 30 outliers final: 23 residues processed: 275 average time/residue: 0.1982 time to fit residues: 69.6096 Evaluate side-chains 269 residues out of total 710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 245 time to evaluate : 0.801 ------------------------------------------------------------------------------- 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 87 GLU Chi-restraints excluded: chain A residue 89 ASP 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 A residue 197 THR 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 58 LEU Chi-restraints excluded: chain B residue 114 ASN Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 197 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 D residue 59 THR 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 53 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 75 optimal weight: 0.0470 chunk 62 optimal weight: 0.0970 chunk 34 optimal weight: 0.7980 chunk 6 optimal weight: 10.0000 chunk 24 optimal weight: 6.9990 chunk 39 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 chunk 42 optimal weight: 6.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 ASN ** B 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7727 moved from start: 0.3074 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= 0.184 Angle : 0.722 15.871 9034 Z= 0.352 Chirality : 0.039 0.226 1012 Planarity : 0.004 0.043 1122 Dihedral : 4.329 18.308 888 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.80 % Allowed : 23.10 % Favored : 73.10 % 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: 0.64 (0.30), residues: 808 helix: 1.53 (0.21), residues: 591 sheet: None (None), residues: 0 loop : -2.82 (0.39), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.002 TRP G 30 HIS 0.003 0.000 HIS D 77 PHE 0.026 0.001 PHE D 61 TYR 0.024 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 296 residues out of total 710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 269 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 ARG cc_start: 0.5637 (ptt-90) cc_final: 0.5189 (ptt-90) REVERT: A 187 MET cc_start: 0.8685 (mtm) cc_final: 0.8451 (ttp) REVERT: B 78 TYR cc_start: 0.7103 (t80) cc_final: 0.6513 (t80) REVERT: B 117 ARG cc_start: 0.7719 (ptt90) cc_final: 0.7155 (ttp-110) REVERT: B 198 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.8017 (pttp) REVERT: B 215 VAL cc_start: 0.9119 (m) cc_final: 0.8882 (p) REVERT: C 12 GLU cc_start: 0.7531 (tm-30) cc_final: 0.7211 (tm-30) REVERT: C 13 MET cc_start: 0.7544 (ptp) cc_final: 0.7152 (ptp) REVERT: C 25 ASN cc_start: 0.9056 (t0) cc_final: 0.8787 (m-40) REVERT: C 60 GLU cc_start: 0.8115 (pp20) cc_final: 0.7817 (pp20) REVERT: D 37 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8823 (tt) REVERT: E 8 LYS cc_start: 0.7004 (mptt) cc_final: 0.6760 (mptt) REVERT: E 61 PHE cc_start: 0.9261 (t80) cc_final: 0.9046 (t80) REVERT: F 37 LEU cc_start: 0.9098 (tp) cc_final: 0.8889 (tp) REVERT: G 76 TYR cc_start: 0.7914 (OUTLIER) cc_final: 0.7462 (m-80) outliers start: 27 outliers final: 21 residues processed: 285 average time/residue: 0.2011 time to fit residues: 74.5845 Evaluate side-chains 274 residues out of total 710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 250 time to evaluate : 0.748 ------------------------------------------------------------------------------- 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 150 LEU Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 197 THR 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 80 ARG Chi-restraints excluded: chain B residue 114 ASN Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 197 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 D residue 59 THR 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 53 LEU Chi-restraints excluded: chain G residue 76 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 3.9990 chunk 42 optimal weight: 7.9990 chunk 63 optimal weight: 8.9990 chunk 75 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.7728 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6710 Z= 0.200 Angle : 0.721 12.273 9034 Z= 0.354 Chirality : 0.040 0.227 1012 Planarity : 0.003 0.044 1122 Dihedral : 4.302 18.028 888 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 3.94 % Allowed : 23.66 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.30), residues: 808 helix: 1.52 (0.21), residues: 593 sheet: None (None), residues: 0 loop : -2.83 (0.40), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP G 30 HIS 0.003 0.000 HIS D 77 PHE 0.021 0.001 PHE D 61 TYR 0.018 0.001 TYR B 78 ARG 0.007 0.000 ARG E 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 285 residues out of total 710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 257 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 ARG cc_start: 0.5728 (ptt-90) cc_final: 0.5260 (ptt-90) REVERT: A 187 MET cc_start: 0.8692 (mtm) cc_final: 0.8474 (ttp) REVERT: B 78 TYR cc_start: 0.7208 (t80) cc_final: 0.6687 (t80) REVERT: B 117 ARG cc_start: 0.7566 (ptt90) cc_final: 0.6972 (ttp-110) REVERT: B 198 LYS cc_start: 0.8381 (OUTLIER) cc_final: 0.8086 (pttp) REVERT: B 215 VAL cc_start: 0.9125 (m) cc_final: 0.8900 (p) REVERT: C 12 GLU cc_start: 0.7511 (tm-30) cc_final: 0.7235 (tm-30) REVERT: C 13 MET cc_start: 0.7518 (ptp) cc_final: 0.7130 (ptp) REVERT: C 25 ASN cc_start: 0.9054 (t0) cc_final: 0.8779 (m-40) REVERT: D 37 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8842 (tt) REVERT: E 30 TRP cc_start: 0.8680 (m100) cc_final: 0.8303 (m100) outliers start: 28 outliers final: 22 residues processed: 270 average time/residue: 0.1857 time to fit residues: 64.7383 Evaluate side-chains 269 residues out of total 710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 245 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 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 150 LEU Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 197 THR 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 80 ARG Chi-restraints excluded: chain B residue 114 ASN Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 197 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 59 THR 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 53 LEU Chi-restraints excluded: chain G residue 76 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 37 optimal weight: 0.0020 chunk 7 optimal weight: 0.0470 chunk 59 optimal weight: 1.9990 chunk 68 optimal weight: 0.0980 chunk 72 optimal weight: 7.9990 chunk 65 optimal weight: 0.6980 chunk 70 optimal weight: 3.9990 chunk 42 optimal weight: 7.9990 overall best weight: 0.3486 ------------------------------------------------------------------------------- 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: 0.7685 moved from start: 0.3532 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= 0.188 Angle : 0.763 13.108 9034 Z= 0.370 Chirality : 0.040 0.242 1012 Planarity : 0.003 0.041 1122 Dihedral : 4.233 17.910 888 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.96 % Allowed : 25.35 % Favored : 71.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.30), residues: 808 helix: 1.46 (0.21), residues: 593 sheet: None (None), residues: 0 loop : -2.85 (0.39), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.088 0.002 TRP G 30 HIS 0.002 0.000 HIS D 77 PHE 0.028 0.001 PHE D 61 TYR 0.016 0.001 TYR C 4 ARG 0.007 0.001 ARG D 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 281 residues out of total 710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 260 time to evaluate : 0.852 Fit side-chains revert: symmetry clash REVERT: A 13 LYS cc_start: 0.8084 (tttt) cc_final: 0.7732 (mtpt) REVERT: A 117 ARG cc_start: 0.5693 (ptt-90) cc_final: 0.5252 (ptt-90) REVERT: B 78 TYR cc_start: 0.7179 (t80) cc_final: 0.6720 (t80) REVERT: B 92 CYS cc_start: 0.6794 (p) cc_final: 0.6541 (p) REVERT: B 117 ARG cc_start: 0.7584 (ptt90) cc_final: 0.6954 (ttp-110) REVERT: B 215 VAL cc_start: 0.9139 (m) cc_final: 0.8915 (p) REVERT: C 12 GLU cc_start: 0.7576 (tm-30) cc_final: 0.7269 (tm-30) REVERT: C 13 MET cc_start: 0.7508 (ptp) cc_final: 0.7132 (ptp) REVERT: C 24 LEU cc_start: 0.9020 (mt) cc_final: 0.8744 (mt) REVERT: C 25 ASN cc_start: 0.8724 (t0) cc_final: 0.8501 (m-40) REVERT: D 37 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8853 (tt) REVERT: E 30 TRP cc_start: 0.8627 (m100) cc_final: 0.8368 (m100) REVERT: F 76 TYR cc_start: 0.7748 (t80) cc_final: 0.7263 (t80) outliers start: 21 outliers final: 12 residues processed: 270 average time/residue: 0.1869 time to fit residues: 65.6510 Evaluate side-chains 260 residues out of total 710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 247 time to evaluate : 0.747 ------------------------------------------------------------------------------- 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 193 ILE 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 114 ASN Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 15 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 chunk 66 optimal weight: 0.6980 chunk 69 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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: 0.7718 moved from start: 0.3609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 6710 Z= 0.217 Angle : 0.795 14.954 9034 Z= 0.382 Chirality : 0.041 0.241 1012 Planarity : 0.004 0.045 1122 Dihedral : 4.303 17.453 888 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 16.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 2.39 % Allowed : 26.76 % 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: 0.57 (0.30), residues: 808 helix: 1.47 (0.21), residues: 593 sheet: None (None), residues: 0 loop : -2.85 (0.39), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 30 HIS 0.002 0.001 HIS D 77 PHE 0.026 0.002 PHE D 61 TYR 0.018 0.001 TYR G 14 ARG 0.007 0.001 ARG E 21 *********************** 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 263 residues out of total 710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 246 time to evaluate : 0.806 Fit side-chains revert: symmetry clash REVERT: A 13 LYS cc_start: 0.8041 (tttt) cc_final: 0.7788 (mtpt) REVERT: A 18 MET cc_start: 0.9143 (tpp) cc_final: 0.8923 (mmt) REVERT: A 117 ARG cc_start: 0.5760 (ptt-90) cc_final: 0.5283 (ptt-90) REVERT: B 78 TYR cc_start: 0.7190 (t80) cc_final: 0.6733 (t80) REVERT: B 80 ARG cc_start: 0.7698 (ptt90) cc_final: 0.7464 (ptt90) REVERT: B 129 MET cc_start: 0.8020 (tpp) cc_final: 0.7769 (tpp) REVERT: B 215 VAL cc_start: 0.9141 (m) cc_final: 0.8906 (p) REVERT: C 12 GLU cc_start: 0.7542 (tm-30) cc_final: 0.7196 (tm-30) REVERT: C 13 MET cc_start: 0.7544 (ptp) cc_final: 0.7133 (ptp) REVERT: C 24 LEU cc_start: 0.8986 (mt) cc_final: 0.8450 (mt) REVERT: C 25 ASN cc_start: 0.8742 (t0) cc_final: 0.8487 (m-40) REVERT: D 37 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8932 (tt) REVERT: F 76 TYR cc_start: 0.7520 (t80) cc_final: 0.7032 (t80) REVERT: G 70 GLU cc_start: 0.7697 (tm-30) cc_final: 0.7482 (tm-30) outliers start: 17 outliers final: 13 residues processed: 255 average time/residue: 0.1899 time to fit residues: 62.7253 Evaluate side-chains 254 residues out of total 710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 240 time to evaluate : 0.760 ------------------------------------------------------------------------------- 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 151 VAL Chi-restraints excluded: chain A residue 193 ILE 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 114 ASN Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 59 THR 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: 0.0370 chunk 71 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 6 optimal weight: 7.9990 chunk 47 optimal weight: 0.9990 chunk 37 optimal weight: 0.0010 chunk 49 optimal weight: 5.9990 chunk 65 optimal weight: 9.9990 chunk 18 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 overall best weight: 0.6068 ------------------------------------------------------------------------------- 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: 0.7690 moved from start: 0.3777 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= 0.217 Angle : 0.817 15.876 9034 Z= 0.389 Chirality : 0.042 0.246 1012 Planarity : 0.004 0.046 1122 Dihedral : 4.337 17.738 888 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 16.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.39 % Allowed : 27.75 % 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: 0.44 (0.30), residues: 808 helix: 1.36 (0.21), residues: 593 sheet: None (None), residues: 0 loop : -2.86 (0.39), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP G 30 HIS 0.002 0.000 HIS F 45 PHE 0.027 0.002 PHE E 41 TYR 0.016 0.001 TYR C 14 ARG 0.007 0.001 ARG E 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 268 residues out of total 710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 251 time to evaluate : 0.829 Fit side-chains revert: symmetry clash REVERT: A 18 MET cc_start: 0.9107 (tpp) cc_final: 0.8878 (mmt) REVERT: A 117 ARG cc_start: 0.5886 (ptt-90) cc_final: 0.5362 (ptt-90) REVERT: B 78 TYR cc_start: 0.7174 (t80) cc_final: 0.6728 (t80) REVERT: B 80 ARG cc_start: 0.7699 (ptt90) cc_final: 0.7465 (ptt90) REVERT: B 117 ARG cc_start: 0.7262 (ptt-90) cc_final: 0.6610 (ttp-110) REVERT: B 205 TYR cc_start: 0.8134 (t80) cc_final: 0.7900 (t80) REVERT: B 215 VAL cc_start: 0.9132 (m) cc_final: 0.8908 (p) REVERT: C 12 GLU cc_start: 0.7516 (tm-30) cc_final: 0.7193 (tm-30) REVERT: C 13 MET cc_start: 0.7518 (ptp) cc_final: 0.7142 (ptp) REVERT: C 25 ASN cc_start: 0.8601 (t0) cc_final: 0.8394 (m-40) REVERT: D 37 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8923 (tt) REVERT: E 30 TRP cc_start: 0.8496 (m100) cc_final: 0.8138 (m100) REVERT: F 76 TYR cc_start: 0.7512 (t80) cc_final: 0.7029 (t80) REVERT: G 30 TRP cc_start: 0.8221 (m100) cc_final: 0.7818 (m100) outliers start: 17 outliers final: 13 residues processed: 259 average time/residue: 0.1906 time to fit residues: 63.6579 Evaluate side-chains 253 residues out of total 710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 239 time to evaluate : 0.708 ------------------------------------------------------------------------------- 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 151 VAL Chi-restraints excluded: chain A residue 193 ILE 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 114 ASN Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain G residue 76 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 63 optimal weight: 6.9990 chunk 7 optimal weight: 0.9990 chunk 11 optimal weight: 6.9990 chunk 54 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 44 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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** C 25 ASN E 25 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.124039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.098798 restraints weight = 13227.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.101289 restraints weight = 8146.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.103042 restraints weight = 5874.984| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 6710 Z= 0.242 Angle : 0.829 17.076 9034 Z= 0.398 Chirality : 0.042 0.238 1012 Planarity : 0.004 0.046 1122 Dihedral : 4.428 17.534 888 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 17.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 2.54 % Allowed : 28.31 % Favored : 69.15 % 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: 0.40 (0.30), residues: 808 helix: 1.27 (0.21), residues: 598 sheet: None (None), residues: 0 loop : -2.78 (0.40), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP G 30 HIS 0.002 0.001 HIS D 77 PHE 0.024 0.002 PHE D 61 TYR 0.019 0.001 TYR D 28 ARG 0.007 0.001 ARG G 21 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1845.53 seconds wall clock time: 34 minutes 13.12 seconds (2053.12 seconds total)